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Lorenzi A, Legeai F, Jouan V, Girard PA, Strand MR, Ravallec M, Eychenne M, Bretaudeau A, Robin S, Rochefort J, Villegas M, Burke GR, Rebollo R, Nègre N, Volkoff AN. Identification of a viral gene essential for the genome replication of a domesticated endogenous virus in ichneumonid parasitoid wasps. PLoS Pathog 2024; 20:e1011980. [PMID: 38662774 DOI: 10.1371/journal.ppat.1011980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/07/2024] [Accepted: 03/22/2024] [Indexed: 05/08/2024] Open
Abstract
Thousands of endoparasitoid wasp species in the families Braconidae and Ichneumonidae harbor "domesticated endogenous viruses" (DEVs) in their genomes. This study focuses on ichneumonid DEVs, named ichnoviruses (IVs). Large quantities of DNA-containing IV virions are produced in ovary calyx cells during the pupal and adult stages of female wasps. Females parasitize host insects by injecting eggs and virions into the body cavity. After injection, virions rapidly infect host cells which is followed by expression of IV genes that promote the successful development of wasp offspring. IV genomes consist of two components: proviral segment loci that serve as templates for circular dsDNAs that are packaged into capsids, and genes from an ancestral virus that produce virions. In this study, we generated a chromosome-scale genome assembly for Hyposoter didymator that harbors H. didymator ichnovirus (HdIV). We identified a total of 67 HdIV loci that are amplified in calyx cells during the wasp pupal stage. We then focused on an HdIV gene, U16, which is transcribed in calyx cells during the initial stages of replication. Sequence analysis indicated that U16 contains a conserved domain in primases from select other viruses. Knockdown of U16 by RNA interference inhibited virion morphogenesis in calyx cells. Genome-wide analysis indicated U16 knockdown also inhibited amplification of HdIV loci in calyx cells. Altogether, our results identified several previously unknown HdIV loci, demonstrated that all HdIV loci are amplified in calyx cells during the pupal stage, and showed that U16 is required for amplification and virion morphogenesis.
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Affiliation(s)
- Ange Lorenzi
- DGIMI, Univ Montpellier, INRAE, Montpellier, France
- Department of Entomology, University of Georgia, Athens, Georgia, United States of America
| | - Fabrice Legeai
- INRAE, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, Rennes, France
- INRIA, IRISA, GenOuest Core Facility, Campus de Beaulieu, Rennes, France
| | | | | | - Michael R Strand
- Department of Entomology, University of Georgia, Athens, Georgia, United States of America
| | | | | | - Anthony Bretaudeau
- INRAE, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, Rennes, France
- INRIA, IRISA, GenOuest Core Facility, Campus de Beaulieu, Rennes, France
| | - Stéphanie Robin
- INRAE, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, Rennes, France
- INRIA, IRISA, GenOuest Core Facility, Campus de Beaulieu, Rennes, France
| | | | | | - Gaelen R Burke
- Department of Entomology, University of Georgia, Athens, Georgia, United States of America
| | - Rita Rebollo
- INRAE, INSA Lyon, BF2I, UMR203, Villeurbanne, France
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2
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Legeai F, Romain S, Capblancq T, Doniol-Valcroze P, Joron M, Lemaitre C, Després L. Chromosome-Level Assembly and Annotation of the Pearly Heath Coenonympha arcania Butterfly Genome. Genome Biol Evol 2024; 16:evae055. [PMID: 38491969 PMCID: PMC10980516 DOI: 10.1093/gbe/evae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/07/2024] [Accepted: 03/13/2024] [Indexed: 03/18/2024] Open
Abstract
We present the first chromosome-level genome assembly and annotation of the pearly heath Coenonympha arcania, generated with a PacBio HiFi sequencing approach and complemented with Hi-C data. We additionally compare synteny, gene, and repeat content between C. arcania and other Lepidopteran genomes. This reference genome will enable future population genomics studies with Coenonympha butterflies, a species-rich genus that encompasses some of the most highly endangered butterfly taxa in Europe.
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Affiliation(s)
- Fabrice Legeai
- Inria, CNRS, IRISA, University of Rennes, 35000 Rennes, France
- IGEPP, INRAE, Institut Agro, University of Rennes, 35653 Le Rheu, France
| | - Sandra Romain
- Inria, CNRS, IRISA, University of Rennes, 35000 Rennes, France
| | - Thibaut Capblancq
- LECA, CNRS, Université Grenoble-Alpes, Université Savoie Mont Blanc, Grenoble, France
| | | | - Mathieu Joron
- CEFE, CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
| | - Claire Lemaitre
- Inria, CNRS, IRISA, University of Rennes, 35000 Rennes, France
| | - Laurence Després
- LECA, CNRS, Université Grenoble-Alpes, Université Savoie Mont Blanc, Grenoble, France
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3
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Huguet MD, Robin S, Hudaverdian S, Tanguy S, Leterme-Prunier N, Cloteau R, Baulande S, Legoix-Né P, Legeai F, Simon JC, Jaquiéry J, Tagu D, Le Trionnaire G. Transcriptomic basis of sex loss in the pea aphid. BMC Genomics 2024; 25:202. [PMID: 38383295 PMCID: PMC10882735 DOI: 10.1186/s12864-023-09776-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 10/31/2023] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND Transitions from sexual to asexual reproduction are common in eukaryotes, but the underlying mechanisms remain poorly known. The pea aphid-Acyrthosiphon pisum-exhibits reproductive polymorphism, with cyclical parthenogenetic and obligate parthenogenetic lineages, offering an opportunity to decipher the genetic basis of sex loss. Previous work on this species identified a single 840 kb region controlling reproductive polymorphism and carrying 32 genes. With the aim of identifying the gene(s) responsible for sex loss and the resulting consequences on the genetic programs controlling sexual or asexual embryogenesis, we compared the transcriptomic response to photoperiod shortening-the main sex-inducing cue-of a sexual and an obligate asexual lineage of the pea aphid, focusing on heads (where the photoperiodic cue is detected) and embryos (the final target of the cue). RESULTS Our analyses revealed that four genes (one expressed in the head, and three in the embryos) of the region responded differently to photoperiod in the two lineages. We also found that the downstream genetic programs expressed during embryonic development of a future sexual female encompass ∼1600 genes, among which miRNAs, piRNAs and histone modification pathways are overrepresented. These genes mainly co-localize in two genomic regions enriched in transposable elements (TEs). CONCLUSIONS Our results suggest that the causal polymorphism(s) in the 840 kb region somehow impair downstream epigenetic and post-transcriptional regulations in obligate asexual lineages, thereby sustaining asexual reproduction.
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Affiliation(s)
- M D Huguet
- Institute for Genetics, Environment and Plant Protection, IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | - S Robin
- Institute for Genetics, Environment and Plant Protection, IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
- Institut National de Recherche en Informatique et en Automatique, Institut de Recherche en Informatique et Systèmes Aléatoires, Genscale, Campus Beaulieu, Rennes, 35042, France
| | - S Hudaverdian
- Institute for Genetics, Environment and Plant Protection, IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | - S Tanguy
- Institute for Genetics, Environment and Plant Protection, IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | - N Leterme-Prunier
- Institute for Genetics, Environment and Plant Protection, IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | - R Cloteau
- Institute for Genetics, Environment and Plant Protection, IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | - S Baulande
- Centre de Recherche, Genomics of Excellence Platform, Institut Curie, PSL Research University, Paris Cedex 05, France
| | - P Legoix-Né
- Centre de Recherche, Genomics of Excellence Platform, Institut Curie, PSL Research University, Paris Cedex 05, France
| | - F Legeai
- Institute for Genetics, Environment and Plant Protection, IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
- Institut National de Recherche en Informatique et en Automatique, Institut de Recherche en Informatique et Systèmes Aléatoires, Genscale, Campus Beaulieu, Rennes, 35042, France
| | - J-C Simon
- Institute for Genetics, Environment and Plant Protection, IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | - J Jaquiéry
- Institute for Genetics, Environment and Plant Protection, IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | - D Tagu
- Institute for Genetics, Environment and Plant Protection, IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France
| | - G Le Trionnaire
- Institute for Genetics, Environment and Plant Protection, IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, 35653, France.
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Arai H, Legeai F, Kageyama D, Sugio A, Simon JC. Genomic insights into Spiroplasma endosymbionts that induce male-killing and protective phenotypes in the pea aphid. FEMS Microbiol Lett 2024; 371:fnae027. [PMID: 38632047 DOI: 10.1093/femsle/fnae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 04/19/2024] Open
Abstract
The endosymbiotic bacteria Spiroplasma (Mollicutes) infect diverse plants and arthropods, and some of which induce male killing, where male hosts are killed during development. Male-killing Spiroplasma strains belong to either the phylogenetically distant Citri-Poulsonii or Ixodetis groups. In Drosophila flies, Spiroplasma poulsonii induces male killing via the Spaid toxin. While Spiroplasma ixodetis infects a wide range of insects and arachnids, little is known about the genetic basis of S. ixodetis-induced male killing. Here, we analyzed the genome of S. ixodetis strains in the pea aphid Acyrthosiphon pisum (Aphididae, Hemiptera). Genome sequencing constructed a complete genome of a male-killing strain, sAp269, consisting of a 1.5 Mb circular chromosome and an 80 Kb plasmid. sAp269 encoded putative virulence factors containing either ankyrin repeat, ovarian tumor-like deubiquitinase, or ribosome inactivating protein domains, but lacked the Spaid toxin. Further comparative genomics of Spiroplasma strains in A. pisum biotypes adapted to different host plants revealed their phylogenetic associations and the diversity of putative virulence factors. Although the mechanisms of S. ixodetis-induced male killing in pea aphids remain elusive, this study underlines the dynamic genome evolution of S. ixodetis and proposes independent acquisition events of male-killing mechanisms in insects.
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Affiliation(s)
- Hiroshi Arai
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-0851, Japan
| | - Fabrice Legeai
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | - Daisuke Kageyama
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-0851, Japan
| | - Akiko Sugio
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
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Rimbault M, Legeai F, Peccoud J, Mieuzet L, Call E, Nouhaud P, Defendini H, Mahéo F, Marande W, Théron N, Tagu D, Le Trionnaire G, Simon JC, Jaquiéry J. Contrasting Evolutionary Patterns Between Sexual and Asexual Lineages in a Genomic Region Linked to Reproductive Mode Variation in the pea aphid. Genome Biol Evol 2023; 15:evad168. [PMID: 37717171 PMCID: PMC10538257 DOI: 10.1093/gbe/evad168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 09/01/2023] [Accepted: 09/12/2023] [Indexed: 09/18/2023] Open
Abstract
Although asexual lineages evolved from sexual lineages in many different taxa, the genetics of sex loss remains poorly understood. We addressed this issue in the pea aphid Acyrthosiphon pisum, whose natural populations encompass lineages performing cyclical parthenogenesis (CP) and producing one sexual generation per year, as well as obligate parthenogenetic (OP) lineages that can no longer produce sexual females but can still produce males. An SNP-based, whole-genome scan of CP and OP populations sequenced in pools (103 individuals from 6 populations) revealed that an X-linked region is associated with the variation in reproductive mode. This 840-kb region is highly divergent between CP and OP populations (FST = 34.9%), with >2,000 SNPs or short Indels showing a high degree of association with the phenotypic trait. In OP populations specifically, this region also shows reduced diversity and Tajima's D, consistent with the OP phenotype being a derived trait in aphids. Interestingly, the low genetic differentiation between CP and OP populations at the rest of the genome (FST = 2.5%) suggests gene flow between them. Males from OP lineages thus likely transmit their op allele to new genomic backgrounds. These genetic exchanges, combined with the selection of the OP and CP reproductive modes under different climates, probably contribute to the long-term persistence of the cp and op alleles.
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Affiliation(s)
- Maud Rimbault
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Fabrice Legeai
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
- University of Rennes, Inria, CNRS, IRISA, Rennes, France
| | - Jean Peccoud
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Unité Mixte de Recherche 7267 Centre National de la Recherche Scientifique, Université de Poitiers, Poitiers CEDEX 9, France
| | - Lucie Mieuzet
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Elsa Call
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Pierre Nouhaud
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Hélène Defendini
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Frédérique Mahéo
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - William Marande
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Nicolas Théron
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Denis Tagu
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Gaël Le Trionnaire
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Jean-Christophe Simon
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Julie Jaquiéry
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
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6
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Guichard A, Legeai F, Tagu D, Lemaitre C. MTG-Link: leveraging barcode information from linked-reads to assemble specific loci. BMC Bioinformatics 2023; 24:284. [PMID: 37452278 PMCID: PMC10347852 DOI: 10.1186/s12859-023-05395-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 06/21/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Local assembly with short and long reads has proven to be very useful in many applications: reconstruction of the sequence of a locus of interest, gap-filling in draft assemblies, as well as alternative allele reconstruction of large Structural Variants. Whereas linked-read technologies have a great potential to assemble specific loci as they provide long-range information while maintaining the power and accuracy of short-read sequencing, there is a lack of local assembly tools for linked-read data. RESULTS We present MTG-Link, a novel local assembly tool dedicated to linked-reads. The originality of the method lies in its read subsampling step which takes advantage of the barcode information contained in linked-reads mapped in flanking regions. We validated our approach on several datasets from different linked-read technologies. We show that MTG-Link is able to assemble successfully large sequences, up to dozens of Kb. We also demonstrate that the read subsampling step of MTG-Link considerably improves the local assembly of specific loci compared to other existing short-read local assembly tools. Furthermore, MTG-Link was able to fully characterize large insertion variants and deletion breakpoints in a human genome and to reconstruct dark regions in clinically-relevant human genes. It also improved the contiguity of a 1.3 Mb locus of biological interest in several individual genomes of the mimetic butterfly Heliconius numata. CONCLUSIONS MTG-Link is an efficient local assembly tool designed for different linked-read sequencing technologies. MTG-Link source code is available at https://github.com/anne-gcd/MTG-Link and as a Bioconda package.
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Affiliation(s)
- Anne Guichard
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France.
- Univ Rennes, Inria, CNRS, IRISA, 35000, Rennes, France.
| | - Fabrice Legeai
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
- Univ Rennes, Inria, CNRS, IRISA, 35000, Rennes, France
| | - Denis Tagu
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
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7
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Gauthier J, Meier J, Legeai F, McClure M, Whibley A, Bretaudeau A, Boulain H, Parrinello H, Mugford ST, Durbin R, Zhou C, McCarthy S, Wheat CW, Piron-Prunier F, Monsempes C, François MC, Jay P, Noûs C, Persyn E, Jacquin-Joly E, Meslin C, Montagné N, Lemaitre C, Elias M. First chromosome scale genomes of ithomiine butterflies (Nymphalidae: Ithomiini): Comparative models for mimicry genetic studies. Mol Ecol Resour 2023; 23:872-885. [PMID: 36533297 DOI: 10.1111/1755-0998.13749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022]
Abstract
The ithomiine butterflies (Nymphalidae: Danainae) represent the largest known radiation of Müllerian mimetic butterflies. They dominate by number the mimetic butterfly communities, which include species such as the iconic neotropical Heliconius genus. Recent studies on the ecology and genetics of speciation in Ithomiini have suggested that sexual pheromones, colour pattern and perhaps hostplant could drive reproductive isolation. However, no reference genome was available for Ithomiini, which has hindered further exploration on the genetic architecture of these candidate traits, and more generally on the genomic patterns of divergence. Here, we generated high-quality, chromosome-scale genome assemblies for two Melinaea species, M. marsaeus and M. menophilus, and a draft genome of the species Ithomia salapia. We obtained genomes with a size ranging from 396 to 503 Mb across the three species and scaffold N50 of 40.5 and 23.2 Mb for the two chromosome-scale assemblies. Using collinearity analyses we identified massive rearrangements between the two closely related Melinaea species. An annotation of transposable elements and gene content was performed, as well as a specialist annotation to target chemosensory genes, which is crucial for host plant detection and mate recognition in mimetic species. A comparative genomic approach revealed independent gene expansions in ithomiines and particularly in gustatory receptor genes. These first three genomes of ithomiine mimetic butterflies constitute a valuable addition and a welcome comparison to existing biological models such as Heliconius, and will enable further understanding of the mechanisms of adaptation in butterflies.
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Affiliation(s)
| | - Joana Meier
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Fabrice Legeai
- BIPAA, IGEPP, INRAE, Institut Agro, Univ Rennes, Rennes, France
- Univ Rennes, Inria, CNRS, IRISA, Rennes, France
| | - Melanie McClure
- Institut Systématique Évolution Biodiversité (ISYEB), Centre National de la Recherche Scientifique, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
- Laboratoire Écologie, Évolution, Interactions des Systèmes Amazoniens (LEEISA), Université de Guyane, CNRS, IFREMER, Cayenne, France
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Anthony Bretaudeau
- BIPAA, IGEPP, INRAE, Institut Agro, Univ Rennes, Rennes, France
- Univ Rennes, Inria, CNRS, IRISA, Rennes, France
| | - Hélène Boulain
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Hugues Parrinello
- MGX-Montpellier GenomiX, Univ. Montpellier, CNRS, INSERM, Montpellier, France
| | - Sam T Mugford
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Chenxi Zhou
- Department of Genetics, University of Cambridge, Cambridge, UK
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Shane McCarthy
- Department of Genetics, University of Cambridge, Cambridge, UK
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, UK
| | | | - Florence Piron-Prunier
- Institut Systématique Évolution Biodiversité (ISYEB), Centre National de la Recherche Scientifique, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
| | - Christelle Monsempes
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Marie-Christine François
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Paul Jay
- Ecologie Systématique Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
| | | | - Emma Persyn
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
- CIRAD, UMR PVBMT, St Pierre, France
| | - Emmanuelle Jacquin-Joly
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Camille Meslin
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Nicolas Montagné
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | | | - Marianne Elias
- Institut Systématique Évolution Biodiversité (ISYEB), Centre National de la Recherche Scientifique, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
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Robin S, Legeai F, Jouan V, Ogliastro M, Darboux I. Genome-wide identification of lncRNAs associated with viral infection in Spodoptera frugiperda. J Gen Virol 2023; 104. [PMID: 36757871 DOI: 10.1099/jgv.0.001827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
The role of lncRNAs in immune defence has been demonstrated in many multicellular and unicellular organisms. However, investigation of the identification and characterization of long non-coding RNAs (lncRNAs) involved in the insect immune response is still limited. In this study, we used RNA sequencing (RNA-seq) to investigate the expression profiles of lncRNAs and mRNAs in the fall armyworm Spodoptera frugiperda in response to virus infection. To assess the tissue- and virus-specificity of lncRNAs, we analysed and compared their expression profiles in haemocytes and fat body of larvae infected with two entomopathogenic viruses with different lifestyles, i.e. the polydnavirus HdIV (Hyposoter didymator IchnoVirus) and the densovirus JcDV (Junonia coenia densovirus). We identified 1883 candidate lncRNAs, of which 529 showed differential expression following viral infection. Expression profiles differed considerably between samples, indicating that many differentially expressed (DE) lncRNAs showed virus- and tissue-specific expression patterns. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and target prediction analyses indicated that DE-LncRNAs were mainly enriched in metabolic process, DNA replication and repair, immune response, metabolism of insect hormone and cell adhesion. In addition, we identified three DE-lncRNAs potentially acting as microRNA host genes, suggesting that they participate in gene regulation by producing miRNAs in response to virus infection. This study provides a catalogue of lncRNAs expressed in two important immune tissues and potential insight into their roles in the antiviral defence in S. frugiperda. The results may help future in-depth functional studies to better understand the biological function of lncRNAs in interaction between viruses and the fall armyworm.
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Affiliation(s)
- Stéphanie Robin
- BIPAA, IGEPP, INRAE, Institut Agro, University of Rennes, Rennes, France.,University of Rennes, INRIA, CNRS, IRISA, Rennes, France
| | - Fabrice Legeai
- BIPAA, IGEPP, INRAE, Institut Agro, University of Rennes, Rennes, France.,University of Rennes, INRIA, CNRS, IRISA, Rennes, France
| | - Véronique Jouan
- INRAE, University of Montpellier, UMR Diversité, Génomes & Interactions Microorganismes-Insectes (DGIMI), Montpellier, France
| | - Mylène Ogliastro
- INRAE, University of Montpellier, UMR Diversité, Génomes & Interactions Microorganismes-Insectes (DGIMI), Montpellier, France
| | - Isabelle Darboux
- INRAE, University of Montpellier, UMR Diversité, Génomes & Interactions Microorganismes-Insectes (DGIMI), Montpellier, France
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9
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Yainna S, Tay WT, Durand K, Fiteni E, Hilliou F, Legeai F, Clamens AL, Gimenez S, Asokan R, Kalleshwaraswamy CM, Deshmukh SS, Meagher RL, Blanco CA, Silvie P, Brévault T, Dassou A, Kergoat GJ, Walsh T, Gordon K, Nègre N, d’Alençon E, Nam K. The evolutionary process of invasion in the fall armyworm (Spodoptera frugiperda). Sci Rep 2022; 12:21063. [PMID: 36473923 PMCID: PMC9727104 DOI: 10.1038/s41598-022-25529-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
The fall armyworm (FAW; Spodoptera frugiperda) is one of the major agricultural pest insects. FAW is native to the Americas, and its invasion was first reported in West Africa in 2016. Then it quickly spread through Africa, Asia, and Oceania, becoming one of the main threats to corn production. We analyzed whole genome sequences of 177 FAW individuals from 12 locations on four continents to infer evolutionary processes of invasion. Principal component analysis from the TPI gene and whole genome sequences shows that invasive FAW populations originated from the corn strain. Ancestry coefficient and phylogenetic analyses from the nuclear genome indicate that invasive populations are derived from a single ancestry, distinct from native populations, while the mitochondrial phylogenetic tree supports the hypothesis of multiple introductions. Adaptive evolution specific to invasive populations was observed in detoxification, chemosensory, and digestion genes. We concluded that extant invasive FAW populations originated from the corn strain with potential contributions of adaptive evolution.
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Affiliation(s)
- Sudeeptha Yainna
- grid.503158.aDGIMI, Univ Montpellier, INRAE, Montpellier, France ,grid.8183.20000 0001 2153 9871CIRAD, UPR AIDA, Montpellier, France
| | - Wee Tek Tay
- grid.1016.60000 0001 2173 2719Black Mountain Laboratories, CSIRO, Canberra, Australia
| | - Karine Durand
- grid.503158.aDGIMI, Univ Montpellier, INRAE, Montpellier, France
| | - Estelle Fiteni
- grid.503158.aDGIMI, Univ Montpellier, INRAE, Montpellier, France
| | - Frédérique Hilliou
- grid.435437.20000 0004 0385 8766INRAE, Institut Sophia Agrobiotech, Université Côte D’Azur, CNRS, Sophia Antipolis, France
| | - Fabrice Legeai
- INRAE, UMR-IGEPP, BioInformatics Platform for Agroecosystems Arthropods, Campus Beaulieu, 35042 Rennes, France ,grid.420225.30000 0001 2298 7270INRIA, IRISA, GenOuest Core Facility, Campus de Beaulieu, Rennes, France
| | - Anne-Laure Clamens
- grid.121334.60000 0001 2097 0141CBGP, INRAE, CIRAD, IRD, Institut Agro, Univ Montpellier, Montpellier, France
| | - Sylvie Gimenez
- grid.503158.aDGIMI, Univ Montpellier, INRAE, Montpellier, France
| | - R. Asokan
- grid.418222.f0000 0000 8663 7600Division of Biotechnology, ICAR - Indian Institute of Horticultural Research, Bengaluru, India
| | - C. M. Kalleshwaraswamy
- grid.509224.8Department of Entomology, College of Agriculture, University of Agricultural and Horticultural Sciences, Shivamogga, India
| | - Sharanabasappa S. Deshmukh
- grid.509224.8Department of Entomology, College of Agriculture, University of Agricultural and Horticultural Sciences, Shivamogga, India
| | - Robert L. Meagher
- grid.463419.d0000 0001 0946 3608United States Department of Agriculture, Agricultural Research Service, Gainesville, FL USA
| | - Carlos A. Blanco
- grid.413759.d0000 0001 0725 8379United States Department of Agriculture, Animal and Plant Health Inspection Service, Maryland, USA
| | - Pierre Silvie
- grid.8183.20000 0001 2153 9871CIRAD, UPR AIDA, Montpellier, France ,grid.121334.60000 0001 2097 0141AIDA, Univ Montpellier, CIRAD, Montpellier, France ,grid.121334.60000 0001 2097 0141PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Thierry Brévault
- grid.8183.20000 0001 2153 9871CIRAD, UPR AIDA, Montpellier, France ,grid.121334.60000 0001 2097 0141AIDA, Univ Montpellier, CIRAD, Montpellier, France
| | - Anicet Dassou
- grid.510426.40000 0004 7470 473XENSBBA, UNSTIM, Dassa, Benin
| | - Gael J. Kergoat
- grid.420225.30000 0001 2298 7270INRIA, IRISA, GenOuest Core Facility, Campus de Beaulieu, Rennes, France
| | - Thomas Walsh
- grid.1016.60000 0001 2173 2719Black Mountain Laboratories, CSIRO, Canberra, Australia
| | - Karl Gordon
- grid.1016.60000 0001 2173 2719Black Mountain Laboratories, CSIRO, Canberra, Australia
| | - Nicolas Nègre
- grid.503158.aDGIMI, Univ Montpellier, INRAE, Montpellier, France
| | | | - Kiwoong Nam
- grid.503158.aDGIMI, Univ Montpellier, INRAE, Montpellier, France
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10
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Fiteni E, Durand K, Gimenez S, Meagher RL, Legeai F, Kergoat GJ, Nègre N, d’Alençon E, Nam K. Host-plant adaptation as a driver of incipient speciation in the fall armyworm (Spodoptera frugiperda). BMC Ecol Evol 2022; 22:133. [DOI: 10.1186/s12862-022-02090-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Divergent selection on host-plants is one of the main evolutionary forces driving ecological speciation in phytophagous insects. The ecological speciation might be challenging in the presence of gene flow and assortative mating because the direction of divergence is not necessarily the same between ecological selection (through host-plant adaptation) and assortative mating. The fall armyworm (FAW), a major lepidopteran pest species, is composed of two sympatric strains, corn and rice strains, named after two of their preferred host-plants. These two strains have been hypothesized to undergo incipient speciation, based on (i) several lines of evidence encompassing both pre- and post-zygotic reproductive isolation, and (ii) the presence of a substantial level of genetic differentiation. Even though the status of these two strains has been established a long time ago, it is still yet to be found whether these two strains indeed exhibit a marked level of genetic differentiation from a large number of genomic loci. Here, we analyzed whole genome sequences from 56 FAW individuals either collected from pasture grasses (a part of the favored host range of the rice strain) or corn to assess the role of host-plant adaptation in incipient speciation.
Results
Principal component analysis of whole genome data shows that the pattern of divergence in the fall armyworm is predominantly explained by the genetic differentiation associated with host-plants. The level of genetic differentiation between corn and rice strains is particularly marked in the Z chromosome. We identified one autosomal locus and two Z chromosome loci targeted by selective sweeps specific to rice strain and corn strain, respectively. The autosomal locus has both increased DXY and FST while the Z chromosome loci had decreased DXY and increased FST.
Conclusion
These results show that the FAW population structure is dominated by the genetic differentiation between corn and rice strains. This differentiation involves divergent selection targeting at least three loci, which include a locus potentially causing reproductive isolation. Taken together, these results suggest the evolutionary scenario that host-plant speciation is a driver of incipient speciation in the fall armyworm.
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11
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Meslin C, Mainet P, Montagné N, Robin S, Legeai F, Bretaudeau A, Johnston JS, Koutroumpa F, Persyn E, Monsempès C, François MC, Jacquin-Joly E. Spodoptera littoralis genome mining brings insights on the dynamic of expansion of gustatory receptors in polyphagous noctuidae. G3 (Bethesda) 2022; 12:6598846. [PMID: 35652787 PMCID: PMC9339325 DOI: 10.1093/g3journal/jkac131] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022]
Abstract
The bitter taste, triggered via gustatory receptors, serves as an important natural defense against the ingestion of poisonous foods in animals, and the increased host breadth is usually linked to an increase in the number of gustatory receptor genes. This has been especially observed in polyphagous insect species, such as noctuid species from the Spodoptera genus. However, the dynamic and physical mechanisms leading to these gene expansions and the evolutionary pressures behind them remain elusive. Among major drivers of genome dynamics are the transposable elements but, surprisingly, their potential role in insect gustatory receptor expansion has not been considered yet. In this work, we hypothesized that transposable elements and possibly positive selection would be involved in the highly dynamic evolution of gustatory receptor in Spodoptera spp. We first sequenced de novo the full 465 Mb genome of S. littoralis, and manually annotated the main chemosensory genes, including a large repertoire of 373 gustatory receptor genes (including 19 pseudogenes). We also improved the completeness of S. frugiperda and S. litura gustatory receptor gene repertoires. Then, we annotated transposable elements and revealed that a particular category of class I retrotransposons, the SINE transposons, was significantly enriched in the vicinity of gustatory receptor gene clusters, suggesting a transposon-mediated mechanism for the formation of these clusters. Selection pressure analyses indicated that positive selection within the gustatory receptor gene family is cryptic, only 7 receptors being identified as positively selected. Altogether, our data provide a new good quality Spodoptera genome, pinpoint interesting gustatory receptor candidates for further functional studies and bring valuable genomic information on the mechanisms of gustatory receptor expansions in polyphagous insect species.
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Affiliation(s)
- Camille Meslin
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), 78026 Versailles, France
| | - Pauline Mainet
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), 78026 Versailles, France
| | - Nicolas Montagné
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), 78026 Versailles, France
| | - Stéphanie Robin
- INRAE, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, 35042 Rennes, France.,INRIA, IRISA, GenOuest Core Facility, Campus de Beaulieu, Rennes 5042, France
| | - Fabrice Legeai
- INRAE, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, 35042 Rennes, France.,INRIA, IRISA, GenOuest Core Facility, Campus de Beaulieu, Rennes 5042, France
| | - Anthony Bretaudeau
- INRAE, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, 35042 Rennes, France.,INRIA, IRISA, GenOuest Core Facility, Campus de Beaulieu, Rennes 5042, France
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Fotini Koutroumpa
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), 78026 Versailles, France.,Present address: INRAE, Université Tours, Infectiologie et Santé Publique (ISP), 37380 Nouzilly, France
| | - Emma Persyn
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), 78026 Versailles, France.,CIRAD, UMR PVBMT, Réunion, France
| | - Christelle Monsempès
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), 78026 Versailles, France
| | - Marie-Christine François
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), 78026 Versailles, France
| | - Emmanuelle Jacquin-Joly
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), 78026 Versailles, France
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12
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Aigu Y, Daval S, Gazengel K, Marnet N, Lariagon C, Laperche A, Legeai F, Manzanares-Dauleux MJ, Gravot A. Multi-Omic Investigation of Low-Nitrogen Conditional Resistance to Clubroot Reveals Brassica napus Genes Involved in Nitrate Assimilation. Front Plant Sci 2022; 13:790563. [PMID: 35222461 PMCID: PMC8874135 DOI: 10.3389/fpls.2022.790563] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/21/2022] [Indexed: 05/10/2023]
Abstract
Nitrogen fertilization has been reported to influence the development of clubroot, a root disease of Brassicaceae species, caused by the obligate protist Plasmodiophora brassicae. Our previous works highlighted that low-nitrogen fertilization induced a strong reduction of clubroot symptoms in some oilseed rape genotypes. To further understand the underlying mechanisms, the response to P. brassicae infection was investigated in two genotypes "Yudal" and HD018 harboring sharply contrasted nitrogen-driven modulation of resistance toward P. brassicae. Targeted hormone and metabolic profiling, as well as RNA-seq analysis, were performed in inoculated and non-inoculated roots at 14 and 27 days post-inoculation, under high and low-nitrogen conditions. Clubroot infection triggered a large increase of SA concentration and an induction of the SA gene markers expression whatever the genotype and nitrogen conditions. Overall, metabolic profiles suggested that N-driven induction of resistance was independent of SA signaling, soluble carbohydrate and amino acid concentrations. Low-nitrogen-driven resistance in "Yudal" was associated with the transcriptional regulation of a small set of genes, among which the induction of NRT2- and NR-encoding genes. Altogether, our results indicate a possible role of nitrate transporters and auxin signaling in the crosstalk between plant nutrition and partial resistance to pathogens.
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Affiliation(s)
- Yoann Aigu
- IGEPP, INRAE, Institut Agro, Université de Rennes 1, Le Rheu, France
| | - Stéphanie Daval
- IGEPP, INRAE, Institut Agro, Université de Rennes 1, Le Rheu, France
| | - Kévin Gazengel
- IGEPP, INRAE, Institut Agro, Université de Rennes 1, Le Rheu, France
| | | | | | - Anne Laperche
- IGEPP, INRAE, Institut Agro, Université de Rennes 1, Le Rheu, France
| | - Fabrice Legeai
- IGEPP, INRAE, Institut Agro, Université de Rennes 1, Le Rheu, France
| | | | - Antoine Gravot
- IGEPP, INRAE, Institut Agro, Université de Rennes 1, Le Rheu, France
- *Correspondence: Gravot Antoine,
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13
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Bianchetti G, Clouet V, Legeai F, Baron C, Gazengel K, Carrillo A, Manzanares-Dauleux MJ, Buitink J, Nesi N. RNA sequencing data for responses to drought stress and/or clubroot infection in developing seeds of Brassica napus. Data Brief 2021; 38:107392. [PMID: 34611536 PMCID: PMC8477133 DOI: 10.1016/j.dib.2021.107392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 11/17/2022] Open
Abstract
Oilseed rape (Brassica napus L.) is the third largest oil crop worldwide. Like other crops, oilseed rape faces unfavorable environmental conditions resulting from multiple and combined actions of abiotic and biotic constraints that occur throughout the growing season. In particular drought severely reduces seed yield but also impacts seed quality in oilseed rape. In addition, clubroot disease, caused by the pathogen Plasmodiophora brassicae, limits the yield of the oilseed rape crops grown in infected areas. Clubroot induces swellings or galls on the roots that decrease the flow of water and nutrients within the plant. Furthermore, combinations of different stresses lead to complex plant responses that can not be predicted by the simple addition of individual stress responses. Indeed, an abiotic constraint can either reduce or stimulate the plant response to a pathogen or pest. Transcriptome datasets from different conditions are key resources to improve our knowledge of environmental stress-resistance mechanisms in plant organs. Here, we describe a RNA-seq dataset consisting of 72 samples of immature B. napus seeds from plants grown either under drought, infected with P. brassicae, or a combination of both stresses. A total of 67.6 Gb of transcriptome paired-end reads were filtered, mapped onto the B. napus reference genome Darmor-bzh and used for identification of differentially expressed genes and gene ontology enrichment. The raw reads are available under accession PRJNA738318 at NCBI Sequence Read Archive (SRA) repository. The dataset is a resource for the scientific community exploring seed plasticity.
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Affiliation(s)
- Grégoire Bianchetti
- IGEPP, INRAE, Institut Agro, Université de Rennes 1, BP35327, Le Rheu 35650, France
| | - Vanessa Clouet
- IGEPP, INRAE, Institut Agro, Université de Rennes 1, BP35327, Le Rheu 35650, France
| | - Fabrice Legeai
- IGEPP, INRAE, Institut Agro, Université de Rennes 1, BP35327, Le Rheu 35650, France
| | - Cécile Baron
- IGEPP, INRAE, Institut Agro, Université de Rennes 1, BP35327, Le Rheu 35650, France
| | - Kévin Gazengel
- IGEPP, INRAE, Institut Agro, Université de Rennes 1, BP35327, Le Rheu 35650, France
| | - Aurélien Carrillo
- IGEPP, INRAE, Institut Agro, Université de Rennes 1, BP35327, Le Rheu 35650, France
| | | | - Julia Buitink
- IRHS, INRAE, Institut Agro, Université d'Angers, SFR4207 QuaSaV, Beaucouzé 49070, France
| | - Nathalie Nesi
- IGEPP, INRAE, Institut Agro, Université de Rennes 1, BP35327, Le Rheu 35650, France
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14
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Piron-Prunier F, Persyn E, Legeai F, McClure M, Meslin C, Robin S, Alves-Carvalho S, Mohammad A, Blugeon C, Jacquin-Joly E, Montagné N, Elias M, Gauthier J. Comparative transcriptome analysis at the onset of speciation in a mimetic butterfly-The Ithomiini Melinaea marsaeus. J Evol Biol 2021; 34:1704-1721. [PMID: 34570954 DOI: 10.1111/jeb.13940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/16/2021] [Accepted: 09/03/2021] [Indexed: 11/28/2022]
Abstract
Ecological speciation entails divergent selection on specific traits and ultimately on the developmental pathways responsible for these traits. Selection can act on gene sequences but also on regulatory regions responsible for gene expression. Mimetic butterflies are a relevant system for speciation studies because wing colour pattern (WCP) often diverges between closely related taxa and is thought to drive speciation through assortative mating and increased predation on hybrids. Here, we generate the first transcriptomic resources for a mimetic butterfly of the tribe Ithomiini, Melinaea marsaeus, to examine patterns of differential expression between two subspecies and between tissues that express traits that likely drive reproductive isolation; WCP and chemosensory genes. We sequenced whole transcriptomes of three life stages to cover a large catalogue of transcripts, and we investigated differential expression between subspecies in pupal wing discs and antennae. Eighteen known WCP genes were expressed in wing discs and 115 chemosensory genes were expressed in antennae, with a remarkable diversity of chemosensory protein genes. Many transcripts were differentially expressed between subspecies, including two WCP genes and one odorant receptor. Our results suggest that in M. marsaeus the same genes as in other mimetic butterflies are involved in traits causing reproductive isolation, and point at possible candidates for the differences in those traits between subspecies. Differential expression analyses of other developmental stages and body organs and functional studies are needed to confirm and expand these results. Our work provides key resources for comparative genomics in mimetic butterflies, and more generally in Lepidoptera.
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Affiliation(s)
- Florence Piron-Prunier
- Institut de Systématique, Evolution, Biodiversité, MNHN, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Emma Persyn
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Fabrice Legeai
- BIPAA, IGEPP, INRAE, Institut Agro, Univ Rennes, Rennes, France.,Univ Rennes, INRIA, CNRS, IRISA, Rennes, France
| | - Melanie McClure
- Institut de Systématique, Evolution, Biodiversité, MNHN, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,Laboratoire Écologie, Évolution,Interactions des Systèmes Amazoniens (LEEISA), Université de Guyane, CNRS, IFREMER, Cayenne, France
| | - Camille Meslin
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Stéphanie Robin
- BIPAA, IGEPP, INRAE, Institut Agro, Univ Rennes, Rennes, France.,Univ Rennes, INRIA, CNRS, IRISA, Rennes, France
| | | | - Ammara Mohammad
- Département de Biologie, Genomics Core Facility, Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Corinne Blugeon
- Département de Biologie, Genomics Core Facility, Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Emmanuelle Jacquin-Joly
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Nicolas Montagné
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Marianne Elias
- Institut de Systématique, Evolution, Biodiversité, MNHN, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Jérémy Gauthier
- Univ Rennes, INRIA, CNRS, IRISA, Rennes, France.,Geneva Natural History Museum, Geneva, Switzerland
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15
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Morisse P, Lemaitre C, Legeai F. LRez: a C++ API and toolkit for analyzing and managing Linked-Reads data. Bioinform Adv 2021; 1:vbab022. [PMID: 36700107 PMCID: PMC9710615 DOI: 10.1093/bioadv/vbab022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/09/2021] [Accepted: 09/20/2021] [Indexed: 01/28/2023]
Abstract
Motivation Linked-Reads technologies combine both the high quality and low cost of short-reads sequencing and long-range information, through the use of barcodes tagging reads which originate from a common long DNA molecule. This technology has been employed in a broad range of applications including genome assembly, phasing and scaffolding, as well as structural variant calling. However, to date, no tool or API dedicated to the manipulation of Linked-Reads data exist. Results We introduce LRez, a C++ API and toolkit that allows easy management of Linked-Reads data. LRez includes various functionalities, for computing numbers of common barcodes between genomic regions, extracting barcodes from BAM files, as well as indexing and querying BAM, FASTQ and gzipped FASTQ files to quickly fetch all reads or alignments containing a given barcode. LRez is compatible with a wide range of Linked-Reads sequencing technologies, and can thus be used in any tool or pipeline requiring barcode processing or indexing, in order to improve their performances. Availability and implementation LRez is implemented in C++, supported on Unix-based platforms and available under AGPL-3.0 License at https://github.com/morispi/LRez, and as a bioconda module. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Pierre Morisse
- Univ Rennes, Inria, CNRS, IRISA, Rennes 35000, France,To whom correspondence should be addressed.
| | | | - Fabrice Legeai
- Univ Rennes, Inria, CNRS, IRISA, Rennes 35000, France,IGEPP, INRAE, Institut Agro, Univ Rennes, Rennes 35000, France
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16
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Gauthier J, Boulain H, van Vugt JJFA, Baudry L, Persyn E, Aury JM, Noel B, Bretaudeau A, Legeai F, Warris S, Chebbi MA, Dubreuil G, Duvic B, Kremer N, Gayral P, Musset K, Josse T, Bigot D, Bressac C, Moreau S, Periquet G, Harry M, Montagné N, Boulogne I, Sabeti-Azad M, Maïbèche M, Chertemps T, Hilliou F, Siaussat D, Amselem J, Luyten I, Capdevielle-Dulac C, Labadie K, Merlin BL, Barbe V, de Boer JG, Marbouty M, Cônsoli FL, Dupas S, Hua-Van A, Le Goff G, Bézier A, Jacquin-Joly E, Whitfield JB, Vet LEM, Smid HM, Kaiser L, Koszul R, Huguet E, Herniou EA, Drezen JM. Author Correction: Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization. Commun Biol 2021; 4:940. [PMID: 34331006 PMCID: PMC8324771 DOI: 10.1038/s42003-021-02480-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Jérémy Gauthier
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200, Tours, France.,Geneva Natural History Museum, 1208, Geneva, Switzerland
| | - Hélène Boulain
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200, Tours, France.,EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Joke J F A van Vugt
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Lyam Baudry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris, 75015, France.,Sorbonne Université, Collège Doctoral, 75005, Paris, France
| | - Emma Persyn
- Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005, Paris, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Anthony Bretaudeau
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35000, Rennes, France.,Univ Rennes, Inria, CNRS, IRISA, 35000, Rennes, France
| | - Fabrice Legeai
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35000, Rennes, France.,Univ Rennes, Inria, CNRS, IRISA, 35000, Rennes, France
| | - Sven Warris
- Applied Bioinformatics, Wageningen University & Research, Wageningen, The Netherlands
| | - Mohamed A Chebbi
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200, Tours, France
| | - Géraldine Dubreuil
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200, Tours, France
| | - Bernard Duvic
- Université Montpellier, INRAE, DGIMI, 34095, Montpellier, France
| | - Natacha Kremer
- Laboratoire de Biométrie et Biologie Evolutive Université de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5558, 43 bd du 11 novembre 1918, bat. G. Mendel, 69622, Villeurbanne Cedex, France
| | - Philippe Gayral
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200, Tours, France
| | - Karine Musset
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200, Tours, France
| | - Thibaut Josse
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200, Tours, France
| | - Diane Bigot
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200, Tours, France
| | - Christophe Bressac
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200, Tours, France
| | - Sébastien Moreau
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200, Tours, France
| | - Georges Periquet
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200, Tours, France
| | - Myriam Harry
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
| | - Nicolas Montagné
- Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005, Paris, France
| | - Isabelle Boulogne
- Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005, Paris, France
| | - Mahnaz Sabeti-Azad
- Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005, Paris, France
| | - Martine Maïbèche
- Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005, Paris, France
| | - Thomas Chertemps
- Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005, Paris, France
| | - Frédérique Hilliou
- Université Côte d'Azur, INRAE, CNRS, ISA, 06903, Sophia-Antipolis, France
| | - David Siaussat
- Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005, Paris, France
| | - Joëlle Amselem
- Université Paris-Saclay, INRAE, URGI, 78026, Versailles, France
| | - Isabelle Luyten
- Université Paris-Saclay, INRAE, URGI, 78026, Versailles, France
| | - Claire Capdevielle-Dulac
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
| | - Karine Labadie
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Bruna Laís Merlin
- Insect Interactions Laboratory, Department of Entomology and Acarology, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, 13418-900, Brazil
| | - Valérie Barbe
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jetske G de Boer
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.,Laboratory of Entomology, Wageningen University, P.O. Box 16, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.,Evolutionary Genetics, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Martial Marbouty
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris, 75015, France
| | - Fernando Luis Cônsoli
- Insect Interactions Laboratory, Department of Entomology and Acarology, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, 13418-900, Brazil
| | - Stéphane Dupas
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
| | - Aurélie Hua-Van
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
| | - Gaelle Le Goff
- Université Côte d'Azur, INRAE, CNRS, ISA, 06903, Sophia-Antipolis, France
| | - Annie Bézier
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200, Tours, France
| | - Emmanuelle Jacquin-Joly
- Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005, Paris, France
| | - James B Whitfield
- Department of Entomology, 320 Morrill Hall, 505 South Goodwin Avenue, University of Illinois, Urbana, IL, 61801, USA
| | - Louise E M Vet
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.,Laboratory of Entomology, Wageningen University, P.O. Box 16, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Hans M Smid
- Laboratory of Entomology, Wageningen University, P.O. Box 16, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Laure Kaiser
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris, 75015, France
| | - Elisabeth Huguet
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200, Tours, France
| | - Elisabeth A Herniou
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200, Tours, France
| | - Jean-Michel Drezen
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200, Tours, France.
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17
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Cusumano A, Urbach S, Legeai F, Ravallec M, Dicke M, Poelman EH, Volkoff AN. Plant-phenotypic changes induced by parasitoid ichnoviruses enhance the performance of both unparasitized and parasitized caterpillars. Mol Ecol 2021; 30:4567-4583. [PMID: 34245612 PMCID: PMC8518489 DOI: 10.1111/mec.16072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 07/02/2021] [Indexed: 12/29/2022]
Abstract
There is increasing awareness that interactions between plants and insects can be mediated by microbial symbionts. Nonetheless, evidence showing that symbionts associated with organisms beyond the second trophic level affect plant‐insect interactions are restricted to a few cases belonging to parasitoid‐associated bracoviruses. Insect parasitoids harbour a wide array of symbionts which, like bracoviruses, can be injected into their herbivorous hosts to manipulate their physiology and behaviour. Yet, the function of these symbionts in plant‐based trophic webs remains largely overlooked. Here, we provide the first evidence of a parasitoid‐associated symbiont belonging to the group of ichnoviruses which affects the strength of plant‐insect interactions. A comparative proteomic analysis shows that, upon parasitoid injection of calyx fluid containing ichnovirus particles, the composition of salivary glands of caterpillars changes both qualitatively (presence of two viral‐encoded proteins) and quantitatively (abundance of several caterpillar‐resident enzymes, including elicitors such as glucose oxidase). In turn, plant phenotypic changes triggered by the altered composition of caterpillar oral secretions affect the performance of herbivores. Ichnovirus manipulation of plant responses to herbivory leads to benefits for their parasitoid partners in terms of reduced developmental time within the parasitized caterpillar. Interestingly, plant‐mediated ichnovirus‐induced effects also enhance the performances of unparasitized herbivores which in natural conditions may feed alongside parasitized ones. We discuss these findings in the context of ecological costs imposed to the plant by the viral symbiont of the parasitoid. Our results provide intriguing novel findings about the role played by carnivore‐associated symbionts on plant‐insect‐parasitoid systems and underline the importance of placing mutualistic associations in an ecological perspective.
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Affiliation(s)
- Antonino Cusumano
- DGIMI Université de Montpellier, INRAE, Montpellier, France.,Laboratory of Entomology, Wageningen University, Wageningen, The Netherlands.,Department of Agricultural, Food and Forest Sciences, University of Palermo, Palermo, Italy
| | - Serge Urbach
- IGF, Univ Montpellier, CNRS, INSERM, Montpellier, France.,BCM, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Fabrice Legeai
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, Le Rheu, France.,Université Rennes 1, INRIA, CNRS, IRISA, Rennes, France
| | - Marc Ravallec
- DGIMI Université de Montpellier, INRAE, Montpellier, France
| | - Marcel Dicke
- Laboratory of Entomology, Wageningen University, Wageningen, The Netherlands
| | - Erik H Poelman
- Laboratory of Entomology, Wageningen University, Wageningen, The Netherlands
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18
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Singh KS, Cordeiro EMG, Troczka BJ, Pym A, Mackisack J, Mathers TC, Duarte A, Legeai F, Robin S, Bielza P, Burrack HJ, Charaabi K, Denholm I, Figueroa CC, ffrench-Constant RH, Jander G, Margaritopoulos JT, Mazzoni E, Nauen R, Ramírez CC, Ren G, Stepanyan I, Umina PA, Voronova NV, Vontas J, Williamson MS, Wilson ACC, Xi-Wu G, Youn YN, Zimmer CT, Simon JC, Hayward A, Bass C. Global patterns in genomic diversity underpinning the evolution of insecticide resistance in the aphid crop pest Myzus persicae. Commun Biol 2021; 4:847. [PMID: 34234279 PMCID: PMC8263593 DOI: 10.1038/s42003-021-02373-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 06/17/2021] [Indexed: 02/06/2023] Open
Abstract
The aphid Myzus persicae is a destructive agricultural pest that displays an exceptional ability to develop resistance to both natural and synthetic insecticides. To investigate the evolution of resistance in this species we generated a chromosome-scale genome assembly and living panel of >110 fully sequenced globally sampled clonal lines. Our analyses reveal a remarkable diversity of resistance mutations segregating in global populations of M. persicae. We show that the emergence and spread of these mechanisms is influenced by host-plant associations, uncovering the widespread co-option of a host-plant adaptation that also offers resistance against synthetic insecticides. We identify both the repeated evolution of independent resistance mutations at the same locus, and multiple instances of the evolution of novel resistance mechanisms against key insecticides. Our findings provide fundamental insights into the genomic responses of global insect populations to strong selective forces, and hold practical relevance for the control of pests and parasites.
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Affiliation(s)
- Kumar Saurabh Singh
- grid.8391.30000 0004 1936 8024College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, Cornwall UK
| | - Erick M. G. Cordeiro
- grid.11899.380000 0004 1937 0722Departamento de Entomologia e Acarologia, Escola Superior de Agricultura “Luiz de Queiroz,”, Universidade de São Paulo, Piracicaba, Brazil
| | - Bartlomiej J. Troczka
- grid.8391.30000 0004 1936 8024College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, Cornwall UK
| | - Adam Pym
- grid.8391.30000 0004 1936 8024College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, Cornwall UK
| | - Joanna Mackisack
- grid.8391.30000 0004 1936 8024College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, Cornwall UK
| | - Thomas C. Mathers
- grid.14830.3e0000 0001 2175 7246Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Ana Duarte
- grid.8391.30000 0004 1936 8024College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, Cornwall UK
| | | | | | - Pablo Bielza
- grid.218430.c0000 0001 2153 2602Departamento de Producción Vegetal, Universidad Politécnica de Cartagena, Cartagena, Spain
| | - Hannah J. Burrack
- grid.40803.3f0000 0001 2173 6074Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC USA
| | - Kamel Charaabi
- Laboratory of Biotechnology and Nuclear Technologies, National Center of Nuclear Sciences and Technologies, Biotechpole of Sidi Thabet, Sidi Thabet, Ariana Tunisia
| | - Ian Denholm
- grid.5846.f0000 0001 2161 9644Department of Biological and Environmental Sciences, University of Hertfordshire, Hatfield, UK
| | - Christian C. Figueroa
- grid.10999.380000 0001 0036 2536Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Richard H. ffrench-Constant
- grid.8391.30000 0004 1936 8024College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, Cornwall UK
| | - Georg Jander
- grid.5386.8000000041936877XBoyce Thompson Institute, Ithaca, NY USA
| | - John T. Margaritopoulos
- Department of Plant Protection at Volos, Institute of Industrial and Fodder Crops, Hellenic Agricultural Organization ‘DEMETER’, Volos, Greece
| | - Emanuele Mazzoni
- grid.8142.f0000 0001 0941 3192Department of Sustainable Crop Production, Section Sustainable Crop and Food Protection, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Ralf Nauen
- grid.420044.60000 0004 0374 4101Bayer AG, Crop Science Division, R&D, Monheim, Germany
| | - Claudio C. Ramírez
- grid.10999.380000 0001 0036 2536Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Guangwei Ren
- grid.410727.70000 0001 0526 1937Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Ilona Stepanyan
- grid.418094.00000 0001 1146 7878Scientific Center of Zoology and Hydroecology, National Academy of Science, Republic of Armenia, Yerevan, Armenia
| | - Paul A. Umina
- Cesar, Parkville, Victoria Australia ,grid.1008.90000 0001 2179 088XSchool of BioSciences, The University of Melbourne, Parkville, Victoria Australia
| | - Nina V. Voronova
- grid.17678.3f0000 0001 1092 255XThe Department of General Ecology and Methods of Biology Teaching, Belarusian State University, Minsk, Republic of Belarus
| | - John Vontas
- grid.4834.b0000 0004 0635 685XInstitute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, Crete, Greece ,grid.10985.350000 0001 0794 1186Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Martin S. Williamson
- grid.418374.d0000 0001 2227 9389Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Alex C. C. Wilson
- grid.26790.3a0000 0004 1936 8606Department of Biology, University of Miami, Coral Gables, FL USA
| | - Gao Xi-Wu
- grid.22935.3f0000 0004 0530 8290Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Young-Nam Youn
- grid.254230.20000 0001 0722 6377Department of Applied Biology, College of Agricultural and Life Science, Chungnam National University, Daejeon, Korea
| | - Christoph T. Zimmer
- grid.8391.30000 0004 1936 8024College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, Cornwall UK ,grid.420222.40000 0001 0669 0426Present Address: Syngenta Crop Protection, Werk Stein, Schaffhauserstrasse, Stein, Switzerland
| | | | - Alex Hayward
- grid.8391.30000 0004 1936 8024College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, Cornwall UK
| | - Chris Bass
- grid.8391.30000 0004 1936 8024College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, Cornwall UK
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19
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Poivet E, Gallot A, Montagné N, Senin P, Monsempès C, Legeai F, Jacquin-Joly E. Transcriptome Profiling of Starvation in the Peripheral Chemosensory Organs of the Crop Pest Spodoptera littoralis Caterpillars. Insects 2021; 12:insects12070573. [PMID: 34201462 PMCID: PMC8303696 DOI: 10.3390/insects12070573] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/05/2021] [Accepted: 06/18/2021] [Indexed: 11/25/2022]
Abstract
Simple Summary Starvation increases olfactory sensitivity in a manner that enhances the search for food in animals, including insects. However, the molecular mechanisms via which starvation modulates olfactory receptor neuron function are poorly understood. In this study, we sequenced and compared the whole transcriptomes of the main olfactory organs (antennae and palps) of fed and starved caterpillars from the species Spodoptera littoralis. We revealed that transcripts involved in several biological processes are regulated upon starvation. These processes include glucose metabolism, immune defense, foraging activity, and olfaction. In this last process, we evidenced regulation of chemosensory proteins and odorant-degrading enzymes, known to play a role in the dynamics and the sensitivity of the olfactory receptor neuron response. Our results identify new elements in the cascade of olfactory neuron modulation, in addition to insulin, GABA, and short neuropeptide F signaling. Abstract Starvation is frequently encountered by animals under fluctuating food conditions in nature, and response to it is vital for life span. Many studies have investigated the behavioral and physiological responses to starvation. In particular, starvation is known to induce changes in olfactory behaviors and olfactory sensitivity to food odorants, but the underlying mechanisms are not well understood. Here, we investigated the transcriptional changes induced by starvation in the chemosensory tissues of the caterpillar Spodoptera littoralis, using Illumina RNA sequencing. Gene expression profiling revealed 81 regulated transcripts associated with several biological processes, such as glucose metabolism, immune defense, response to stress, foraging activity, and olfaction. Focusing on the olfactory process, we observed changes in transcripts encoding proteins putatively involved in the peri-receptor events, namely, chemosensory proteins and odorant-degrading enzymes. Such modulation of their expression may drive fluctuations in the dynamics and the sensitivity of the olfactory receptor neuron response. In combination with the enhanced presynaptic activity mediated via the short neuropeptide F expressed during fasting periods, this could explain an enhanced olfactory detection process. Our observations suggest that a coordinated transcriptional response of peripheral chemosensory organs participates in the regulation of olfactory signal reception and olfactory-driven behaviors upon starvation.
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Affiliation(s)
- Erwan Poivet
- Institute of Ecology and Environmental Sciences of Paris, INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, 78000 Versailles, France; (E.P.); (A.G.); (N.M.); (C.M.)
| | - Aurore Gallot
- Institute of Ecology and Environmental Sciences of Paris, INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, 78000 Versailles, France; (E.P.); (A.G.); (N.M.); (C.M.)
| | - Nicolas Montagné
- Institute of Ecology and Environmental Sciences of Paris, INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, 78000 Versailles, France; (E.P.); (A.G.); (N.M.); (C.M.)
| | - Pavel Senin
- IRISA, INRIA, CNRS, Université de Rennes, 35000 Rennes, France; (P.S.); (F.L.)
| | - Christelle Monsempès
- Institute of Ecology and Environmental Sciences of Paris, INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, 78000 Versailles, France; (E.P.); (A.G.); (N.M.); (C.M.)
| | - Fabrice Legeai
- IRISA, INRIA, CNRS, Université de Rennes, 35000 Rennes, France; (P.S.); (F.L.)
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35000 Rennes, France
| | - Emmanuelle Jacquin-Joly
- Institute of Ecology and Environmental Sciences of Paris, INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, 78000 Versailles, France; (E.P.); (A.G.); (N.M.); (C.M.)
- Correspondence:
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20
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Fernández R, Marcet-Houben M, Legeai F, Richard G, Robin S, Wucher V, Pegueroles C, Gabaldón T, Tagu D. Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum. Mol Biol Evol 2021; 37:2601-2615. [PMID: 32359152 PMCID: PMC7475028 DOI: 10.1093/molbev/msaa110] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Ecology of insects is as wide as their diversity, which reflects their high capacity of adaptation in most of the environments of our planet. Aphids, with over 4,000 species, have developed a series of adaptations including a high phenotypic plasticity and the ability to feed on the phloem sap of plants, which is enriched in sugars derived from photosynthesis. Recent analyses of aphid genomes have indicated a high level of shared ancestral gene duplications that might represent a basis for genetic innovation and broad adaptations. In addition, there are a large number of recent, species-specific gene duplications whose role in adaptation remains poorly understood. Here, we tested whether duplicates specific to the pea aphid Acyrthosiphon pisum are related to genomic innovation by combining comparative genomics, transcriptomics, and chromatin accessibility analyses. Consistent with large levels of neofunctionalization, we found that most of the recent pairs of gene duplicates evolved asymmetrically, showing divergent patterns of positive selection and gene expression. Genes under selection involved a plethora of biological functions, suggesting that neofunctionalization and tissue specificity, among other evolutionary mechanisms, have orchestrated the evolution of recent paralogs in the pea aphid and may have facilitated host-symbiont cooperation. Our comprehensive phylogenomics analysis allowed us to tackle the history of duplicated genes to pave the road toward understanding the role of gene duplication in ecological adaptation.
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Affiliation(s)
- Rosa Fernández
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Animal Biodiversity and Evolution, Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Marina Marcet-Houben
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain.,Department of Life Sciences, Barcelona Supercomputing Center, Barcelona, Spain
| | - Fabrice Legeai
- IGEPP, INRAE, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France.,INRIA, IRISA, Genscale, Campus Beaulieu, Rennes, France
| | - Gautier Richard
- IGEPP, INRAE, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France.,Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Stéphanie Robin
- IGEPP, INRAE, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France.,INRIA, IRISA, GenOuest Core Facility, Campus Beaulieu, Rennes, France
| | - Valentin Wucher
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Cinta Pegueroles
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain.,Department of Life Sciences, Barcelona Supercomputing Center, Barcelona, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Department of Life Sciences, Barcelona Supercomputing Center, Barcelona, Spain
| | - Denis Tagu
- IGEPP, INRAE, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
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21
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Gauthier J, Boulain H, van Vugt JJFA, Baudry L, Persyn E, Aury JM, Noel B, Bretaudeau A, Legeai F, Warris S, Chebbi MA, Dubreuil G, Duvic B, Kremer N, Gayral P, Musset K, Josse T, Bigot D, Bressac C, Moreau S, Periquet G, Harry M, Montagné N, Boulogne I, Sabeti-Azad M, Maïbèche M, Chertemps T, Hilliou F, Siaussat D, Amselem J, Luyten I, Capdevielle-Dulac C, Labadie K, Merlin BL, Barbe V, de Boer JG, Marbouty M, Cônsoli FL, Dupas S, Hua-Van A, Le Goff G, Bézier A, Jacquin-Joly E, Whitfield JB, Vet LEM, Smid HM, Kaiser L, Koszul R, Huguet E, Herniou EA, Drezen JM. Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization. Commun Biol 2021; 4:104. [PMID: 33483589 PMCID: PMC7822920 DOI: 10.1038/s42003-020-01623-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023] Open
Abstract
Endogenous viruses form an important proportion of eukaryote genomes and a source of novel functions. How large DNA viruses integrated into a genome evolve when they confer a benefit to their host, however, remains unknown. Bracoviruses are essential for the parasitism success of parasitoid wasps, into whose genomes they integrated ~103 million years ago. Here we show, from the assembly of a parasitoid wasp genome at a chromosomal scale, that bracovirus genes colonized all ten chromosomes of Cotesia congregata. Most form clusters of genes involved in particle production or parasitism success. Genomic comparison with another wasp, Microplitis demolitor, revealed that these clusters were already established ~53 mya and thus belong to remarkably stable genomic structures, the architectures of which are evolutionary constrained. Transcriptomic analyses highlight temporal synchronization of viral gene expression without resulting in immune gene induction, suggesting that no conflicts remain between ancient symbiotic partners when benefits to them converge.
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Affiliation(s)
- Jérémy Gauthier
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France ,grid.466902.f0000 0001 2248 6951Geneva Natural History Museum, 1208 Geneva, Switzerland
| | - Hélène Boulain
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France ,grid.418656.80000 0001 1551 0562EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Joke J. F. A. van Vugt
- grid.418375.c0000 0001 1013 0288Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Lyam Baudry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris, 75015 France ,grid.462844.80000 0001 2308 1657Sorbonne Université, Collège Doctoral, 75005 Paris, France
| | - Emma Persyn
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Jean-Marc Aury
- grid.8390.20000 0001 2180 5818Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Benjamin Noel
- grid.8390.20000 0001 2180 5818Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Anthony Bretaudeau
- grid.410368.80000 0001 2191 9284IGEPP, INRAE, Institut Agro, Univ Rennes, 35000 Rennes, France ,grid.420225.30000 0001 2298 7270Univ Rennes, Inria, CNRS, IRISA, 35000 Rennes, France
| | - Fabrice Legeai
- grid.410368.80000 0001 2191 9284IGEPP, INRAE, Institut Agro, Univ Rennes, 35000 Rennes, France ,grid.420225.30000 0001 2298 7270Univ Rennes, Inria, CNRS, IRISA, 35000 Rennes, France
| | - Sven Warris
- grid.4818.50000 0001 0791 5666Applied Bioinformatics, Wageningen University & Research, Wageningen, The Netherlands
| | - Mohamed A. Chebbi
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Géraldine Dubreuil
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Bernard Duvic
- grid.503158.aUniversité Montpellier, INRAE, DGIMI, 34095 Montpellier, France
| | - Natacha Kremer
- grid.462854.90000 0004 0386 3493Laboratoire de Biométrie et Biologie Evolutive Université de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5558, 43 bd du 11 novembre 1918, bat. G. Mendel, 69622 Villeurbanne Cedex, France
| | - Philippe Gayral
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Karine Musset
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Thibaut Josse
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Diane Bigot
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Christophe Bressac
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Sébastien Moreau
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Georges Periquet
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Myriam Harry
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Nicolas Montagné
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Isabelle Boulogne
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Mahnaz Sabeti-Azad
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Martine Maïbèche
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Thomas Chertemps
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Frédérique Hilliou
- grid.435437.20000 0004 0385 8766Université Côte d’Azur, INRAE, CNRS, ISA, 06903 Sophia-Antipolis, France
| | - David Siaussat
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - Joëlle Amselem
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France
| | - Isabelle Luyten
- grid.507621.7Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France
| | - Claire Capdevielle-Dulac
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Karine Labadie
- grid.8390.20000 0001 2180 5818Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Bruna Laís Merlin
- grid.11899.380000 0004 1937 0722Insect Interactions Laboratory, Department of Entomology and Acarology, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo 13418-900 Brazil
| | - Valérie Barbe
- grid.8390.20000 0001 2180 5818Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Jetske G. de Boer
- grid.418375.c0000 0001 1013 0288Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands ,grid.4818.50000 0001 0791 5666Laboratory of Entomology, Wageningen University, P.O. Box 16, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands ,grid.4830.f0000 0004 0407 1981Evolutionary Genetics, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Martial Marbouty
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris, 75015 France
| | - Fernando Luis Cônsoli
- grid.11899.380000 0004 1937 0722Insect Interactions Laboratory, Department of Entomology and Acarology, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo 13418-900 Brazil
| | - Stéphane Dupas
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Aurélie Hua-Van
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Gaelle Le Goff
- grid.435437.20000 0004 0385 8766Université Côte d’Azur, INRAE, CNRS, ISA, 06903 Sophia-Antipolis, France
| | - Annie Bézier
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Emmanuelle Jacquin-Joly
- grid.462350.6Sorbonne Université, INRAE, CNRS, IRD, UPEC, Univ. de Paris, Institute of Ecology and Environmental Science of Paris (iEES-Paris), 75005 Paris, France
| | - James B. Whitfield
- Department of Entomology, 320 Morrill Hall, 505 South Goodwin Avenue, University of Illinois, Urbana, IL 61801 USA
| | - Louise E. M. Vet
- grid.418375.c0000 0001 1013 0288Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands ,grid.4818.50000 0001 0791 5666Laboratory of Entomology, Wageningen University, P.O. Box 16, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Hans M. Smid
- grid.4818.50000 0001 0791 5666Laboratory of Entomology, Wageningen University, P.O. Box 16, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Laure Kaiser
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris, 75015 France
| | - Elisabeth Huguet
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Elisabeth A. Herniou
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
| | - Jean-Michel Drezen
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261 CNRS-Université de Tours, Faculté des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
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22
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Gimenez S, Abdelgaffar H, Goff GL, Hilliou F, Blanco CA, Hänniger S, Bretaudeau A, Legeai F, Nègre N, Jurat-Fuentes JL, d'Alençon E, Nam K. Adaptation by copy number variation increases insecticide resistance in the fall armyworm. Commun Biol 2020; 3:664. [PMID: 33184418 PMCID: PMC7661717 DOI: 10.1038/s42003-020-01382-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 10/14/2020] [Indexed: 12/19/2022] Open
Abstract
Understanding the genetic basis of insecticide resistance is a key topic in agricultural ecology. The adaptive evolution of multi-copy detoxification genes has been interpreted as a cause of insecticide resistance, yet the same pattern can also be generated by the adaptation to host-plant defense toxins. In this study, we tested in the fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae), if adaptation by copy number variation caused insecticide resistance in two geographically distinct populations with different levels of resistance and the two host-plant strains. We observed a significant allelic differentiation of genomic copy number variations between the two geographic populations, but not between host-plant strains. A locus with positively selected copy number variation included a CYP gene cluster. Toxicological tests supported a central role for CYP enzymes in deltamethrin resistance. Our results indicate that copy number variation of detoxification genes might be responsible for insecticide resistance in fall armyworm and that evolutionary forces causing insecticide resistance could be independent of host-plant adaptation.
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Affiliation(s)
- Sylvie Gimenez
- DGIMI, Univ of Montpellier, INRA, Place Eugène Bataillon, 34095, Montpellier, France
| | - Heba Abdelgaffar
- Department of Entomology and Plant Pathology, University of Tennessee, 370 Plant Biotechnology Building, 2505 E J. Chapman Dr, Knoxville, TN, 37996, USA
| | - Gaelle Le Goff
- Université Côte d'Azur, INRAE, CNRS, ISA, 400 Route des Chappes, 06903, Sophia Antipolis, France
| | - Frédérique Hilliou
- Université Côte d'Azur, INRAE, CNRS, ISA, 400 Route des Chappes, 06903, Sophia Antipolis, France
| | - Carlos A Blanco
- United States Department of Agriculture, Animal and Plant Health Inspection Service, 4700 River Rd, Riverdale, 20737, MD, USA
| | - Sabine Hänniger
- Max Planck Institute for Chemical Ecology, Hans-Knoell-Straße 8, 07745, Jena, Germany
| | - Anthony Bretaudeau
- IGEPP, INRAE, Institut Agro, Univ Rennes, Campus de Beaulieu, 263 Avenue Général Leclerc, 35042, Rennes, France
- GenOuest Core Facility, Univ Rennes, Inria, CNRS, IRISA, Campus de Beaulieu, 263 Avenue Général Leclerc, 35042, Rennes, France
| | - Fabrice Legeai
- IGEPP, INRAE, Institut Agro, Univ Rennes, Campus de Beaulieu, 263 Avenue Général Leclerc, 35042, Rennes, France
- GenOuest Core Facility, Univ Rennes, Inria, CNRS, IRISA, Campus de Beaulieu, 263 Avenue Général Leclerc, 35042, Rennes, France
| | - Nicolas Nègre
- DGIMI, Univ of Montpellier, INRA, Place Eugène Bataillon, 34095, Montpellier, France
| | - Juan Luis Jurat-Fuentes
- Department of Entomology and Plant Pathology, University of Tennessee, 370 Plant Biotechnology Building, 2505 E J. Chapman Dr, Knoxville, TN, 37996, USA
| | - Emmanuelle d'Alençon
- DGIMI, Univ of Montpellier, INRA, Place Eugène Bataillon, 34095, Montpellier, France
| | - Kiwoong Nam
- DGIMI, Univ of Montpellier, INRA, Place Eugène Bataillon, 34095, Montpellier, France.
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23
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Rispe C, Legeai F, Nabity PD, Fernández R, Arora AK, Baa-Puyoulet P, Banfill CR, Bao L, Barberà M, Bouallègue M, Bretaudeau A, Brisson JA, Calevro F, Capy P, Catrice O, Chertemps T, Couture C, Delière L, Douglas AE, Dufault-Thompson K, Escuer P, Feng H, Forneck A, Gabaldón T, Guigó R, Hilliou F, Hinojosa-Alvarez S, Hsiao YM, Hudaverdian S, Jacquin-Joly E, James EB, Johnston S, Joubard B, Le Goff G, Le Trionnaire G, Librado P, Liu S, Lombaert E, Lu HL, Maïbèche M, Makni M, Marcet-Houben M, Martínez-Torres D, Meslin C, Montagné N, Moran NA, Papura D, Parisot N, Rahbé Y, Lopes MR, Ripoll-Cladellas A, Robin S, Roques C, Roux P, Rozas J, Sánchez-Gracia A, Sánchez-Herrero JF, Santesmasses D, Scatoni I, Serre RF, Tang M, Tian W, Umina PA, van Munster M, Vincent-Monégat C, Wemmer J, Wilson ACC, Zhang Y, Zhao C, Zhao J, Zhao S, Zhou X, Delmotte F, Tagu D. Correction to: The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest. BMC Biol 2020; 18:123. [PMID: 32917281 PMCID: PMC7488435 DOI: 10.1186/s12915-020-00864-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Affiliation(s)
| | - Fabrice Legeai
- BIPAA, IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France.
| | - Paul D Nabity
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Rosa Fernández
- Bioinformatics and Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain.,Present address: Institute of Evolutionary Biology (CSIC-UPF), Passeig marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Arinder K Arora
- Department of Entomology, Cornell University, Ithaca, NY, 14853, USA
| | | | - Celeste R Banfill
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | | | - Miquel Barberà
- Institut de Biologia Integrativa de Sistemes, Parc Cientific Universitat de Valencia, C/ Catedrático José Beltrán n° 2, 46980, Paterna, València, Spain
| | - Maryem Bouallègue
- Université de Tunis El Manar, Faculté des Sciences de Tunis, LR01ES05 Biochimie et Biotechnologie, 2092, Tunis, Tunisia
| | - Anthony Bretaudeau
- BIPAA, IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France
| | | | - Federica Calevro
- Univ Lyon, INSA-Lyon, INRAE, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Pierre Capy
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS, Univ. Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Olivier Catrice
- LIPM, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Thomas Chertemps
- Sorbonne Université, UPEC, Université Paris 7, INRAE, CNRS, IRD, Institute of Ecology and Environmental Sciences, Paris, France
| | - Carole Couture
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d'Ornon, France
| | - Laurent Delière
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d'Ornon, France
| | - Angela E Douglas
- Department of Entomology, Cornell University, Ithaca, NY, 14853, USA.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Keith Dufault-Thompson
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI, USA
| | - Paula Escuer
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028, Barcelona, Spain
| | - Honglin Feng
- Department of Biology, University of Miami, Coral Gables, USA.,Current affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, USA
| | | | - Toni Gabaldón
- Bioinformatics and Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra, 08003, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Frédérique Hilliou
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
| | - Silvia Hinojosa-Alvarez
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028, Barcelona, Spain
| | - Yi-Min Hsiao
- Institute of Biotechnology and Department of Entomology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan.,Present affiliation: Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Sylvie Hudaverdian
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France
| | | | - Edward B James
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA
| | | | - Gaëlle Le Goff
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
| | - Gaël Le Trionnaire
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France
| | - Pablo Librado
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Shanlin Liu
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083, Guangdong Province, People's Republic of China.,BGI-Shenzhen, Shenzhen, 518083, Guangdong Province, People's Republic of China.,Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Eric Lombaert
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Hsiao-Ling Lu
- Department of Post-Modern Agriculture, MingDao University, Changhua, Taiwan
| | - Martine Maïbèche
- Sorbonne Université, UPEC, Université Paris 7, INRAE, CNRS, IRD, Institute of Ecology and Environmental Sciences, Paris, France
| | - Mohamed Makni
- Université de Tunis El Manar, Faculté des Sciences de Tunis, LR01ES05 Biochimie et Biotechnologie, 2092, Tunis, Tunisia
| | - Marina Marcet-Houben
- Bioinformatics and Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain
| | - David Martínez-Torres
- Institut de Biologia Integrativa de Sistemes, Parc Cientific Universitat de Valencia, C/ Catedrático José Beltrán n° 2, 46980, Paterna, València, Spain
| | - Camille Meslin
- INRAE, Institute of Ecology and Environmental Sciences, Versailles, France
| | - Nicolas Montagné
- Sorbonne Université, Institute of Ecology and Environmental Sciences, Paris, France
| | - Nancy A Moran
- Department of Integrative Biology, University of Texas at Austin, Austin, USA
| | - Daciana Papura
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d'Ornon, France
| | - Nicolas Parisot
- Univ Lyon, INSA-Lyon, INRAE, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Yvan Rahbé
- Univ Lyon, INRAE, INSA-Lyon, CNRS, UCBL, UMR5240 MAP, F-69622, Villeurbanne, France
| | | | - Aida Ripoll-Cladellas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Stéphanie Robin
- BIPAA IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France
| | - Céline Roques
- Plateforme Génomique GeT-PlaGe, Centre INRAE de Toulouse Midi-Pyrénées, 24 Chemin de Borde Rouge, Auzeville, CS 52627, 31326, Castanet-Tolosan Cedex, France
| | - Pascale Roux
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d'Ornon, France
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028, Barcelona, Spain
| | - Alejandro Sánchez-Gracia
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028, Barcelona, Spain
| | - Jose F Sánchez-Herrero
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028, Barcelona, Spain
| | - Didac Santesmasses
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | | | - Rémy-Félix Serre
- Plateforme Génomique GeT-PlaGe, Centre INRAE de Toulouse Midi-Pyrénées, 24 Chemin de Borde Rouge, Auzeville, CS 52627, 31326, Castanet-Tolosan Cedex, France
| | - Ming Tang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Wenhua Tian
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Paul A Umina
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Manuella van Munster
- BGPI, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | | | - Joshua Wemmer
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Alex C C Wilson
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI, USA
| | - Chaoyang Zhao
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Jing Zhao
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083, Guangdong Province, People's Republic of China.,BGI-Shenzhen, Shenzhen, 518083, Guangdong Province, People's Republic of China
| | - Serena Zhao
- Department of Integrative Biology, University of Texas at Austin, Austin, USA
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, People's Republic of China
| | | | - Denis Tagu
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France.
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Dommel M, Oh J, Huguet-Tapia JC, Guy E, Boulain H, Sugio A, Murugan M, Legeai F, Heck M, Smith CM, White FF. Big Genes, Small Effectors: Pea Aphid Cassette Effector Families Composed From Miniature Exons. Front Plant Sci 2020; 11:1230. [PMID: 33013944 PMCID: PMC7495047 DOI: 10.3389/fpls.2020.01230] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 07/27/2020] [Indexed: 05/25/2023]
Abstract
Aphids secrete proteins from their stylets that evidence indicates function similar to pathogen effectors for virulence. Here, we describe two small candidate effector gene families of the pea aphid, Acyrthosiphon pisum, that share highly conserved secretory signal peptide coding regions and divergent non-secretory coding sequences derived from miniature exons. The KQY candidate effector family contains eleven members with additional isoforms, generated by alternative splicing. Pairwise comparisons indicate possible four unique KQY families based on coding regions without the secretory signal region. KQY1a, a representative of the family, is encoded by a 968 bp mRNA and a gene that spans 45.7 kbp of the genome. The locus consists of 37 exons, 33 of which are 15 bp or smaller. Additional KQY members, as well as members of the KHI family, share similar features. Differential expression analyses indicate that the genes are expressed preferentially in salivary glands. Proteomic analysis on salivary glands and saliva revealed 11 KQY members in salivary proteins, and KQY1a was detected in an artificial diet solution after aphid feeding. A single KQY locus and two KHI loci were identified in Myzus persicae, the peach aphid. Of the genes that can be anchored to chromosomes, loci are mostly scattered throughout the genome, except a two-gene region (KQY4/KQY6). We propose that the KQY family expanded in A. pisum through combinatorial assemblies of a common secretory signal cassette and novel coding regions, followed by classical gene duplication and divergence.
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Affiliation(s)
- Matthew Dommel
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Jonghee Oh
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | | | - Endrick Guy
- INRAE, UMR Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Hélène Boulain
- INRAE, UMR Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Akiko Sugio
- INRAE, UMR Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Marimuthu Murugan
- Department of Entomology, Kansas State University, Manhattan, KS, United States
| | - Fabrice Legeai
- INRAE, UMR Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Michelle Heck
- USDA-ARS, Cornell University, Ithaca, NY, United States
| | - C. Michael Smith
- Department of Entomology, Kansas State University, Manhattan, KS, United States
| | - Frank F. White
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
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25
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Wenger JA, Cassone BJ, Legeai F, Johnston JS, Bansal R, Yates AD, Coates BS, Pavinato VAC, Michel A. Whole genome sequence of the soybean aphid, Aphis glycines. Insect Biochem Mol Biol 2020; 123:102917. [PMID: 28119199 DOI: 10.1016/j.ibmb.2017.01.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 01/03/2017] [Accepted: 01/14/2017] [Indexed: 05/09/2023]
Abstract
Aphids are emerging as model organisms for both basic and applied research. Of the 5,000 estimated species, only three aphids have published whole genome sequences: the pea aphid Acyrthosiphon pisum, the Russian wheat aphid, Diuraphis noxia, and the green peach aphid, Myzus persicae. We present the whole genome sequence of a fourth aphid, the soybean aphid (Aphis glycines), which is an extreme specialist and an important invasive pest of soybean (Glycine max). The availability of genomic resources is important to establish effective and sustainable pest control, as well as to expand our understanding of aphid evolution. We generated a 302.9 Mbp draft genome assembly for Ap. glycines using a hybrid sequencing approach. This assembly shows high completeness with 19,182 predicted genes, 92% of known Ap. glycines transcripts mapping to contigs, and substantial continuity with a scaffold N50 of 174,505 bp. The assembly represents 95.5% of the predicted genome size of 317.1 Mbp based on flow cytometry. Ap. glycines contains the smallest known aphid genome to date, based on updated genome sizes for 19 aphid species. The repetitive DNA content of the Ap. glycines genome assembly (81.6 Mbp or 26.94% of the 302.9 Mbp assembly) shows a reduction in the number of classified transposable elements compared to Ac. pisum, and likely contributes to the small estimated genome size. We include comparative analyses of gene families related to host-specificity (cytochrome P450's and effectors), which may be important in Ap. glycines evolution. This Ap. glycines draft genome sequence will provide a resource for the study of aphid genome evolution, their interaction with host plants, and candidate genes for novel insect control methods.
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Affiliation(s)
- Jacob A Wenger
- Department of Entomology, Ohio Agricultural Research and Development Center, The Ohio State University, USA; Center for Applied Plant Sciences, The Ohio State University, Wooster, OH, USA
| | - Bryan J Cassone
- Department of Entomology, Ohio Agricultural Research and Development Center, The Ohio State University, USA; Center for Applied Plant Sciences, The Ohio State University, Wooster, OH, USA
| | - Fabrice Legeai
- Ecology and Genetics of Insects & INRIA/IRISA, Genscale, Campus Beaulieu, Rennes, INRA, UMR IGEPP 1349, France
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - Raman Bansal
- Department of Entomology, Ohio Agricultural Research and Development Center, The Ohio State University, USA
| | - Ashley D Yates
- Department of Entomology, Ohio Agricultural Research and Development Center, The Ohio State University, USA; Center for Applied Plant Sciences, The Ohio State University, Wooster, OH, USA
| | - Brad S Coates
- USDA-ARS, Corn Insects & Crop Genetics Research Unit, Ames, IA, USA
| | - Vitor A C Pavinato
- Department of Entomology, Ohio Agricultural Research and Development Center, The Ohio State University, USA
| | - Andy Michel
- Department of Entomology, Ohio Agricultural Research and Development Center, The Ohio State University, USA; Center for Applied Plant Sciences, The Ohio State University, Wooster, OH, USA.
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26
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Legeai F, Santos BF, Robin S, Bretaudeau A, Dikow RB, Lemaitre C, Jouan V, Ravallec M, Drezen JM, Tagu D, Baudat F, Gyapay G, Zhou X, Liu S, Webb BA, Brady SG, Volkoff AN. Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps. BMC Biol 2020; 18:89. [PMID: 32703219 PMCID: PMC7379367 DOI: 10.1186/s12915-020-00822-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/29/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Polydnaviruses (PDVs) are mutualistic endogenous viruses inoculated by some lineages of parasitoid wasps into their hosts, where they facilitate successful wasp development. PDVs include the ichnoviruses and bracoviruses that originate from independent viral acquisitions in ichneumonid and braconid wasps respectively. PDV genomes are fully incorporated into the wasp genomes and consist of (1) genes involved in viral particle production, which derive from the viral ancestor and are not encapsidated, and (2) proviral segments harboring virulence genes, which are packaged into the viral particle. To help elucidating the mechanisms that have facilitated viral domestication in ichneumonid wasps, we analyzed the structure of the viral insertions by sequencing the whole genome of two ichnovirus-carrying wasp species, Hyposoter didymator and Campoletis sonorensis. RESULTS Assemblies with long scaffold sizes allowed us to unravel the organization of the endogenous ichnovirus and revealed considerable dispersion of the viral loci within the wasp genomes. Proviral segments contained species-specific sets of genes and occupied distinct genomic locations in the two ichneumonid wasps. In contrast, viral machinery genes were organized in clusters showing highly conserved gene content and order, with some loci located in collinear wasp genomic regions. This genomic architecture clearly differs from the organization of PDVs in braconid wasps, in which proviral segments are clustered and viral machinery elements are more dispersed. CONCLUSIONS The contrasting structures of the two types of ichnovirus genomic elements are consistent with their different functions: proviral segments are vehicles for virulence proteins expected to adapt according to different host defense systems, whereas the genes involved in virus particle production in the wasp are likely more stable and may reflect ancestral viral architecture. The distinct genomic architectures seen in ichnoviruses versus bracoviruses reveal different evolutionary trajectories that have led to virus domestication in the two wasp lineages.
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Affiliation(s)
- Fabrice Legeai
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France
- Université Rennes 1, INRIA, CNRS, IRISA, F-35000, Rennes, France
| | - Bernardo F Santos
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Avenue NW, Washington, DC, 20560-0165, USA
| | - Stéphanie Robin
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France
- Université Rennes 1, INRIA, CNRS, IRISA, F-35000, Rennes, France
| | - Anthony Bretaudeau
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France
- Université Rennes 1, INRIA, CNRS, IRISA, F-35000, Rennes, France
| | - Rebecca B Dikow
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Avenue NW, Washington, DC, 20560-0165, USA
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, 10th and Constitution Avenue NW, Washington, DC, 20560-0165, USA
| | - Claire Lemaitre
- Université Rennes 1, INRIA, CNRS, IRISA, F-35000, Rennes, France
| | - Véronique Jouan
- DGIMI, INRAE, University of Montpellier, 34095, Montpellier, France
| | - Marc Ravallec
- DGIMI, INRAE, University of Montpellier, 34095, Montpellier, France
| | - Jean-Michel Drezen
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS - Université de Tours, UFR des Sciences et Techniques, Parc de Grandmont, Tours, France
| | - Denis Tagu
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France
| | - Frédéric Baudat
- Institut de Génétique Humaine, CNRS, University of Montpellier, 34396, Montpellier, France
| | - Gabor Gyapay
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, 2 rue Gaston Crémieux, BP5706, 91057, Evry, France
| | - Xin Zhou
- Department of Entomology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Shanlin Liu
- Department of Entomology, China Agricultural University, Beijing, 100193, People's Republic of China
- China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong Province, 518083, People's Republic of China
| | - Bruce A Webb
- Department of Entomology, University of Kentucky, Lexington, USA
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Avenue NW, Washington, DC, 20560-0165, USA
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27
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Rispe C, Legeai F, Nabity PD, Fernández R, Arora AK, Baa-Puyoulet P, Banfill CR, Bao L, Barberà M, Bouallègue M, Bretaudeau A, Brisson JA, Calevro F, Capy P, Catrice O, Chertemps T, Couture C, Delière L, Douglas AE, Dufault-Thompson K, Escuer P, Feng H, Forneck A, Gabaldón T, Guigó R, Hilliou F, Hinojosa-Alvarez S, Hsiao YM, Hudaverdian S, Jacquin-Joly E, James EB, Johnston S, Joubard B, Le Goff G, Le Trionnaire G, Librado P, Liu S, Lombaert E, Lu HL, Maïbèche M, Makni M, Marcet-Houben M, Martínez-Torres D, Meslin C, Montagné N, Moran NA, Papura D, Parisot N, Rahbé Y, Lopes MR, Ripoll-Cladellas A, Robin S, Roques C, Roux P, Rozas J, Sánchez-Gracia A, Sánchez-Herrero JF, Santesmasses D, Scatoni I, Serre RF, Tang M, Tian W, Umina PA, van Munster M, Vincent-Monégat C, Wemmer J, Wilson ACC, Zhang Y, Zhao C, Zhao J, Zhao S, Zhou X, Delmotte F, Tagu D. The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest. BMC Biol 2020; 18:90. [PMID: 32698880 PMCID: PMC7376646 DOI: 10.1186/s12915-020-00820-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 06/22/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Although native to North America, the invasion of the aphid-like grape phylloxera Daktulosphaira vitifoliae across the globe altered the course of grape cultivation. For the past 150 years, viticulture relied on grafting-resistant North American Vitis species as rootstocks, thereby limiting genetic stocks tolerant to other stressors such as pathogens and climate change. Limited understanding of the insect genetics resulted in successive outbreaks across the globe when rootstocks failed. Here we report the 294-Mb genome of D. vitifoliae as a basic tool to understand host plant manipulation, nutritional endosymbiosis, and enhance global viticulture. RESULTS Using a combination of genome, RNA, and population resequencing, we found grape phylloxera showed high duplication rates since its common ancestor with aphids, but similarity in most metabolic genes, despite lacking obligate nutritional symbioses and feeding from parenchyma. Similarly, no enrichment occurred in development genes in relation to viviparity. However, phylloxera evolved > 2700 unique genes that resemble putative effectors and are active during feeding. Population sequencing revealed the global invasion began from the upper Mississippi River in North America, spread to Europe and from there to the rest of the world. CONCLUSIONS The grape phylloxera genome reveals genetic architecture relative to the evolution of nutritional endosymbiosis, viviparity, and herbivory. The extraordinary expansion in effector genes also suggests novel adaptations to plant feeding and how insects induce complex plant phenotypes, for instance galls. Finally, our understanding of the origin of this invasive species and its genome provide genetics resources to alleviate rootstock bottlenecks restricting the advancement of viticulture.
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Affiliation(s)
| | - Fabrice Legeai
- BIPAA, IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
| | - Paul D. Nabity
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Rosa Fernández
- Bioinformatics and Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003 Barcelona, Spain
- Present address: Institute of Evolutionary Biology (CSIC-UPF), Passeig marítim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - Arinder K. Arora
- Department of Entomology, Cornell University, Ithaca, NY 14853 USA
| | | | | | | | - Miquel Barberà
- Institut de Biologia Integrativa de Sistemes, Parc Cientific Universitat de Valencia, C/ Catedrático José Beltrán n° 2, 46980 Paterna, València Spain
| | - Maryem Bouallègue
- Université de Tunis El Manar, Faculté des Sciences de Tunis, LR01ES05 Biochimie et Biotechnologie, 2092 Tunis, Tunisia
| | - Anthony Bretaudeau
- BIPAA, IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
| | | | - Federica Calevro
- Univ Lyon, INSA-Lyon, INRAE, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Pierre Capy
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS, Univ. Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Olivier Catrice
- LIPM, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Thomas Chertemps
- Sorbonne Université, UPEC, Université Paris 7, INRAE, CNRS, IRD, Institute of Ecology and Environmental Sciences, Paris, France
| | - Carole Couture
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d’Ornon, France
| | - Laurent Delière
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d’Ornon, France
| | - Angela E. Douglas
- Department of Entomology, Cornell University, Ithaca, NY 14853 USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853 USA
| | - Keith Dufault-Thompson
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI USA
| | - Paula Escuer
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Honglin Feng
- Department of Biology, University of Miami, Coral Gables, USA
- Current affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, USA
| | | | - Toni Gabaldón
- Bioinformatics and Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Frédérique Hilliou
- Université Côte d’Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
| | - Silvia Hinojosa-Alvarez
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Yi-min Hsiao
- Institute of Biotechnology and Department of Entomology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Present affiliation: Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Sylvie Hudaverdian
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
| | | | - Edward B. James
- Department of Biology, University of Miami, Coral Gables, FL 33146 USA
| | - Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX 77843 USA
| | | | - Gaëlle Le Goff
- Université Côte d’Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
| | - Gaël Le Trionnaire
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
| | - Pablo Librado
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Shanlin Liu
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083 Guangdong Province People’s Republic of China
- BGI-Shenzhen, Shenzhen, 518083 Guangdong Province People’s Republic of China
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Eric Lombaert
- Université Côte d’Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Hsiao-ling Lu
- Department of Post-Modern Agriculture, MingDao University, Changhua, Taiwan
| | - Martine Maïbèche
- Sorbonne Université, UPEC, Université Paris 7, INRAE, CNRS, IRD, Institute of Ecology and Environmental Sciences, Paris, France
| | - Mohamed Makni
- Université de Tunis El Manar, Faculté des Sciences de Tunis, LR01ES05 Biochimie et Biotechnologie, 2092 Tunis, Tunisia
| | - Marina Marcet-Houben
- Bioinformatics and Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003 Barcelona, Spain
| | - David Martínez-Torres
- Institut de Biologia Integrativa de Sistemes, Parc Cientific Universitat de Valencia, C/ Catedrático José Beltrán n° 2, 46980 Paterna, València Spain
| | - Camille Meslin
- INRAE, Institute of Ecology and Environmental Sciences, Versailles, France
| | - Nicolas Montagné
- Sorbonne Université, Institute of Ecology and Environmental Sciences, Paris, France
| | - Nancy A. Moran
- Department of Integrative Biology, University of Texas at Austin, Austin, USA
| | - Daciana Papura
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d’Ornon, France
| | - Nicolas Parisot
- Univ Lyon, INSA-Lyon, INRAE, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Yvan Rahbé
- Univ Lyon, INRAE, INSA-Lyon, CNRS, UCBL, UMR5240 MAP, F-69622 Villeurbanne, France
| | | | - Aida Ripoll-Cladellas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Stéphanie Robin
- BIPAA IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
| | - Céline Roques
- Plateforme Génomique GeT-PlaGe, Centre INRAE de Toulouse Midi-Pyrénées, 24 Chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Pascale Roux
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d’Ornon, France
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Alejandro Sánchez-Gracia
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Jose F. Sánchez-Herrero
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Didac Santesmasses
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | | | - Rémy-Félix Serre
- Plateforme Génomique GeT-PlaGe, Centre INRAE de Toulouse Midi-Pyrénées, 24 Chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Ming Tang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Wenhua Tian
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Paul A. Umina
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Manuella van Munster
- BGPI, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | | | - Joshua Wemmer
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Alex C. C. Wilson
- Department of Biology, University of Miami, Coral Gables, FL 33146 USA
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI USA
| | - Chaoyang Zhao
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Jing Zhao
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083 Guangdong Province People’s Republic of China
- BGI-Shenzhen, Shenzhen, 518083 Guangdong Province People’s Republic of China
| | - Serena Zhao
- Department of Integrative Biology, University of Texas at Austin, Austin, USA
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193 People’s Republic of China
| | | | - Denis Tagu
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
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28
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Guyomar C, Delage W, Legeai F, Mougel C, Simon JC, Lemaitre C. MinYS: mine your symbiont by targeted genome assembly in symbiotic communities. NAR Genom Bioinform 2020; 2:lqaa047. [PMID: 33575599 PMCID: PMC7671366 DOI: 10.1093/nargab/lqaa047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 05/20/2020] [Accepted: 06/17/2020] [Indexed: 12/17/2022] Open
Abstract
Most metazoans are associated with symbionts. Characterizing the effect of a particular symbiont often requires getting access to its genome, which is usually done by sequencing the whole community. We present MinYS, a targeted assembly approach to assemble a particular genome of interest from such metagenomic data. First, taking advantage of a reference genome, a subset of the reads is assembled into a set of backbone contigs. Then, this draft assembly is completed using the whole metagenomic readset in a de novo manner. The resulting assembly is output as a genome graph, enabling different strains with potential structural variants coexisting in the sample to be distinguished. MinYS was applied to 50 pea aphid resequencing samples, with variable diversity in symbiont communities, in order to recover the genome sequence of its obligatory bacterial symbiont, Buchnera aphidicola. It was able to return high-quality assemblies (one contig assembly in 90% of the samples), even when using increasingly distant reference genomes, and to retrieve large structural variations in the samples. Because of its targeted essence, it outperformed standard metagenomic assemblers in terms of both time and assembly quality.
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Affiliation(s)
- Cervin Guyomar
- Univ. Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France
| | - Wesley Delage
- Univ. Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France
| | - Fabrice Legeai
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), INRAE, Institut Agro, Univ. Rennes, F-35653 Le Rheu, France
| | - Christophe Mougel
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), INRAE, Institut Agro, Univ. Rennes, F-35653 Le Rheu, France
| | - Jean-Christophe Simon
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), INRAE, Institut Agro, Univ. Rennes, F-35653 Le Rheu, France
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Dennis AB, Ballesteros GI, Robin S, Schrader L, Bast J, Berghöfer J, Beukeboom LW, Belghazi M, Bretaudeau A, Buellesbach J, Cash E, Colinet D, Dumas Z, Errbii M, Falabella P, Gatti JL, Geuverink E, Gibson JD, Hertaeg C, Hartmann S, Jacquin-Joly E, Lammers M, Lavandero BI, Lindenbaum I, Massardier-Galata L, Meslin C, Montagné N, Pak N, Poirié M, Salvia R, Smith CR, Tagu D, Tares S, Vogel H, Schwander T, Simon JC, Figueroa CC, Vorburger C, Legeai F, Gadau J. Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum. BMC Genomics 2020; 21:376. [PMID: 32471448 PMCID: PMC7257214 DOI: 10.1186/s12864-020-6764-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/30/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Parasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group with the potential for biological control. Their success depends on adapting to develop inside aphids and overcoming both host aphid defenses and their protective endosymbionts. RESULTS We present the de novo genome assemblies, detailed annotation, and comparative analysis of two closely related parasitoid wasps that target pest aphids: Aphidius ervi and Lysiphlebus fabarum (Hymenoptera: Braconidae: Aphidiinae). The genomes are small (139 and 141 Mbp) and the most AT-rich reported thus far for any arthropod (GC content: 25.8 and 23.8%). This nucleotide bias is accompanied by skewed codon usage and is stronger in genes with adult-biased expression. AT-richness may be the consequence of reduced genome size, a near absence of DNA methylation, and energy efficiency. We identify missing desaturase genes, whose absence may underlie mimicry in the cuticular hydrocarbon profile of L. fabarum. We highlight key gene groups including those underlying venom composition, chemosensory perception, and sex determination, as well as potential losses in immune pathway genes. CONCLUSIONS These findings are of fundamental interest for insect evolution and biological control applications. They provide a strong foundation for further functional studies into coevolution between parasitoids and their hosts. Both genomes are available at https://bipaa.genouest.org.
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Affiliation(s)
- Alice B Dennis
- Department of Aquatic Ecology, Eawag, 8600, Dübendorf, Switzerland.
- Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland.
- Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.
| | - Gabriel I Ballesteros
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Centre for Molecular and Functional Ecology in Agroecosystems, Universidad de Talca, Talca, Chile
- Laboratorio de Control Biológico, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Stéphanie Robin
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
- Université de Rennes 1, INRIA, CNRS, IRISA, 35000, Rennes, France
| | - Lukas Schrader
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Jens Bast
- Department of Ecology and Evolution, Université de Lausanne, 1015, Lausanne, Switzerland
- Institute of Zoology, Universität zu Köln, 50674, Köln, Germany
| | - Jan Berghöfer
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Leo W Beukeboom
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Maya Belghazi
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, PINT, PFNT, Marseille, France
| | - Anthony Bretaudeau
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
- Université de Rennes 1, INRIA, CNRS, IRISA, 35000, Rennes, France
| | - Jan Buellesbach
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Elizabeth Cash
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, CA, 94720, USA
| | | | - Zoé Dumas
- Department of Ecology and Evolution, Université de Lausanne, 1015, Lausanne, Switzerland
| | - Mohammed Errbii
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | | | - Jean-Luc Gatti
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Elzemiek Geuverink
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Joshua D Gibson
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, CA, 94720, USA
- Department of Biology, Georgia Southern University, Statesboro, GA, 30460, USA
| | - Corinne Hertaeg
- Department of Aquatic Ecology, Eawag, 8600, Dübendorf, Switzerland
- Department of Environmental Systems Sciences, D-USYS, ETH Zürich, Zürich, Switzerland
| | - Stefanie Hartmann
- Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Emmanuelle Jacquin-Joly
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université Paris Diderot, Institute of Ecology and Environmental Sciences of Paris, iEES-Paris, F-78000, Versailles, France
| | - Mark Lammers
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Blas I Lavandero
- Laboratorio de Control Biológico, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Ina Lindenbaum
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | | | - Camille Meslin
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université Paris Diderot, Institute of Ecology and Environmental Sciences of Paris, iEES-Paris, F-78000, Versailles, France
| | - Nicolas Montagné
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université Paris Diderot, Institute of Ecology and Environmental Sciences of Paris, iEES-Paris, F-78000, Versailles, France
| | - Nina Pak
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Marylène Poirié
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Rosanna Salvia
- Department of Sciences, University of Basilicata, 85100, Potenza, Italy
| | - Chris R Smith
- Department of Biology, Earlham College, Richmond, IN, 47374, USA
| | - Denis Tagu
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
| | - Sophie Tares
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Tanja Schwander
- Department of Ecology and Evolution, Université de Lausanne, 1015, Lausanne, Switzerland
| | | | - Christian C Figueroa
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Centre for Molecular and Functional Ecology in Agroecosystems, Universidad de Talca, Talca, Chile
| | - Christoph Vorburger
- Department of Aquatic Ecology, Eawag, 8600, Dübendorf, Switzerland
- Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Fabrice Legeai
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
- Université de Rennes 1, INRIA, CNRS, IRISA, 35000, Rennes, France
| | - Jürgen Gadau
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany.
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Gauthier J, de Silva DL, Gompert Z, Whibley A, Houssin C, Le Poul Y, McClure M, Lemaitre C, Legeai F, Mallet J, Elias M. Contrasting genomic and phenotypic outcomes of hybridization between pairs of mimetic butterfly taxa across a suture zone. Mol Ecol 2020; 29:1328-1343. [PMID: 32145112 DOI: 10.1111/mec.15403] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 02/03/2020] [Accepted: 02/21/2020] [Indexed: 11/28/2022]
Abstract
Hybrid zones, whereby divergent lineages come into contact and eventually hybridize, can provide insights on the mechanisms involved in population differentiation and reproductive isolation, and ultimately speciation. Suture zones offer the opportunity to compare these processes across multiple species. In this paper we use reduced-complexity genomic data to compare the genetic and phenotypic structure and hybridization patterns of two mimetic butterfly species, Ithomia salapia and Oleria onega (Nymphalidae: Ithomiini), each consisting of a pair of lineages differentiated for their wing colour pattern and that come into contact in the Andean foothills of Peru. Despite similarities in their life history, we highlight major differences, both at the genomic and phenotypic level, between the two species. These differences include the presence of hybrids, variations in wing phenotype, and genomic patterns of introgression and differentiation. In I. salapia, the two lineages appear to hybridize only rarely, whereas in O. onega the hybrids are not only more common, but also genetically and phenotypically more variable. We also detected loci statistically associated with wing colour pattern variation, but in both species these loci were not over-represented among the candidate barrier loci, suggesting that traits other than wing colour pattern may be important for reproductive isolation. Our results contrast with the genomic patterns observed between hybridizing lineages in the mimetic Heliconius butterflies, and call for a broader investigation into the genomics of speciation in Ithomiini - the largest radiation of mimetic butterflies.
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Affiliation(s)
- Jérémy Gauthier
- Inria, CNRS, IRISA, University Rennes, Rennes, France.,Geneva Natural History Museum, Geneva, Switzerland
| | - Donna Lisa de Silva
- Institut de Systématique, Évolution, Biodiversité, CNRS, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
| | | | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Céline Houssin
- Institut de Systématique, Évolution, Biodiversité, CNRS, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
| | - Yann Le Poul
- Institut de Systématique, Évolution, Biodiversité, CNRS, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France.,Fakultat für Biologie, Biozentrum, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Melanie McClure
- Institut de Systématique, Évolution, Biodiversité, CNRS, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
| | | | | | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Marianne Elias
- Institut de Systématique, Évolution, Biodiversité, CNRS, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
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31
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Lorenzi A, Ravallec M, Eychenne M, Jouan V, Robin S, Darboux I, Legeai F, Gosselin-Grenet AS, Sicard M, Stoltz D, Volkoff AN. RNA interference identifies domesticated viral genes involved in assembly and trafficking of virus-derived particles in ichneumonid wasps. PLoS Pathog 2019; 15:e1008210. [PMID: 31834912 PMCID: PMC6957214 DOI: 10.1371/journal.ppat.1008210] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/13/2020] [Accepted: 11/13/2019] [Indexed: 02/07/2023] Open
Abstract
There are many documented examples of viral genes retained in the genomes of multicellular organisms that may in some cases bring new beneficial functions to the receivers. The ability of certain ichneumonid parasitic wasps to produce virus-derived particles, the so-called ichnoviruses (IVs), not only results from the capture and domestication of single viral genes but of almost entire ancestral virus genome(s). Indeed, following integration into wasp chromosomal DNA, the putative and still undetermined IV ancestor(s) evolved into encoding a ‘virulence gene delivery vehicle’ that is now required for successful infestation of wasp hosts. Several putative viral genes, which are clustered in distinct regions of wasp genomes referred to as IVSPERs (Ichnovirus Structural Protein Encoding Regions), have been assumed to be involved in virus-derived particles morphogenesis, but this question has not been previously functionally addressed. In the present study, we have successfully combined RNA interference and transmission electron microscopy to specifically identify IVSPER genes that are responsible for the morphogenesis and trafficking of the virus-derived particles in ovarian cells of the ichneumonid wasp Hyposoter didymator. We suggest that ancestral viral genes retained within the genomes of certain ichneumonid parasitoids possess conserved functions which were domesticated for the purpose of assembling viral vectors for the delivery of virulence genes to parasitized host animals. Thousands of parasitic wasp from the ichneumonid family rely on virus-derived particles, named Ichnoviruses (Polydnavirus family), to ensure their successful development. The particles are produced in a specialized ovarian tissue of the female wasp named calyx. Virions are assembled in the calyx cell nuclei and stored in the oviduct before being transferred to the parasitoid host upon female wasp oviposition. Genes encoding proteins associated with the particles had been previously identified. These genes are localized in clusters of genes in the wasp genome (named IVSPER for “Ichnovirus structural proteins encoding regions”), they are specifically transcribed in the calyx but not encapsidated. IVSPER genes were thus hypothesized to derive from the integration of a virus, however still undetermined. Indeed, none of the identified genes had similarity to known sequence, making in addition unclear their function in particle production. In this work, we use the RNA interference technology to decipher the function of six IVSPER genes from the ichneumonid wasp Hyposoter didymator. Thanks to this approach, combined with transmission electron microscopy, we show that the studied IVSPER genes are required in different steps of particle morphogenesis and trafficking, and that their functions are those expected of a typical virus.
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Affiliation(s)
- Ange Lorenzi
- DGIMI, INRA, University of Montpellier, Montpellier, France
| | - Marc Ravallec
- DGIMI, INRA, University of Montpellier, Montpellier, France
| | | | | | - Stéphanie Robin
- UMR 1349 INRA/Agrocampus Ouest/Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Le Rheu, France
- Université Rennes 1, INRIA, CNRS, IRISA, Rennes, France
| | | | - Fabrice Legeai
- UMR 1349 INRA/Agrocampus Ouest/Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Le Rheu, France
- Université Rennes 1, INRIA, CNRS, IRISA, Rennes, France
| | | | - Mathieu Sicard
- ISEM, University of Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Don Stoltz
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Canada
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32
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Ferreira de Carvalho J, Lucas J, Deniot G, Falentin C, Filangi O, Gilet M, Legeai F, Lode M, Morice J, Trotoux G, Aury JM, Barbe V, Keller J, Snowdon R, He Z, Denoeud F, Wincker P, Bancroft I, Chèvre AM, Rousseau-Gueutin M. Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole-genome duplications in Brassica. Plant J 2019; 98:434-447. [PMID: 30604905 DOI: 10.1111/tpj.14228] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 12/14/2018] [Accepted: 01/02/2019] [Indexed: 06/09/2023]
Abstract
Several plastid macromolecular protein complexes are encoded by both nuclear and plastid genes. Therefore, cytonuclear interactions are held in place to prevent genomic conflicts that may lead to incompatibilities. Allopolyploidy resulting from hybridization and genome doubling of two divergent species can disrupt these fine-tuned interactions, as newly formed allopolyploid species confront biparental nuclear chromosomes with a uniparentally inherited plastid genome. To avoid any deleterious effects of unequal genome inheritance, preferential transcription of the plastid donor over the other donor has been hypothesized to occur in allopolyploids. We used Brassica as a model to study the effects of paleopolyploidy in diploid parental species, as well as the effects of recent and ancient allopolyploidy in Brassica napus, on genes implicated in plastid protein complexes. We first identified redundant nuclear copies involved in those complexes. Compared with cytosolic protein complexes and with genome-wide retention rates, genes involved in plastid protein complexes show a higher retention of genes in duplicated and triplicated copies. Those redundant copies are functional and are undergoing strong purifying selection. We then compared transcription patterns and sequences of those redundant gene copies between resynthesized allopolyploids and their diploid parents. The neopolyploids showed no biased subgenome expression or maternal homogenization via gene conversion, despite the presence of some non-synonymous substitutions between plastid genomes of parental progenitors. Instead, subgenome dominance was observed regardless of the maternal progenitor. Our results provide new insights on the evolution of plastid protein complexes that could be tested and generalized in other allopolyploid species.
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Affiliation(s)
| | - Jérémy Lucas
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Gwenaëlle Deniot
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Cyril Falentin
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Olivier Filangi
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Marie Gilet
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Fabrice Legeai
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Maryse Lode
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Jérôme Morice
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Gwenn Trotoux
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique, Genoscope, Institut de biologie François-Jacob, Evry, 91057, France
| | - Valérie Barbe
- Commissariat à l'Energie Atomique, Genoscope, Institut de biologie François-Jacob, Evry, 91057, France
| | - Jean Keller
- UMR CNRS 6553 ECOBIO, OSUR, Université de Rennes 1, Rennes, 35042, France
| | - Rod Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany
| | - Zhesi He
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - France Denoeud
- Commissariat à l'Energie Atomique, Genoscope, Institut de biologie François-Jacob, Evry, 91057, France
- UMR CNRS 8030, Evry, CP5706, France
- Université d'Evry-Val-d'Essonne, Université Paris-Saclay, Evry, 91000, France
| | - Patrick Wincker
- Commissariat à l'Energie Atomique, Genoscope, Institut de biologie François-Jacob, Evry, 91057, France
- UMR CNRS 8030, Evry, CP5706, France
- Université d'Evry-Val-d'Essonne, Université Paris-Saclay, Evry, 91000, France
| | - Ian Bancroft
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Anne-Marie Chèvre
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
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Robin S, Ravallec M, Frayssinet M, Whitfield J, Jouan V, Legeai F, Volkoff AN. Evidence for an ichnovirus machinery in parasitoids of coleopteran larvae. Virus Res 2019; 263:189-206. [DOI: 10.1016/j.virusres.2019.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/03/2019] [Accepted: 02/05/2019] [Indexed: 11/30/2022]
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Boulain H, Legeai F, Jaquiéry J, Guy E, Morlière S, Simon JC, Sugio A. Differential Expression of Candidate Salivary Effector Genes in Pea Aphid Biotypes With Distinct Host Plant Specificity. Front Plant Sci 2019; 10:1301. [PMID: 31695713 PMCID: PMC6818229 DOI: 10.3389/fpls.2019.01301] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/18/2019] [Indexed: 05/13/2023]
Abstract
Effector proteins play crucial roles in determining the outcome of various plant-parasite interactions. Aphids inject salivary effector proteins into plants to facilitate phloem feeding, but some proteins might trigger defense responses in certain plants. The pea aphid, Acyrthosiphon pisum, forms multiple biotypes, and each biotype is specialized to feed on a small number of closely related legume species. Interestingly, all the previously identified biotypes can feed on Vicia faba; hence, it serves as a universal host plant of A. pisum. We hypothesized that the salivary effector proteins have a key role in determining the compatibility between specific host species and A. pisum biotypes and that each biotype produces saliva containing a specific mixture of effector proteins due to differential expression of encoding genes. As the first step to address these hypotheses, we conducted two sets of RNA-seq experiments. RNA-seq analysis of dissected salivary glands (SGs) from reference alfalfa- and pea-specialized A. pisum lines revealed common and line-specific repertoires of candidate salivary effector genes. Based on the results, we created an extended catalogue of A. pisum salivary effector candidates. Next, we used aphid head samples, which contain SGs, to examine biotype-specific expression patterns of candidate salivary genes. RNA-seq analysis of head samples of alfalfa- and pea-specialized biotypes, each represented by three genetically distinct aphid lines reared on either a universal or specific host plant, showed that a majority of the candidate salivary effector genes was expressed in both biotypes at a similar level. Nonetheless, we identified small sets of genes that were differentially regulated in a biotype-specific manner. Little host plant effect (universal vs. specific) was observed on the expression of candidate salivary genes. Analysis of previously obtained genome re-sequenced data of the two biotypes revealed the copy number variations that might explain the differential expression of some candidate salivary genes. In addition, at least four candidate effector genes that were present in the alfalfa biotype but might not be encoded in the pea biotype were identified. This work sets the stage for future functional characterization of candidate genes potentially involved in the determination of plant specificity of pea aphid biotypes.
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Affiliation(s)
- Hélène Boulain
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Fabrice Legeai
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
- University of Rennes 1, Inria, CNRS, IRISA, Rennes, France
| | - Julie Jaquiéry
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Endrick Guy
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Stéphanie Morlière
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Jean-Christophe Simon
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Akiko Sugio
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
- *Correspondence: Akiko Sugio,
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Robertson HM, Waterhouse RM, Walden KKO, Ruzzante L, Reijnders MJMF, Coates BS, Legeai F, Gress JC, Biyiklioglu S, Weaver DK, Wanner KW, Budak H. Genome Sequence of the Wheat Stem Sawfly, Cephus cinctus, Representing an Early-Branching Lineage of the Hymenoptera, Illuminates Evolution of Hymenopteran Chemoreceptors. Genome Biol Evol 2018; 10:2997-3011. [PMID: 30335145 PMCID: PMC6250288 DOI: 10.1093/gbe/evy232] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2018] [Indexed: 02/06/2023] Open
Abstract
The wheat stem sawfly, Cephus cinctus, is a major pest of wheat and key ecological player in the grasslands of western North America. It also represents the distinctive Cephoidea superfamily of sawflies (Symphyta) that appeared early during the hymenopteran radiation, but after three early-branching eusymphytan superfamilies that form the base of the order Hymenoptera. We present a high-quality draft genome assembly of 162 Mb in 1,976 scaffolds with a scaffold N50 of 622 kb. Automated gene annotation identified 11,210 protein-coding gene models and 1,307 noncoding RNA models. Thirteen percent of the assembly consists of ∼58,000 transposable elements partitioned equally between Class-I and Class-II elements. Orthology analysis reveals that 86% of Cephus proteins have identifiable orthologs in other insects. Phylogenomic analysis of conserved subsets of these proteins supports the placement of the Cephoidea between the Eusymphyta and the parasitic woodwasp superfamily Orussoidea. Manual annotation and phylogenetic analysis of families of odorant, gustatory, and ionotropic receptors, plus odorant-binding proteins, shows that Cephus has representatives for most conserved and expanded gene lineages in the Apocrita (wasps, ants, and bees). Cephus has also maintained several insect gene lineages that have been lost from the Apocrita, most prominently the carbon dioxide receptor subfamily. Furthermore, Cephus encodes a few small lineage-specific chemoreceptor gene family expansions that might be involved in adaptations to new grasses including wheat. These comparative analyses identify gene family members likely to have been present in the hymenopteran ancestor and provide a new perspective on the evolution of the chemosensory gene repertoire.
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Affiliation(s)
- Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Livio Ruzzante
- Department of Ecology and Evolution, University of Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Maarten J M F Reijnders
- Department of Ecology and Evolution, University of Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Brad S Coates
- United States Department of Agriculture, Agricultural Research Service (USDA ARS), Corn Insects & Crop Genetics Research Unit, Ames, Iowa
| | - Fabrice Legeai
- Ecology and Genetics of Insects, INRA, UMR IGEPP 1349, Rennes, France
| | - Joanna C Gress
- Department of Science and Mathematics, Abraham Baldwin Agricultural College, Tifton, Georgia
- Department of Plant Sciences and Plant Pathology, Montana State University
| | - Sezgi Biyiklioglu
- Department of Plant Sciences and Plant Pathology, Montana State University
| | - David K Weaver
- Department of Land Resources and Environmental Sciences, Montana State University
| | - Kevin W Wanner
- Department of Plant Sciences and Plant Pathology, Montana State University
| | - Hikmet Budak
- Department of Plant Sciences and Plant Pathology, Montana State University
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Boulain H, Legeai F, Guy E, Morlière S, Douglas NE, Oh J, Murugan M, Smith M, Jaquiéry J, Peccoud J, White FF, Carolan JC, Simon JC, Sugio A. Fast Evolution and Lineage-Specific Gene Family Expansions of Aphid Salivary Effectors Driven by Interactions with Host-Plants. Genome Biol Evol 2018; 10:1554-1572. [PMID: 29788052 PMCID: PMC6012102 DOI: 10.1093/gbe/evy097] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2018] [Indexed: 12/31/2022] Open
Abstract
Effector proteins play crucial roles in plant-parasite interactions by suppressing plant defenses and hijacking plant physiological responses to facilitate parasite invasion and propagation. Although effector proteins have been characterized in many microbial plant pathogens, their nature and role in adaptation to host plants are largely unknown in insect herbivores. Aphids rely on salivary effector proteins injected into the host plants to promote phloem sap uptake. Therefore, gaining insight into the repertoire and evolution of aphid effectors is key to unveiling the mechanisms responsible for aphid virulence and host plant specialization. With this aim in mind, we assembled catalogues of putative effectors in the legume specialist aphid, Acyrthosiphon pisum, using transcriptomics and proteomics approaches. We identified 3,603 candidate effector genes predicted to be expressed in A. pisum salivary glands (SGs), and 740 of which displayed up-regulated expression in SGs in comparison to the alimentary tract. A search for orthologs in 17 arthropod genomes revealed that SG-up-regulated effector candidates of A. pisum are enriched in aphid-specific genes and tend to evolve faster compared with the whole gene set. We also found that a large fraction of proteins detected in the A. pisum saliva belonged to three gene families, of which certain members show evidence consistent with positive selection. Overall, this comprehensive analysis suggests that the large repertoire of effector candidates in A. pisum constitutes a source of novelties promoting plant adaptation to legumes.
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Affiliation(s)
- Hélène Boulain
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Fabrice Legeai
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France.,Inria/IRISA GenScale, Campus de Beaulieu, Rennes, France
| | - Endrick Guy
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Stéphanie Morlière
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Nadine E Douglas
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.,UCD School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Jonghee Oh
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas
| | - Marimuthu Murugan
- Community Science College and Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Michael Smith
- Department of Entomology, Kansas State University, Manhattan, Kansas
| | - Julie Jaquiéry
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Jean Peccoud
- UMR CNRS 7267 Ecologie et Biologie des Interactions, équipe Ecologie Evolution Symbiose, Université de Poitiers, Poitiers, France
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, Florida
| | - James C Carolan
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Jean-Christophe Simon
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Akiko Sugio
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
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Jaquiéry J, Peccoud J, Ouisse T, Legeai F, Prunier-Leterme N, Gouin A, Nouhaud P, Brisson JA, Bickel R, Purandare S, Poulain J, Battail C, Lemaitre C, Mieuzet L, Le Trionnaire G, Simon JC, Rispe C. Disentangling the Causes for Faster-X Evolution in Aphids. Genome Biol Evol 2018; 10:507-520. [PMID: 29360959 PMCID: PMC5798017 DOI: 10.1093/gbe/evy015] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2018] [Indexed: 12/22/2022] Open
Abstract
The faster evolution of X chromosomes has been documented in several species, and results from the increased efficiency of selection on recessive alleles in hemizygous males and/or from increased drift due to the smaller effective population size of X chromosomes. Aphids are excellent models for evaluating the importance of selection in faster-X evolution because their peculiar life cycle and unusual inheritance of sex chromosomes should generally lead to equivalent effective population sizes for X and autosomes. Because we lack a high-density genetic map for the pea aphid, whose complete genome has been sequenced, we first assigned its entire genome to the X or autosomes based on ratios of sequencing depth in males (X0) to females (XX). Then, we computed nonsynonymous to synonymous substitutions ratios (dN/dS) for the pea aphid gene set and found faster evolution of X-linked genes. Our analyses of substitution rates, together with polymorphism and expression data, showed that relaxed selection is likely to be the greatest contributor to faster-X because a large fraction of X-linked genes are expressed at low rates and thus escape selection. Yet, a minor role for positive selection is also suggested by the difference between substitution rates for X and autosomes for male-biased genes (but not for asexual female-biased genes) and by lower Tajima’s D for X-linked compared with autosomal genes with highly male-biased expression patterns. This study highlights the relevance of organisms displaying alternative chromosomal inheritance to the understanding of forces shaping genome evolution.
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Affiliation(s)
- Julie Jaquiéry
- INRA UMR IGEPP Domaine de la Motte, Le Rheu, France.,CNRS UMR 6553 ECOBIO, Université de Rennes 1, France
| | - Jean Peccoud
- CNRS UMR 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, France
| | | | - Fabrice Legeai
- INRA UMR IGEPP Domaine de la Motte, Le Rheu, France.,INRIA Centre Rennes - Bretagne Atlantique, GenOuest, Rennes, France
| | | | - Anais Gouin
- INRA UMR IGEPP Domaine de la Motte, Le Rheu, France.,INRIA Centre Rennes - Bretagne Atlantique, GenOuest, Rennes, France
| | - Pierre Nouhaud
- Institute of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | | | - Ryan Bickel
- Department of Biology, University of Rochester
| | - Swapna Purandare
- Multidisciplinary Center for Advance Research and Studies (MCARS), Jamia Millia Islamia, New Delhi, India
| | - Julie Poulain
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Christophe Battail
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Centre National de Génotypage (CNG), Evry, France
| | - Claire Lemaitre
- INRIA Centre Rennes - Bretagne Atlantique, GenOuest, Rennes, France
| | | | | | | | - Claude Rispe
- BIOEPAR, INRA, ONIRIS, La Chantrerie, Nantes, France
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38
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Guyomar C, Legeai F, Jousselin E, Mougel C, Lemaitre C, Simon JC. Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches. Microbiome 2018; 6:181. [PMID: 30305166 PMCID: PMC6180509 DOI: 10.1186/s40168-018-0562-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/20/2018] [Indexed: 05/27/2023]
Abstract
BACKGROUND Most metazoans are involved in durable relationships with microbes which can take several forms, from mutualism to parasitism. The advances of NGS technologies and bioinformatics tools have opened opportunities to shed light on the diversity of microbial communities and to give some insights into the functions they perform in a broad array of hosts. The pea aphid is a model system for the study of insect-bacteria symbiosis. It is organized in a complex of biotypes, each adapted to specific host plants. It harbors both an obligatory symbiont supplying key nutrients and several facultative symbionts bringing additional functions to the host, such as protection against biotic and abiotic stresses. However, little is known on how the symbiont genomic diversity is structured at different scales: across host biotypes, among individuals of the same biotype, or within individual aphids, which limits our understanding on how these multi-partner symbioses evolve and interact. RESULTS We present a framework well adapted to the study of genomic diversity and evolutionary dynamics of the pea aphid holobiont from metagenomic read sets, based on mapping to reference genomes and whole genome variant calling. Our results revealed that the pea aphid microbiota is dominated by a few heritable bacterial symbionts reported in earlier works, with no discovery of new microbial associates. However, we detected a large and heterogeneous genotypic diversity associated with the different symbionts of the pea aphid. Partitioning analysis showed that this fine resolution diversity is distributed across the three considered scales. Phylogenetic analyses highlighted frequent horizontal transfers of facultative symbionts between host lineages, indicative of flexible associations between the pea aphid and its microbiota. However, the evolutionary dynamics of symbiotic associations strongly varied depending on the symbiont, reflecting different histories and possible constraints. In addition, at the intra-host scale, we showed that different symbiont strains may coexist inside the same aphid host. CONCLUSIONS We present a methodological framework for the detailed analysis of NGS data from microbial communities of moderate complexity and gave major insights into the extent of diversity in pea aphid-symbiont associations and the range of evolutionary trajectories they could take.
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Affiliation(s)
- Cervin Guyomar
- INRA, UMR 1349 INRA/Agrocampus Ouest/Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Le Rheu, France
- Université Rennes 1, Inria, CNRS, IRISA, F-35000, Rennes, France
| | - Fabrice Legeai
- INRA, UMR 1349 INRA/Agrocampus Ouest/Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Le Rheu, France
- Université Rennes 1, Inria, CNRS, IRISA, F-35000, Rennes, France
| | - Emmanuelle Jousselin
- INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet, Montpellier, France
| | - Christophe Mougel
- INRA, UMR 1349 INRA/Agrocampus Ouest/Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Le Rheu, France
| | - Claire Lemaitre
- Université Rennes 1, Inria, CNRS, IRISA, F-35000, Rennes, France
| | - Jean-Christophe Simon
- INRA, UMR 1349 INRA/Agrocampus Ouest/Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Le Rheu, France.
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39
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Gay S, Bugeon J, Bouchareb A, Henry L, Delahaye C, Legeai F, Montfort J, Le Cam A, Siegel A, Bobe J, Thermes V. MiR-202 controls female fecundity by regulating medaka oogenesis. PLoS Genet 2018; 14:e1007593. [PMID: 30199527 PMCID: PMC6147661 DOI: 10.1371/journal.pgen.1007593] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 09/20/2018] [Accepted: 07/26/2018] [Indexed: 12/12/2022] Open
Abstract
Female gamete production relies on coordinated molecular and cellular processes that occur in the ovary throughout oogenesis. In fish, as in other vertebrates, these processes have been extensively studied both in terms of endocrine/paracrine regulation and protein expression and activity. The role of small non-coding RNAs in the regulation of animal reproduction remains however largely unknown and poorly investigated, despite a growing interest for the importance of miRNAs in a wide variety of biological processes. Here, we analyzed the role of miR-202, a miRNA predominantly expressed in male and female gonads in several vertebrate species. We studied its expression in the medaka ovary and generated a mutant line (using CRISPR/Cas9 genome editing) to determine its importance for reproductive success with special interest for egg production. Our results show that miR-202-5p is the most abundant mature form of the miRNA and that it is expressed in granulosa cells and in the unfertilized egg. The knock out (KO) of mir-202 gene resulted in a strong phenotype both in terms of number and quality of eggs produced. Mutant females exhibited either no egg production or produced a dramatically reduced number of eggs that could not be fertilized, ultimately leading to no reproductive success. We quantified the size distribution of the oocytes in the ovary of KO females and performed a large-scale transcriptomic analysis approach to identified dysregulated molecular pathways. Together, cellular and molecular analyses indicate that the lack of miR-202 impairs the early steps of oogenesis/folliculogenesis and decreases the number of large (i.e. vitellogenic) follicles, ultimately leading to dramatically reduced female fecundity. This study sheds new light on the regulatory mechanisms that control the early steps of follicular development, including possible targets of miR-202-5p, and provides the first in vivo functional evidence that a gonad-predominant microRNA may have a major role in female reproduction. The role of small non-coding RNAs in the regulation of animal reproduction remains poorly investigated, despite a growing interest for the importance of miRNAs in a wide variety of biological processes. Here, we analyzed the role of miR-202, a miRNA predominantly expressed in gonads in vertebrate. We studied its expression in the medaka ovary and knocked out the mir-202 gene to study its importance for reproductive success. We showed that the lack of miR-202 results in the sterility of both females and males. In particular, it led to a drastic reduction of both the number and the quality of eggs produced by females. Mutant females exhibited either no egg production or produced a drastically reduced number of eggs that could not be fertilized, ultimately leading to no reproductive success. Quantitative histological and molecular analyses indicated that mir-202 KO impairs oocyte development and is also associated with the dysregulation of many genes that are critical for reproduction. This study sheds new light on the regulatory mechanisms that control oogenesis, including possible targets of miR-202-5p, and provides the first in vivo functional evidence that a gonad-predominant microRNA may have a major role in female reproduction.
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Affiliation(s)
| | | | | | | | - Clara Delahaye
- LPGP, INRA, Rennes, France
- Univ Rennes, INRIA, CNRS, IRISA, Rennes, France
| | - Fabrice Legeai
- Univ Rennes, INRIA, CNRS, IRISA, Rennes, France
- IGEPP, INRA BP35327, Le Rheu, France
| | | | | | - Anne Siegel
- Univ Rennes, INRIA, CNRS, IRISA, Rennes, France
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40
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Nouhaud P, Gautier M, Gouin A, Jaquiéry J, Peccoud J, Legeai F, Mieuzet L, Smadja CM, Lemaitre C, Vitalis R, Simon JC. Identifying genomic hotspots of differentiation and candidate genes involved in the adaptive divergence of pea aphid host races. Mol Ecol 2018; 27:3287-3300. [PMID: 30010213 DOI: 10.1111/mec.14799] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 06/01/2018] [Accepted: 06/11/2018] [Indexed: 01/01/2023]
Abstract
Identifying the genomic bases of adaptation to novel environments is a long-term objective in evolutionary biology. Because genetic differentiation is expected to increase between locally adapted populations at the genes targeted by selection, scanning the genome for elevated levels of differentiation is a first step towards deciphering the genomic architecture underlying adaptive divergence. The pea aphid Acyrthosiphon pisum is a model of choice to address this question, as it forms a large complex of plant-specialized races and cryptic species, resulting from recent adaptive radiation. Here, we characterized genomewide polymorphisms in three pea aphid races specialized on alfalfa, clover and pea crops, respectively, which we sequenced in pools (poolseq). Using a model-based approach that explicitly accounts for selection, we identified 392 genomic hotspots of differentiation spanning 47.3 Mb and 2,484 genes (respectively, 9.12% of the genome size and 8.10% of its genes). Most of these highly differentiated regions were located on the autosomes, and overall differentiation was weaker on the X chromosome. Within these hotspots, high levels of absolute divergence between races suggest that these regions experienced less gene flow than the rest of the genome, most likely by contributing to reproductive isolation. Moreover, population-specific analyses showed evidence of selection in every host race, depending on the hotspot considered. These hotspots were significantly enriched for candidate gene categories that control host-plant selection and use. These genes encode 48 salivary proteins, 14 gustatory receptors, 10 odorant receptors, five P450 cytochromes and one chemosensory protein, which represent promising candidates for the genetic basis of host-plant specialization and ecological isolation in the pea aphid complex. Altogether, our findings open new research directions towards functional studies, for validating the role of these genes on adaptive phenotypes.
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Affiliation(s)
| | - Mathieu Gautier
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
- Institut de Biologie Computationnelle, Univ Montpellier, Montpellier, France
| | - Anaïs Gouin
- INRA, UMR 1349 IGEPP, Le Rheu, France
- Inria/IRISA GenScale, Rennes, France
| | | | - Jean Peccoud
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers, Poitiers, France
| | - Fabrice Legeai
- INRA, UMR 1349 IGEPP, Le Rheu, France
- Inria/IRISA GenScale, Rennes, France
| | | | - Carole M Smadja
- Institut des Sciences de l'Evolution (UMR 5554) - CNRS - IRD - EPHE - CIRAD -Université de Montpellier, Montpellier, France
| | | | - Renaud Vitalis
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
- Institut de Biologie Computationnelle, Univ Montpellier, Montpellier, France
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Cusumano A, Duvic B, Jouan V, Ravallec M, Legeai F, Peri E, Colazza S, Volkoff AN. First extensive characterization of the venom gland from an egg parasitoid: structure, transcriptome and functional role. J Insect Physiol 2018; 107:68-80. [PMID: 29477467 DOI: 10.1016/j.jinsphys.2018.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 12/23/2017] [Accepted: 02/21/2018] [Indexed: 06/08/2023]
Abstract
The venom gland is a ubiquitous organ in Hymenoptera. In insect parasitoids, the venom gland has been shown to have multiple functions including regulation of host immune response, host paralysis, host castration and developmental alteration. However, the role played by the venom gland has been mainly studied in parasitoids developing in larval or pupal hosts while little is known for parasitoids developing in insect eggs. We conducted the first extensive characterization of the venom of the endoparasitoid Ooencyrtus telenomicida (Vassiliev), a species that develops in eggs of the stink bug Nezara viridula (L.). In particular we investigated the structure of the venom apparatus, its functional role and conducted a transcriptomic analysis of the venom gland. We found that injection of O. telenomicida venom induces: 1) a melanized-like process in N. viridula host eggs (host-parasitoid interaction), 2) impairment of the larval development of the competitor Trissolcus basalis (Wollaston) (parasitoid-parasitoid interaction). The O. telenomicida venom gland transcriptome reveals a majority of digestive enzymes (peptidases and glycosylases) and oxidoreductases (laccases) among the most expressed genes. The former enzymes are likely to be involved in degradation of the host resources for the specific benefit of the O. telenomicida offspring. In turn, alteration of host resources caused by these enzymes may negatively affect the larval development of the competitor T. basalis. We hypothesize that the melanization process induced by venom injection could be related to the presence of laccases, which are multicopper oxidases that belong to the phenoloxidases group. This work contributed to a better understanding of the venom in insect parasitoids and allowed to identify candidate genes whose functional role can be investigated in future studies.
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Affiliation(s)
- Antonino Cusumano
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Viale delle Scienze edificio 5, 90128 Palermo, Italy; Laboratory of Entomology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
| | - Bernard Duvic
- UMR DGIMI INRA 1333 - Université de Montpellier, Place Eugène Bataillon, CC101, 34095 Montpellier Cedex, France
| | - Véronique Jouan
- UMR DGIMI INRA 1333 - Université de Montpellier, Place Eugène Bataillon, CC101, 34095 Montpellier Cedex, France
| | - Marc Ravallec
- UMR DGIMI INRA 1333 - Université de Montpellier, Place Eugène Bataillon, CC101, 34095 Montpellier Cedex, France
| | - Fabrice Legeai
- BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, 35042 Rennes Cedex, France
| | - Ezio Peri
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Viale delle Scienze edificio 5, 90128 Palermo, Italy
| | - Stefano Colazza
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Viale delle Scienze edificio 5, 90128 Palermo, Italy
| | - Anne-Nathalie Volkoff
- UMR DGIMI INRA 1333 - Université de Montpellier, Place Eugène Bataillon, CC101, 34095 Montpellier Cedex, France
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42
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Gouin A, Bretaudeau A, Nam K, Gimenez S, Aury JM, Duvic B, Hilliou F, Durand N, Montagné N, Darboux I, Kuwar S, Chertemps T, Siaussat D, Bretschneider A, Moné Y, Ahn SJ, Hänniger S, Grenet ASG, Neunemann D, Maumus F, Luyten I, Labadie K, Xu W, Koutroumpa F, Escoubas JM, Llopis A, Maïbèche-Coisne M, Salasc F, Tomar A, Anderson AR, Khan SA, Dumas P, Orsucci M, Guy J, Belser C, Alberti A, Noel B, Couloux A, Mercier J, Nidelet S, Dubois E, Liu NY, Boulogne I, Mirabeau O, Le Goff G, Gordon K, Oakeshott J, Consoli FL, Volkoff AN, Fescemyer HW, Marden JH, Luthe DS, Herrero S, Heckel DG, Wincker P, Kergoat GJ, Amselem J, Quesneville H, Groot AT, Jacquin-Joly E, Nègre N, Lemaitre C, Legeai F, d'Alençon E, Fournier P. Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges. Sci Rep 2017; 7:11816. [PMID: 28947760 PMCID: PMC5613006 DOI: 10.1038/s41598-017-10461-4] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/19/2017] [Indexed: 12/30/2022] Open
Abstract
Emergence of polyphagous herbivorous insects entails significant adaptation to recognize, detoxify and digest a variety of host-plants. Despite of its biological and practical importance - since insects eat 20% of crops - no exhaustive analysis of gene repertoires required for adaptations in generalist insect herbivores has previously been performed. The noctuid moth Spodoptera frugiperda ranks as one of the world’s worst agricultural pests. This insect is polyphagous while the majority of other lepidopteran herbivores are specialist. It consists of two morphologically indistinguishable strains (“C” and “R”) that have different host plant ranges. To describe the evolutionary mechanisms that both enable the emergence of polyphagous herbivory and lead to the shift in the host preference, we analyzed whole genome sequences from laboratory and natural populations of both strains. We observed huge expansions of genes associated with chemosensation and detoxification compared with specialist Lepidoptera. These expansions are largely due to tandem duplication, a possible adaptation mechanism enabling polyphagy. Individuals from natural C and R populations show significant genomic differentiation. We found signatures of positive selection in genes involved in chemoreception, detoxification and digestion, and copy number variation in the two latter gene families, suggesting an adaptive role for structural variation.
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Affiliation(s)
- Anaïs Gouin
- INRIA, IRISA, GenScale, Campus de Beaulieu, Rennes, 35042, France
| | - Anthony Bretaudeau
- INRA, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, Rennes, 35042, France.,INRIA, IRISA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | - Kiwoong Nam
- DGIMI, INRA, Univ. Montpellier, 34095, Montpellier, France
| | - Sylvie Gimenez
- DGIMI, INRA, Univ. Montpellier, 34095, Montpellier, France
| | - Jean-Marc Aury
- CEA, Genoscope, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Bernard Duvic
- DGIMI, INRA, Univ. Montpellier, 34095, Montpellier, France
| | - Frédérique Hilliou
- Université Côte d'Azur, INRA, CNRS, Institut Sophia Agrobiotech, 06903 Sophia-Antipolis, France
| | - Nicolas Durand
- Sorbonne Universités, UPMC University Paris 06, Institute of Ecology and Environmental Sciences of Paris, 75005, Paris, France
| | - Nicolas Montagné
- Sorbonne Universités, UPMC University Paris 06, Institute of Ecology and Environmental Sciences of Paris, 75005, Paris, France
| | | | - Suyog Kuwar
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745, Jena, Germany
| | - Thomas Chertemps
- Sorbonne Universités, UPMC University Paris 06, Institute of Ecology and Environmental Sciences of Paris, 75005, Paris, France
| | - David Siaussat
- Sorbonne Universités, UPMC University Paris 06, Institute of Ecology and Environmental Sciences of Paris, 75005, Paris, France
| | - Anne Bretschneider
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745, Jena, Germany
| | - Yves Moné
- DGIMI, INRA, Univ. Montpellier, 34095, Montpellier, France
| | - Seung-Joon Ahn
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745, Jena, Germany
| | - Sabine Hänniger
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745, Jena, Germany
| | | | - David Neunemann
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745, Jena, Germany
| | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Isabelle Luyten
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Karine Labadie
- CEA, Genoscope, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Wei Xu
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, 6150, Australia
| | - Fotini Koutroumpa
- INRA, Institute of Ecology and Environmental Sciences, 78000, Versailles, France.,Laboratory of Mammalian Genetics, Center for DNA Fingerprinting and Diagnostics (CDFD), Lab block: Tuljaguda (Opp. MJ Market), Nampally, Hyderabad, 500 001, India
| | | | - Angel Llopis
- Department of Genetics, Universitat de València, 46100, Burjassot, Valencia, Spain.,Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI-BIOTECMED), Universitat de València, 46100, Burjassot, Valencia, Spain
| | - Martine Maïbèche-Coisne
- Sorbonne Universités, UPMC University Paris 06, Institute of Ecology and Environmental Sciences of Paris, 75005, Paris, France
| | - Fanny Salasc
- DGIMI, INRA, Univ. Montpellier, 34095, Montpellier, France.,EPHE, PSL Research University, UMR1333 - DGIMI, Pathologie comparée des Invertébrés CC101, F-34095, Montpellier cedex 5, France
| | - Archana Tomar
- Laboratory of Mammalian Genetics, Center for DNA Fingerprinting and Diagnostics (CDFD), Lab block: Tuljaguda (Opp. MJ Market), Nampally, Hyderabad, 500 001, India
| | - Alisha R Anderson
- CSIRO Ecosystem Sciences, Black Mountain, Canberra, ACT 2600, Australia
| | - Sher Afzal Khan
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745, Jena, Germany
| | - Pascaline Dumas
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Science Park 904, 1090 GE, Amsterdam, The Netherlands
| | - Marion Orsucci
- DGIMI, INRA, Univ. Montpellier, 34095, Montpellier, France
| | - Julie Guy
- CEA, Genoscope, 2 rue Gaston Crémieux, 91000, Evry, France
| | | | | | - Benjamin Noel
- CEA, Genoscope, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Arnaud Couloux
- CEA, Genoscope, 2 rue Gaston Crémieux, 91000, Evry, France
| | | | - Sabine Nidelet
- Plateforme MGX, C/o institut de Génomique Fonctionnelle, 141, rue de la Cardonille, 34094, Montpellier cedex 05, France
| | - Emeric Dubois
- Plateforme MGX, C/o institut de Génomique Fonctionnelle, 141, rue de la Cardonille, 34094, Montpellier cedex 05, France
| | - Nai-Yong Liu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, 650224, China
| | - Isabelle Boulogne
- Sorbonne Universités, UPMC University Paris 06, Institute of Ecology and Environmental Sciences of Paris, 75005, Paris, France
| | - Olivier Mirabeau
- INRA, Institute of Ecology and Environmental Sciences, 78000, Versailles, France
| | - Gaelle Le Goff
- Université Côte d'Azur, INRA, CNRS, Institut Sophia Agrobiotech, 06903 Sophia-Antipolis, France
| | - Karl Gordon
- CSIRO, Clunies Ross St, (GPO Box 1700), Acton, ACT 2601, Australia
| | - John Oakeshott
- CSIRO, Clunies Ross St, (GPO Box 1700), Acton, ACT 2601, Australia
| | - Fernando L Consoli
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av. Pádua Dias 11, 13418-900, Piracicaba, Brazil
| | | | - Howard W Fescemyer
- Department of Biology, 208 Mueller Laboratory, The Pennsylvania State University, University Park, 16802, Pennsylvania, USA
| | - James H Marden
- Department of Biology, 208 Mueller Laboratory, The Pennsylvania State University, University Park, 16802, Pennsylvania, USA
| | - Dawn S Luthe
- Department of Plant Science, 102 Tyson Building, The Pennsylvania State University, University Park, 16802, Pennsylvania, USA
| | - Salvador Herrero
- Department of Genetics, Universitat de València, 46100, Burjassot, Valencia, Spain
| | - David G Heckel
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745, Jena, Germany
| | - Patrick Wincker
- CEA, Genoscope, 2 rue Gaston Crémieux, 91000, Evry, France.,CNRS UMR 8030, 2 rue Gaston Crémieux, 91000, Evry, France.,Université d'Evry Val D'Essonne, 91000, Evry, France
| | - Gael J Kergoat
- INRA, UMR1062 CBGP, IRD, CIRAD, Montpellier SupAgro, 755 Avenue du campus Agropolis, 34988, Montferrier/Lez, France
| | - Joelle Amselem
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | | | - Astrid T Groot
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745, Jena, Germany.,Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Science Park 904, 1090 GE, Amsterdam, The Netherlands
| | | | - Nicolas Nègre
- DGIMI, INRA, Univ. Montpellier, 34095, Montpellier, France.
| | - Claire Lemaitre
- INRIA, IRISA, GenScale, Campus de Beaulieu, Rennes, 35042, France.
| | - Fabrice Legeai
- INRIA, IRISA, GenScale, Campus de Beaulieu, Rennes, 35042, France
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Ballesteros GI, Gadau J, Legeai F, Gonzalez-Gonzalez A, Lavandero B, Simon JC, Figueroa CC. Expression differences in Aphidius ervi (Hymenoptera: Braconidae) females reared on different aphid host species. PeerJ 2017; 5:e3640. [PMID: 28852588 PMCID: PMC5572533 DOI: 10.7717/peerj.3640] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/12/2017] [Indexed: 01/25/2023] Open
Abstract
The molecular mechanisms that allow generalist parasitoids to exploit many, often very distinct hosts are practically unknown. The wasp Aphidius ervi, a generalist koinobiont parasitoid of aphids, was introduced from Europe into Chile in the late 1970s to control agriculturally important aphid species. A recent study showed significant differences in host preference and host acceptance (infectivity) depending on the host A. ervi were reared on. In contrast, no genetic differentiation between A. ervi populations parasitizing different aphid species and aphids of the same species reared on different host plants was found in Chile. Additionally, the same study did not find any fitness effects in A. ervi if offspring were reared on a different host as their mothers. Here, we determined the effect of aphid host species (Sitobion avenae versus Acyrthosiphon pisum reared on two different host plants alfalfa and pea) on the transcriptome of adult A. ervi females. We found a large number of differentially expressed genes (between host species: head: 2,765; body: 1,216; within the same aphid host species reared on different host plants: alfalfa versus pea: head 593; body 222). As expected, the transcriptomes from parasitoids reared on the same host species (pea aphid) but originating from different host plants (pea versus alfalfa) were more similar to each other than the transcriptomes of parasitoids reared on a different aphid host and host plant (head: 648 and 1,524 transcripts; body: 566 and 428 transcripts). We found several differentially expressed odorant binding proteins and olfactory receptor proteins in particular, when we compared parasitoids from different host species. Additionally, we found differentially expressed genes involved in neuronal growth and development as well as signaling pathways. These results point towards a significant rewiring of the transcriptome of A. ervi depending on aphid-plant complex where parasitoids develop, even if different biotypes of a certain aphid host species (A. pisum) are reared on the same host plant. This difference seems to persist even after the different wasp populations were reared on the same aphid host in the laboratory for more than 50 generations. This indicates that either the imprinting process is very persistent or there is enough genetic/allelic variation between A. ervi populations. The role of distinct molecular mechanisms is discussed in terms of the formation of host fidelity.
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Affiliation(s)
- Gabriel I Ballesteros
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile.,Millennium Nucleus Centre in Molecular Ecology and Evolutionary Applications in the Agroecosystems, Universidad de Talca, Talca, Chile
| | - Jürgen Gadau
- School of Life Sciences, Arizona State University, Tempe, AZ, United States of America.,Institute for Evolution and Biodiversity, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Fabrice Legeai
- GenScale, INRIA Centre Rennes, Rennes, France.,Institute of Genetics, Environment and Plant Protection, INRA, Le Rheu, France
| | - Angelica Gonzalez-Gonzalez
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile.,Millennium Nucleus Centre in Molecular Ecology and Evolutionary Applications in the Agroecosystems, Universidad de Talca, Talca, Chile
| | - Blas Lavandero
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | | | - Christian C Figueroa
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile.,Millennium Nucleus Centre in Molecular Ecology and Evolutionary Applications in the Agroecosystems, Universidad de Talca, Talca, Chile
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44
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Eoche-Bosy D, Gautier M, Esquibet M, Legeai F, Bretaudeau A, Bouchez O, Fournet S, Grenier E, Montarry J. Genome scans on experimentally evolved populations reveal candidate regions for adaptation to plant resistance in the potato cyst nematode Globodera pallida. Mol Ecol 2017; 26:4700-4711. [PMID: 28734070 DOI: 10.1111/mec.14240] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 07/13/2017] [Accepted: 07/17/2017] [Indexed: 12/30/2022]
Abstract
Improving resistance durability involves to be able to predict the adaptation speed of pathogen populations. Identifying the genetic bases of pathogen adaptation to plant resistances is a useful step to better understand and anticipate this phenomenon. Globodera pallida is a major pest of potato crop for which a resistance QTL, GpaVvrn , has been identified in Solanum vernei. However, its durability is threatened as G. pallida populations are able to adapt to the resistance in few generations. The aim of this study was to investigate the genomic regions involved in the resistance breakdown by coupling experimental evolution and high-density genome scan. We performed a whole-genome resequencing of pools of individuals (Pool-Seq) belonging to G. pallida lineages derived from two independent populations having experimentally evolved on susceptible and resistant potato cultivars. About 1.6 million SNPs were used to perform the genome scan using a recent model testing for adaptive differentiation and association to population-specific covariables. We identified 275 outliers and 31 of them, which also showed a significant reduction in diversity in adapted lineages, were investigated for their genic environment. Some candidate genomic regions contained genes putatively encoding effectors and were enriched in SPRYSECs, known in cyst nematodes to be involved in pathogenicity and in (a)virulence. Validated candidate SNPs will provide a useful molecular tool to follow frequencies of virulence alleles in natural G. pallida populations and define efficient strategies of use of potato resistances maximizing their durability.
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Affiliation(s)
- D Eoche-Bosy
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - M Gautier
- CBGP, INRA, IRD, CIRAD, Montpellier SupAgro, Montferrier-sur-Lez, France.,IBC, Montpellier, France
| | - M Esquibet
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - F Legeai
- IGEPP, BIPAA, INRA, Agrocampus Ouest, Université de Rennes 1, Rennes, France.,IRISA, GenScale, INRIA, Rennes, France
| | - A Bretaudeau
- IGEPP, BIPAA, INRA, Agrocampus Ouest, Université de Rennes 1, Rennes, France.,IRISA, GenOuest COre Facility, INRIA, Rennes, France
| | - O Bouchez
- GeT-PlaGe, Genotoul, INRA, Castanet-Tolosan, France.,GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet-Tolosan, France
| | - S Fournet
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - E Grenier
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - J Montarry
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
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45
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Richard G, Legeai F, Prunier-Leterme N, Bretaudeau A, Tagu D, Jaquiéry J, Le Trionnaire G. Dosage compensation and sex-specific epigenetic landscape of the X chromosome in the pea aphid. Epigenetics Chromatin 2017. [PMID: 28638443 PMCID: PMC5471693 DOI: 10.1186/s13072-017-0137-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Background Heterogametic species display a differential number of sex chromosomes resulting in imbalanced transcription levels for these chromosomes between males and females. To correct this disequilibrium, dosage compensation mechanisms involving gene expression and chromatin accessibility regulations have emerged throughout evolution. In insects, these mechanisms have been extensively characterized only in Drosophila but not in insects of agronomical importance. Aphids are indeed major pests of a wide range of crops. Their remarkable ability to switch from asexual to sexual reproduction during their life cycle largely explains the economic losses they can cause. As heterogametic insects, male aphids are X0, while females (asexual and sexual) are XX. Results Here, we analyzed transcriptomic and open chromatin data obtained from whole male and female individuals to evaluate the putative existence of a dosage compensation mechanism involving differential chromatin accessibility of the pea aphid’s X chromosome. Transcriptomic analyses first showed X/AA and XX/AA expression ratios for expressed genes close to 1 in males and females, respectively, suggesting dosage compensation in the pea aphid. Analyses of open chromatin data obtained by Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE-seq) revealed a X chromosome chromatin accessibility globally and significantly higher in males than in females, while autosomes’ chromatin accessibility is similar between sexes. Moreover, chromatin environment of X-linked genes displaying similar expression levels in males and females—and thus likely to be compensated—is significantly more accessible in males. Conclusions Our results suggest the existence of an underlying epigenetic mechanism enhancing the X chromosome chromatin accessibility in males to allow X-linked gene dose correction between sexes in the pea aphid, similar to Drosophila. Our study gives new evidence into the comprehension of dosage compensation in link with chromatin biology in insects and newly in a major crop pest, taking benefits from both transcriptomic and open chromatin data. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0137-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gautier Richard
- EGI, UMR 1349, INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Domaine de la Motte, BP 35327, Le Rheu, France
| | - Fabrice Legeai
- BIPAA, UMR 1349, INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Campus Beaulieu, Rennes, France.,Genscale, INRIA, IRISA, Campus Beaulieu, Rennes, France
| | - Nathalie Prunier-Leterme
- EGI, UMR 1349, INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Domaine de la Motte, BP 35327, Le Rheu, France
| | - Anthony Bretaudeau
- BIPAA, UMR 1349, INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Campus Beaulieu, Rennes, France.,Genouest, INRIA, IRISA, Campus Beaulieu, Rennes, France
| | - Denis Tagu
- EGI, UMR 1349, INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Domaine de la Motte, BP 35327, Le Rheu, France
| | - Julie Jaquiéry
- CNRS, UMR 6553, EcoBio, University of Rennes 1, 35042 Rennes, France
| | - Gaël Le Trionnaire
- EGI, UMR 1349, INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Domaine de la Motte, BP 35327, Le Rheu, France
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46
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Wucher V, Legeai F, Hédan B, Rizk G, Lagoutte L, Leeb T, Jagannathan V, Cadieu E, David A, Lohi H, Cirera S, Fredholm M, Botherel N, Leegwater PA, Le Béguec C, Fieten H, Johnson J, Alföldi J, André C, Lindblad-Toh K, Hitte C, Derrien T. FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome. Nucleic Acids Res 2017; 45:e57. [PMID: 28053114 PMCID: PMC5416892 DOI: 10.1093/nar/gkw1306] [Citation(s) in RCA: 181] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/13/2016] [Accepted: 12/14/2016] [Indexed: 12/13/2022] Open
Abstract
Whole transcriptome sequencing (RNA-seq) has become a standard for cataloguing and monitoring RNA populations. One of the main bottlenecks, however, is to correctly identify the different classes of RNAs among the plethora of reconstructed transcripts, particularly those that will be translated (mRNAs) from the class of long non-coding RNAs (lncRNAs). Here, we present FEELnc (FlExible Extraction of LncRNAs), an alignment-free program that accurately annotates lncRNAs based on a Random Forest model trained with general features such as multi k-mer frequencies and relaxed open reading frames. Benchmarking versus five state-of-the-art tools shows that FEELnc achieves similar or better classification performance on GENCODE and NONCODE data sets. The program also provides specific modules that enable the user to fine-tune classification accuracy, to formalize the annotation of lncRNA classes and to identify lncRNAs even in the absence of a training set of non-coding RNAs. We used FEELnc on a real data set comprising 20 canine RNA-seq samples produced by the European LUPA consortium to substantially expand the canine genome annotation to include 10 374 novel lncRNAs and 58 640 mRNA transcripts. FEELnc moves beyond conventional coding potential classifiers by providing a standardized and complete solution for annotating lncRNAs and is freely available at https://github.com/tderrien/FEELnc.
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Affiliation(s)
- Valentin Wucher
- Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France
| | - Fabrice Legeai
- IGEPP, BIPAA, INRA, Campus Beaulieu, Le Rheu 35653, France
- Institut National de Recherche en Informatique et en Automatique, Institut de Recherche en Informatique et Systèmes Aléatoires, Genscale, Campus Beaulieu, Rennes 35042, France
| | - Benoît Hédan
- Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France
| | - Guillaume Rizk
- Institut National de Recherche en Informatique et en Automatique, Institut de Recherche en Informatique et Systèmes Aléatoires, Genscale, Campus Beaulieu, Rennes 35042, France
| | - Lætitia Lagoutte
- Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland
| | - Edouard Cadieu
- Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France
| | - Audrey David
- IGEPP, BIPAA, INRA, Campus Beaulieu, Le Rheu 35653, France
| | - Hannes Lohi
- Department of Veterinary Biosciences and Research Programs Unit, Molecular Neurology, University of Helsinki, PO Box 63, Helsinki 00014, Finland
- The Folkhälsan Institute of Genetics, Helsinki 00014, Finland
| | - Susanna Cirera
- Department of Veterinary Clinical and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1870, Denmark
| | - Merete Fredholm
- Department of Veterinary Clinical and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1870, Denmark
| | - Nadine Botherel
- Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France
| | - Peter A.J. Leegwater
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht 3584CM, the Netherlands
| | - Céline Le Béguec
- Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France
| | - Hille Fieten
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht 3584CM, the Netherlands
| | - Jeremy Johnson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jessica Alföldi
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Catherine André
- Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 751 23, Sweden
| | - Christophe Hitte
- Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France
| | - Thomas Derrien
- Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France
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47
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Mathers TC, Chen Y, Kaithakottil G, Legeai F, Mugford ST, Baa-Puyoulet P, Bretaudeau A, Clavijo B, Colella S, Collin O, Dalmay T, Derrien T, Feng H, Gabaldón T, Jordan A, Julca I, Kettles GJ, Kowitwanich K, Lavenier D, Lenzi P, Lopez-Gomollon S, Loska D, Mapleson D, Maumus F, Moxon S, Price DRG, Sugio A, van Munster M, Uzest M, Waite D, Jander G, Tagu D, Wilson ACC, van Oosterhout C, Swarbreck D, Hogenhout SA. Erratum to: Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species. Genome Biol 2017; 18:63. [PMID: 28376841 PMCID: PMC5381131 DOI: 10.1186/s13059-017-1202-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 03/29/2017] [Indexed: 11/10/2022] Open
Affiliation(s)
- Thomas C Mathers
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK.,The International Aphid Genomics Consortium, Miami, USA
| | - Yazhou Chen
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,The International Aphid Genomics Consortium, Miami, USA
| | | | - Fabrice Legeai
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France.,IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | - Sam T Mugford
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,The International Aphid Genomics Consortium, Miami, USA
| | - Patrice Baa-Puyoulet
- The International Aphid Genomics Consortium, Miami, USA.,Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Anthony Bretaudeau
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France.,IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | | | - Stefano Colella
- The International Aphid Genomics Consortium, Miami, USA.,Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France.,Present Address: INRA, UMR1342 IRD-CIRAD-INRA-SupAgro-Université de Montpellier, Laboratoire des Symbioses Tropicales et Méditéranéennes, Campus International de Baillarguet, TA-A82/J, F-34398, Montpellier cedex 5, France
| | - Olivier Collin
- IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Thomas Derrien
- CNRS, UMR 6290, Institut de Génétique et Developpement de Rennes, Université de Rennes 1, 2 Avenue du Pr. Léon Bernard, 35000, Rennes, France
| | - Honglin Feng
- The International Aphid Genomics Consortium, Miami, USA.,Department of Biology, University of Miami, Coral Gables, FL 33146, USA
| | - Toni Gabaldón
- The International Aphid Genomics Consortium, Miami, USA.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Anna Jordan
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Irene Julca
- The International Aphid Genomics Consortium, Miami, USA.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Graeme J Kettles
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Present address: Rothamsted Research, Harpenden, Hertforshire, ALF5 2JQ, UK
| | - Krissana Kowitwanich
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Present address: J. R. Simplot Company, Boise, ID, USA
| | - Dominique Lavenier
- IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | - Paolo Lenzi
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Present address: Alson H. Smith Jr. Agriculture and Extension Center, Virginia Tech, Winchester, 22602, VA, USA
| | - Sara Lopez-Gomollon
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,Present address: Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Damian Loska
- The International Aphid Genomics Consortium, Miami, USA.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Daniel Mapleson
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Florian Maumus
- The International Aphid Genomics Consortium, Miami, USA.,Unité de Recherche Génomique-Info (URGI), INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Simon Moxon
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Daniel R G Price
- The International Aphid Genomics Consortium, Miami, USA.,Department of Biology, University of Miami, Coral Gables, FL 33146, USA.,Present address: Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian, EH26 0PZ, UK
| | - Akiko Sugio
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France
| | - Manuella van Munster
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR BGPI, CIRAD TA-A54K, Campus International de Baillarguet, 34398, Montpellier Cedex 5, France
| | - Marilyne Uzest
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR BGPI, CIRAD TA-A54K, Campus International de Baillarguet, 34398, Montpellier Cedex 5, France
| | - Darren Waite
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Georg Jander
- The International Aphid Genomics Consortium, Miami, USA.,Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA
| | - Denis Tagu
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France
| | - Alex C C Wilson
- The International Aphid Genomics Consortium, Miami, USA.,Department of Biology, University of Miami, Coral Gables, FL 33146, USA
| | - Cock van Oosterhout
- The International Aphid Genomics Consortium, Miami, USA.,School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - David Swarbreck
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK. .,The International Aphid Genomics Consortium, Miami, USA. .,School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Saskia A Hogenhout
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK. .,The International Aphid Genomics Consortium, Miami, USA. .,School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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48
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Mathers TC, Chen Y, Kaithakottil G, Legeai F, Mugford ST, Baa-Puyoulet P, Bretaudeau A, Clavijo B, Colella S, Collin O, Dalmay T, Derrien T, Feng H, Gabaldón T, Jordan A, Julca I, Kettles GJ, Kowitwanich K, Lavenier D, Lenzi P, Lopez-Gomollon S, Loska D, Mapleson D, Maumus F, Moxon S, Price DRG, Sugio A, van Munster M, Uzest M, Waite D, Jander G, Tagu D, Wilson ACC, van Oosterhout C, Swarbreck D, Hogenhout SA. Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species. Genome Biol 2017; 18:27. [PMID: 28190401 PMCID: PMC5304397 DOI: 10.1186/s13059-016-1145-3] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 12/22/2016] [Indexed: 12/04/2022] Open
Abstract
Background The prevailing paradigm of host-parasite evolution is that arms races lead to increasing specialisation via genetic adaptation. Insect herbivores are no exception and the majority have evolved to colonise a small number of closely related host species. Remarkably, the green peach aphid, Myzus persicae, colonises plant species across 40 families and single M. persicae clonal lineages can colonise distantly related plants. This remarkable ability makes M. persicae a highly destructive pest of many important crop species. Results To investigate the exceptional phenotypic plasticity of M. persicae, we sequenced the M. persicae genome and assessed how one clonal lineage responds to host plant species of different families. We show that genetically identical individuals are able to colonise distantly related host species through the differential regulation of genes belonging to aphid-expanded gene families. Multigene clusters collectively upregulate in single aphids within two days upon host switch. Furthermore, we demonstrate the functional significance of this rapid transcriptional change using RNA interference (RNAi)-mediated knock-down of genes belonging to the cathepsin B gene family. Knock-down of cathepsin B genes reduced aphid fitness, but only on the host that induced upregulation of these genes. Conclusions Previous research has focused on the role of genetic adaptation of parasites to their hosts. Here we show that the generalist aphid pest M. persicae is able to colonise diverse host plant species in the absence of genetic specialisation. This is achieved through rapid transcriptional plasticity of genes that have duplicated during aphid evolution. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1145-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas C Mathers
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK.,The International Aphid Genomics Consortium, Miami, USA
| | - Yazhou Chen
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,The International Aphid Genomics Consortium, Miami, USA
| | | | - Fabrice Legeai
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France.,IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | - Sam T Mugford
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,The International Aphid Genomics Consortium, Miami, USA
| | - Patrice Baa-Puyoulet
- The International Aphid Genomics Consortium, Miami, USA.,Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Anthony Bretaudeau
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France.,IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | | | - Stefano Colella
- The International Aphid Genomics Consortium, Miami, USA.,Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France.,Present Address: INRA, UMR1342 IRD-CIRAD-INRA-SupAgro-Université de Montpellier, Laboratoire des Symbioses Tropicales et Méditéranéennes, Campus International de Baillarguet, TA-A82/J, F-34398, Montpellier cedex 5, France
| | - Olivier Collin
- IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Thomas Derrien
- CNRS, UMR 6290, Institut de Génétique et Developpement de Rennes, Université de Rennes 1, 2 Avenue du Pr. Léon Bernard, 35000, Rennes, France
| | - Honglin Feng
- The International Aphid Genomics Consortium, Miami, USA.,Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Toni Gabaldón
- The International Aphid Genomics Consortium, Miami, USA.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Anna Jordan
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Irene Julca
- The International Aphid Genomics Consortium, Miami, USA.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Graeme J Kettles
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Present address: Rothamsted Research, Harpenden, Hertforshire, ALF5 2JQ, UK
| | - Krissana Kowitwanich
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Present address: J. R. Simplot Company, Boise, ID, USA
| | - Dominique Lavenier
- IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | - Paolo Lenzi
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Present address: Alson H. Smith Jr. Agriculture and Extension Center, Virginia Tech, Winchester, 22602, VA, USA
| | - Sara Lopez-Gomollon
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,Present address: Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Damian Loska
- The International Aphid Genomics Consortium, Miami, USA.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Daniel Mapleson
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Florian Maumus
- The International Aphid Genomics Consortium, Miami, USA.,Unité de Recherche Génomique-Info (URGI), INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Simon Moxon
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Daniel R G Price
- The International Aphid Genomics Consortium, Miami, USA.,Department of Biology, University of Miami, Coral Gables, FL, 33146, USA.,Present address: Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian, EH26 0PZ, UK
| | - Akiko Sugio
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France
| | - Manuella van Munster
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR BGPI, CIRAD TA-A54K, Campus International de Baillarguet, 34398, Montpellier Cedex 5, France
| | - Marilyne Uzest
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR BGPI, CIRAD TA-A54K, Campus International de Baillarguet, 34398, Montpellier Cedex 5, France
| | - Darren Waite
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Georg Jander
- The International Aphid Genomics Consortium, Miami, USA.,Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA
| | - Denis Tagu
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France
| | - Alex C C Wilson
- The International Aphid Genomics Consortium, Miami, USA.,Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Cock van Oosterhout
- The International Aphid Genomics Consortium, Miami, USA.,School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - David Swarbreck
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK. .,The International Aphid Genomics Consortium, Miami, USA. .,School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Saskia A Hogenhout
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK. .,The International Aphid Genomics Consortium, Miami, USA. .,School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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49
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Muret K, Klopp C, Wucher V, Esquerré D, Legeai F, Lecerf F, Désert C, Boutin M, Jehl F, Acloque H, Giuffra E, Djebali S, Foissac S, Derrien T, Lagarrigue S. Long noncoding RNA repertoire in chicken liver and adipose tissue. Genet Sel Evol 2017; 49:6. [PMID: 28073357 PMCID: PMC5225574 DOI: 10.1186/s12711-016-0275-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 11/29/2016] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Improving functional annotation of the chicken genome is a key challenge in bridging the gap between genotype and phenotype. Among all transcribed regions, long noncoding RNAs (lncRNAs) are a major component of the transcriptome and its regulation, and whole-transcriptome sequencing (RNA-Seq) has greatly improved their identification and characterization. We performed an extensive profiling of the lncRNA transcriptome in the chicken liver and adipose tissue by RNA-Seq. We focused on these two tissues because of their importance in various economical traits for which energy storage and mobilization play key roles and also because of their high cell homogeneity. To predict lncRNAs, we used a recently developed tool called FEELnc, which also classifies them with respect to their distance and strand orientation to the closest protein-coding genes. Moreover, to confidently identify the genes/transcripts expressed in each tissue (a complex task for weakly expressed molecules such as lncRNAs), we probed a particularly large number of biological replicates (16 per tissue) compared to common multi-tissue studies with a larger set of tissues but less sampling. RESULTS We predicted 2193 lncRNA genes, among which 1670 were robustly expressed across replicates in the liver and/or adipose tissue and which were classified into 1493 intergenic and 177 intragenic lncRNAs located between and within protein-coding genes, respectively. We observed similar structural features between chickens and mammals, with strong synteny conservation but without sequence conservation. As previously reported, we confirm that lncRNAs have a lower and more tissue-specific expression than mRNAs. Finally, we showed that adjacent lncRNA-mRNA genes in divergent orientation have a higher co-expression level when separated by less than 1 kb compared to more distant divergent pairs. Among these, we highlighted for the first time a novel lncRNA candidate involved in lipid metabolism, lnc_DHCR24, which is highly correlated with the DHCR24 gene that encodes a key enzyme of cholesterol biosynthesis. CONCLUSIONS We provide a comprehensive lncRNA repertoire in the chicken liver and adipose tissue, which shows interesting patterns of co-expression between mRNAs and lncRNAs. It contributes to improving the structural and functional annotation of the chicken genome and provides a basis for further studies on energy storage and mobilization traits in the chicken.
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Affiliation(s)
- Kévin Muret
- UMR PEGASE, INRA, 35042, Rennes, France.,UMR PEGASE, AGROCAMPUS OUEST, 35042, Rennes, France
| | | | - Valentin Wucher
- UMR6290 IGDR, CNRS, Université Rennes 1, 35000, Rennes, France
| | - Diane Esquerré
- Plateforme GENOTOUL, INRA, 31326, Castanet-Tolosan, France.,GenPhySE, INPT, ENVT, INRA, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Fabrice Legeai
- UMR IGEPP, INRA, 35042, Rennes, France.,UMR IGEPP, AGROCAMPUS OUEST, 35042, Rennes, France
| | - Frédéric Lecerf
- UMR PEGASE, INRA, 35042, Rennes, France.,UMR PEGASE, AGROCAMPUS OUEST, 35042, Rennes, France
| | - Colette Désert
- UMR PEGASE, INRA, 35042, Rennes, France.,UMR PEGASE, AGROCAMPUS OUEST, 35042, Rennes, France
| | - Morgane Boutin
- UMR PEGASE, INRA, 35042, Rennes, France.,UMR PEGASE, AGROCAMPUS OUEST, 35042, Rennes, France
| | - Frédéric Jehl
- UMR PEGASE, INRA, 35042, Rennes, France.,UMR PEGASE, AGROCAMPUS OUEST, 35042, Rennes, France
| | - Hervé Acloque
- GenPhySE, INPT, ENVT, INRA, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Elisabetta Giuffra
- GABI, AgroParisTech, INRA, Université Paris Saclay, 78350, Jouy-en-Josas, France
| | - Sarah Djebali
- GenPhySE, INPT, ENVT, INRA, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Sylvain Foissac
- GenPhySE, INPT, ENVT, INRA, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Thomas Derrien
- UMR6290 IGDR, CNRS, Université Rennes 1, 35000, Rennes, France.
| | - Sandrine Lagarrigue
- UMR PEGASE, INRA, 35042, Rennes, France. .,UMR PEGASE, AGROCAMPUS OUEST, 35042, Rennes, France.
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50
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Eyres I, Jaquiéry J, Sugio A, Duvaux L, Gharbi K, Zhou JJ, Legeai F, Nelson M, Simon JC, Smadja CM, Butlin R, Ferrari J. Differential gene expression according to race and host plant in the pea aphid. Mol Ecol 2016; 25:4197-215. [PMID: 27474484 DOI: 10.1111/mec.13771] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 07/07/2016] [Accepted: 07/11/2016] [Indexed: 12/28/2022]
Abstract
Host-race formation in phytophagous insects is thought to provide the opportunity for local adaptation and subsequent ecological speciation. Studying gene expression differences amongst host races may help to identify phenotypes under (or resulting from) divergent selection and their genetic, molecular and physiological bases. The pea aphid (Acyrthosiphon pisum) comprises host races specializing on numerous plants in the Fabaceae and provides a unique system for examining the early stages of diversification along a gradient of genetic and associated adaptive divergence. In this study, we examine transcriptome-wide gene expression both in response to environment and across pea aphid races selected to cover the range of genetic divergence reported in this species complex. We identify changes in expression in response to host plant, indicating the importance of gene expression in aphid-plant interactions. Races can be distinguished on the basis of gene expression, and higher numbers of differentially expressed genes are apparent between more divergent races; these expression differences between host races may result from genetic drift and reproductive isolation and possibly divergent selection. Expression differences related to plant adaptation include a subset of chemosensory and salivary genes. Genes showing expression changes in response to host plant do not make up a large portion of between-race expression differences, providing confirmation of previous studies' findings that genes involved in expression differences between diverging populations or species are not necessarily those showing initial plasticity in the face of environmental change.
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Affiliation(s)
- Isobel Eyres
- Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield, S10 2TN, UK
| | - Julie Jaquiéry
- CNRS UMR 6553 ECOBIO, Université de Rennes 1, Avenue du Général Leclerc, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Akiko Sugio
- INRA, Institut de Génétique, Environnement et Protection des Plantes, UMR 1349 IGEPP, Domaine de la Motte, 35653, Le Rheu Cedex, France
| | - Ludovic Duvaux
- Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield, S10 2TN, UK
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
| | - Jing-Jiang Zhou
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Fabrice Legeai
- INRA, Institut de Génétique, Environnement et Protection des Plantes, UMR 1349 IGEPP, Domaine de la Motte, 35653, Le Rheu Cedex, France
| | | | - Jean-Christophe Simon
- INRA, Institut de Génétique, Environnement et Protection des Plantes, UMR 1349 IGEPP, Domaine de la Motte, 35653, Le Rheu Cedex, France
| | - Carole M Smadja
- Institut des Sciences de l'Evolution (UMR 5554 CNRS-IRD-CIRAD-Université de Montpellier), Université Montpellier 2, cc065, Place Bataillon, 34095, Montpellier Cedex 05, France
| | - Roger Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield, S10 2TN, UK
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