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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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Galinier R, Roger E, Moné Y, Duval D, Portet A, Pinaud S, Chaparro C, Grunau C, Genthon C, Dubois E, Rognon A, Arancibia N, Dejean B, Théron A, Gourbal B, Mitta G. A multistrain approach to studying the mechanisms underlying compatibility in the interaction between Biomphalaria glabrata and Schistosoma mansoni. PLoS Negl Trop Dis 2017; 11:e0005398. [PMID: 28253264 PMCID: PMC5349689 DOI: 10.1371/journal.pntd.0005398] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [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: 10/21/2016] [Revised: 03/14/2017] [Accepted: 02/07/2017] [Indexed: 12/03/2022] Open
Abstract
In recent decades, numerous studies have sought to better understand the mechanisms underlying the compatibility between Biomphalaria glabrata and Schistosoma mansoni. The developments of comparative transcriptomics, comparative genomics, interactomics and more targeted approaches have enabled researchers to identify a series of candidate genes. However, no molecular comparative work has yet been performed on multiple populations displaying different levels of compatibility. Here, we seek to fill this gap in the literature. We focused on B. glabrata FREPs and S. mansoni SmPoMucs, which were previously demonstrated to be involved in snail/schistosome compatibility. We studied the expression and polymorphisms of these factors in combinations of snail and schistosome isolates that display different levels of compatibility. We found that the polymorphism and expression levels of FREPs and SmPoMucs could be linked to the compatibility level of S. mansoni. These data and our complementary results obtained by RNA-seq of samples from various snail strains indicate that the mechanism of compatibility is much more complex than previously thought, and that it is likely to be highly variable within and between populations. This complexity must be taken into account if we hope to identify the molecular pathways that are most likely to be good targets for strategies aimed at blocking transmission of the parasite through the snail intermediate host. Schistosomiasis is the second most widespread human tropical parasitic disease after malaria. It is caused by flatworms of the genus Schistosoma, and poses a considerable threat for human health in numerous Asian, African and South American countries. The World Health Organization has set the goal of eradicating schistosomiasis by 2025. However, no vaccine is available, and we currently have only one drug (praziquantel) that can effectively and efficiently treat the disease. As treatment by mass drug administration would enhance the risk of drug resistance in schistosome parasites, complementary strategies to fight this parasitic disease are urgently needed. Freshwater snails of the Biomphalaria genus act as intermediate hosts in the transmission of the schistosome species. Thus, learning more about the mechanisms of the interaction between these snails and the schistosomes could critically facilitate the identification of potential new candidate molecules that may be targeted to prevent schistosome transmission in the field.
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Affiliation(s)
- Richard Galinier
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Emmanuel Roger
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Yves Moné
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - David Duval
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Anaïs Portet
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Silvain Pinaud
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Cristian Chaparro
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Christoph Grunau
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Clémence Genthon
- MGX-Montpellier GenomiX, Montpellier Genomics and Bioinformatics Facility, Montpellier, France
| | - Emeric Dubois
- MGX-Montpellier GenomiX, Montpellier Genomics and Bioinformatics Facility, Montpellier, France
| | - Anne Rognon
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Nathalie Arancibia
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Bernard Dejean
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - André Théron
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Benjamin Gourbal
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
- * E-mail: (BG); (GM)
| | - Guillaume Mitta
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
- * E-mail: (BG); (GM)
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4
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Masson F, Moné Y, Vigneron A, Vallier A, Parisot N, Vincent-Monégat C, Balmand S, Carpentier MC, Zaidman-Rémy A, Heddi A. Weevil endosymbiont dynamics is associated with a clamping of immunity. BMC Genomics 2015; 16:819. [PMID: 26482132 PMCID: PMC4617454 DOI: 10.1186/s12864-015-2048-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [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: 06/30/2015] [Accepted: 10/08/2015] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Insects subsisting on nutritionally unbalanced diets have evolved long-term mutualistic relationships with intracellular symbiotic bacteria (endosymbionts). The endosymbiont population load undergoes changes along with insect development. In the cereal weevil Sitophilus oryzae, the midgut endosymbionts Sodalis pierantonius drastically multiply following adult metamorphosis and rapidly decline until total elimination when the insect achieves its cuticle synthesis. Whilst symbiont load was shown to timely meet insect metabolic needs, little is known about the host molecular and immune processes underlying this dynamics. METHODS We performed RNA sequencing analysis on weevil midguts at three representative phases of the endosymbiont dynamics (i.e. increase, climax and decrease). To screen genes which transcriptional changes are specifically related to symbiont dynamics and not to the intrinsic development of the midgut, we further have monitored by RT-qPCR sixteen gene transcript levels in symbiotic and artificially non-symbiotic (aposymbiotic) weevils. We also localized the endosymbionts during the elimination process by fluorescence microscopy. RESULTS Functional analysis of the host differentially expressed genes by RNA sequencing showed that the main transcriptional changes occur during endosymbiont growth phase and affect cell proliferation, apoptosis, autophagy, phagocytosis, and metabolism of fatty acids and nucleic acids. We also showed that symbiont dynamics alters the expression of several genes involved in insect development. Our results strengthened the implication of apoptosis and autophagy processes in symbiont elimination and recycling. Remarkably, apart from the coleoptericin A that is known to target endosymbionts and controls their division and location, no gene coding antimicrobial peptide was upregulated during the symbiont growth and elimination phases. CONCLUSION We show that endosymbiont dynamics parallels numerous transcriptional changes in weevil developing adults and affects several biological processes, including metabolism and development. It also triggers cell apoptosis, autophagy and gut epithelial cell swelling and delamination. Strikingly, immunity is repressed during the whole process, presumably avoiding tissue inflammation and allowing insects to optimize nutrient recovery from recycled endosymbiont.
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Affiliation(s)
- Florent Masson
- Université de Lyon, INSA-Lyon, INRA, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621, Villeurbanne, France.
| | - Yves Moné
- Université de Lyon, INSA-Lyon, INRA, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621, Villeurbanne, France. .,Present address: Université Montpellier 2, INRA, UMR 1333 DGIMI, Diversité, Génomes et Interactions Micro-Organismes Insectes, F-34095, Montpellier, France.
| | - Aurélien Vigneron
- Université de Lyon, INSA-Lyon, INRA, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621, Villeurbanne, France. .,Present address: Department of Epidemiology and Public Health, Division of Epidemiology of Microbial Diseases, Yale University School of Medicine, New Haven, CT, USA.
| | - Agnès Vallier
- Université de Lyon, INSA-Lyon, INRA, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621, Villeurbanne, France.
| | - Nicolas Parisot
- Université de Lyon, INSA-Lyon, INRA, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621, Villeurbanne, France.
| | - Carole Vincent-Monégat
- Université de Lyon, INSA-Lyon, INRA, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621, Villeurbanne, France.
| | - Séverine Balmand
- Université de Lyon, INSA-Lyon, INRA, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621, Villeurbanne, France.
| | - Marie-Christine Carpentier
- Université de Lyon, CNRS, UMR5558 LBBE, Laboratoire de Biométrie et de Biologie Évolutive, F-69621, Villeurbanne, France.
| | - Anna Zaidman-Rémy
- Université de Lyon, INSA-Lyon, INRA, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621, Villeurbanne, France.
| | - Abdelaziz Heddi
- Université de Lyon, INSA-Lyon, INRA, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621, Villeurbanne, France.
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