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Fonseca-González I, Velasquez-Agudelo E, Londoño-Mesa MH, Álvarez JC. De novo transcriptome sequencing and annotation of the Antarctic polychaete Microspio moorei (Spionidae) with its characterization of the heat stress-related proteins (HSP, SOD & CAT). Mar Genomics 2024; 73:101085. [PMID: 38301367 DOI: 10.1016/j.margen.2024.101085] [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: 09/26/2023] [Revised: 12/07/2023] [Accepted: 01/22/2024] [Indexed: 02/03/2024]
Abstract
We present a de novo transcriptome assembly for the non-model Antarctic polychaete worm Microspio moorei (Spionidae) collected during Antarctic field expedition in Fildes Bay, King George Island, Antarctic Peninsula, in 2017. Here, we report the first transcriptome reference array for Microspio spp. The gene sequences of the spionid worm were annotated from a wide range of functions (i.e., biological, and metabolic processes, catalytic processes, and catalytic activity). HSP70, HSP90 SOD and CAT families were compared to reported annelid transcriptomes and proteomes. The phylogenetic analysis using COI, 16S, and 18S markers effectively clusters the species within the family. However, it also casts uncertainty on the monophyletic nature of the Microspio genera, indicating the necessity for additional data and potentially requiring a reevaluation of its grouping. Within these protein families, 3D model software was used to create one representative of their protein structures. Structural predictions were compared with related reported annelids living at different temperatures and a human X-ray reference. We found structural differences (RMSE >1.8) between the human HSP proteins but no significant differences between the polychaete-predicted proteins (RMSE <1.2). These results encourage further research of heat stress-related proteins, the development of genetic markers for climate change-induced temperature stress, and the study of the underlying mechanisms of the heat response. Moreover, these results motivate the extension of these findings to congeneric species.
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Affiliation(s)
- Idalyd Fonseca-González
- LimnoBasE & Biotamar Research Group, Institute of Biology, University of Antioquia, Medellín 050010, Colombia
| | - Esteban Velasquez-Agudelo
- Research Group in Biodiversity, Evolution and Conservation (BEC), EAFIT University, Medellín 050022, Colombia
| | - Mario H Londoño-Mesa
- LimnoBasE & Biotamar Research Group, Institute of Biology, University of Antioquia, Medellín 050010, Colombia
| | - Javier C Álvarez
- Research Group in Biodiversity, Evolution and Conservation (BEC), EAFIT University, Medellín 050022, Colombia.
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2
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Chiari Y, Howard L, Moreno N, Relyea S, Dunnigan J, Boyer MC, Kardos M, Glaberman S, Luikart G. Influence of RNA-Seq library construction, sampling methods, and tissue harvesting time on gene expression estimation. Mol Ecol Resour 2023; 23:803-817. [PMID: 36704853 DOI: 10.1111/1755-0998.13757] [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] [Received: 01/19/2021] [Revised: 12/14/2022] [Accepted: 01/17/2023] [Indexed: 01/28/2023]
Abstract
RNA sequencing (RNA-Seq) is popular for measuring gene expression in non-model organisms, including wild populations. While RNA-Seq can detect gene expression variation among wild-caught individuals and yield important insights into biological function, sampling methods can also affect gene expression estimates. We examined the influence of multiple technical variables on estimated gene expression in a non-model fish, the westslope cutthroat trout (Oncorhynchus clarkii lewisi), using two RNA-Seq library types: 3' RNA-Seq (QuantSeq) and whole mRNA-Seq (NEB). We evaluated effects of dip netting versus electrofishing, and of harvesting tissue immediately versus 5 min after euthanasia on estimated gene expression in blood, gill, and muscle. We found no significant differences in gene expression between sampling methods or tissue collection times with either library type. When library types were compared using the same blood samples, 58% of genes detected by both NEB and QuantSeq showed significantly different expression between library types, and NEB detected 31% more genes than QuantSeq. Although the two library types recovered different numbers of genes and expression levels, results with NEB and QuantSeq were consistent in that neither library type showed differences in gene expression between sampling methods and tissue harvesting times. Our study suggests that researchers can safely rely on different fish sampling strategies in the field. In addition, while QuantSeq is more cost effective, NEB detects more expressed genes. Therefore, when it is crucial to detect as many genes as possible (especially low expressed genes), when alternative splicing is of interest, or when working with an organism lacking good genomic resources, whole mRNA-Seq is more powerful.
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Affiliation(s)
- Ylenia Chiari
- Department of Biology, George Mason University, Fairfax, Virginia, USA
| | - Leif Howard
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Science, University of Montana, Missoula, Montana, USA.,Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, Montana, USA
| | - Nickolas Moreno
- Department of Biology, George Mason University, Fairfax, Virginia, USA
| | - Scott Relyea
- Sekokini Springs Hatchery, Montana Fish Wildlife and Parks, Bozeman, Montana, USA
| | - James Dunnigan
- Sekokini Springs Hatchery, Montana Fish Wildlife and Parks, Bozeman, Montana, USA
| | | | - Marty Kardos
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
| | - Scott Glaberman
- Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
| | - Gordon Luikart
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Science, University of Montana, Missoula, Montana, USA.,Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, Montana, USA
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3
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Zhang Z, Kryvokhyzha D, Orsucci M, Glémin S, Milesi P, Lascoux M. How broad is the selfing syndrome? Insights from convergent evolution of gene expression across species and tissues in the Capsella genus. New Phytol 2022; 236:2344-2357. [PMID: 36089898 PMCID: PMC9828073 DOI: 10.1111/nph.18477] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
The shift from outcrossing to selfing is one of the main evolutionary transitions in plants. It is accompanied by profound effects on reproductive traits, the so-called selfing syndrome. Because the transition to selfing also implies deep genomic and ecological changes, one also expects to observe a genomic selfing syndrome. We took advantage of the three independent transitions from outcrossing to selfing in the Capsella genus to characterize the overall impact of mating system change on RNA expression, in flowers but also in leaves and roots. We quantified the extent of both selfing and genomic syndromes, and tested whether changes in expression corresponded to adaptation to selfing or to relaxed selection on traits that were constrained in outcrossers. Mating system change affected gene expression in all three tissues but more so in flowers than in roots and leaves. Gene expression in selfing species tended to converge in flowers but diverged in the two other tissues. Hence, convergent adaptation to selfing dominates in flowers, whereas genetic drift plays a more important role in leaves and roots. The effect of mating system transition is not limited to reproductive tissues and corresponds to both adaptation to selfing and relaxed selection on previously constrained traits.
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Affiliation(s)
- Zebin Zhang
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityNorbyvägen 18D752 36UppsalaSweden
| | - Dmytro Kryvokhyzha
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityNorbyvägen 18D752 36UppsalaSweden
- Department of Clinical SciencesLund University Diabetes Centre214 28MalmöSweden
| | - Marion Orsucci
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityNorbyvägen 18D752 36UppsalaSweden
- Department of Plant BiologySwedish University of Agricultural Sciences, Uppsala BioCenter750 07UppsalaSweden
| | - Sylvain Glémin
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityNorbyvägen 18D752 36UppsalaSweden
- Université de Rennes, Centre National de la Recherche Scientifique (CNRS), ECOBIO (Ecosystèmes, Biodiversité, Evolution) – Unité Mixte de Recherche (UMR) 6553F‐35042RennesFrance
| | - Pascal Milesi
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityNorbyvägen 18D752 36UppsalaSweden
- Science For Life Laboratory (SciLifeLab)752 37UppsalaSweden
| | - Martin Lascoux
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityNorbyvägen 18D752 36UppsalaSweden
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Levin M, Butter F. Proteotranscriptomics - A facilitator in omics research. Comput Struct Biotechnol J 2022; 20:3667-75. [PMID: 35891789 DOI: 10.1016/j.csbj.2022.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 11/26/2022] Open
Abstract
Applications in omics research, such as comparative transcriptomics and proteomics, require the knowledge of the species-specific gene sequence and benefit from a comprehensive high-quality annotation of the coding genes to achieve high coverage. While protein-coding genes can in simple cases be detected by scanning the genome for open reading frames, in more complex genomes exonic sequences are separated by introns. Despite advances in sequencing technologies that allow for ever-growing numbers of genomes, the quality of many of the provided genome assemblies do not reach reference quality. These non-contiguous assemblies with gaps and the necessity to predict splice sites limit accurate gene annotation from solely genomic data. In contrast, the transcriptome only contains transcribed gene regions, is devoid of introns and thus provides the optimal basis for the identification of open reading frames. The additional integration of proteomics data to validate predicted protein-coding genes further enriches for accurate gene models. This review outlines the principles of the proteotranscriptomics approach, discusses common challenges and suggests methods for improvement.
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Linheiro R, Archer J. CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure. PLoS Comput Biol 2021; 17:e1009631. [PMID: 34813594 DOI: 10.1371/journal.pcbi.1009631] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 12/07/2021] [Accepted: 11/11/2021] [Indexed: 11/19/2022] Open
Abstract
With the exponential growth of sequence information stored over the last decade, including that of de novo assembled contigs from RNA-Seq experiments, quantification of chimeric sequences has become essential when assembling read data. In transcriptomics, de novo assembled chimeras can closely resemble underlying transcripts, but patterns such as those seen between co-evolving sites, or mapped read counts, become obscured. We have created a de Bruijn based de novo assembler for RNA-Seq data that utilizes a classification system to describe the complexity of underlying graphs from which contigs are created. Each contig is labelled with one of three levels, indicating whether or not ambiguous paths exist. A by-product of this is information on the range of complexity of the underlying gene families present. As a demonstration of CStones ability to assemble high-quality contigs, and to label them in this manner, both simulated and real data were used. For simulated data, ten million read pairs were generated from cDNA libraries representing four species, Drosophila melanogaster, Panthera pardus, Rattus norvegicus and Serinus canaria. These were assembled using CStone, Trinity and rnaSPAdes; the latter two being high-quality, well established, de novo assembers. For real data, two RNA-Seq datasets, each consisting of ≈30 million read pairs, representing two adult D. melanogaster whole-body samples were used. The contigs that CStone produced were comparable in quality to those of Trinity and rnaSPAdes in terms of length, sequence identity of aligned regions and the range of cDNA transcripts represented, whilst providing additional information on chimerism. Here we describe the details of CStones assembly and classification process, and propose that similar classification systems can be incorporated into other de novo assembly tools. Within a related side study, we explore the effects that chimera’s within reference sets have on the identification of differentially expression genes. CStone is available at: https://sourceforge.net/projects/cstone/. Within transcriptome reference sets, non-chimeric sequences are representations of transcribed genes, while artificially generated chimeric ones are mosaics of two or more pieces of DNA incorrectly pieced together. One area where such sets are utilized is in the quantification of gene expression patterns; where RNA-Seq reads are mapped to the sequences within, and subsequent count values reflect expression levels. Artificial chimeras can have a negative impact on count values by erroneously increasing variation in relation to the reads being mapped. Reference sets can be created from de novo assembled contigs, but chimeras can be introduced during the assembly process via the required traversal of graphs, representing gene families, constructed from the RNA-Seq data. Graph complexity determines how likely chimeras will arise. We have created CStone, a de novo assembler that utilizes a classification system to describe such complexity. Contigs created by CStone are labelled in a manner that indicates whether or not they are non-chimeric. This encourages contig dependent results to be presented with increased objectivity by maintaining the context of ambiguity associated with the assembly process. CStone has been tested extensively. Additionally, we have quantified the relationship between chimeras within reference sets and the identification of differentially expressed genes.
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Lipaeva P, Vereshchagina K, Drozdova P, Jakob L, Kondrateva E, Lucassen M, Bedulina D, Timofeyev M, Stadler P, Luckenbach T. Different ways to play it cool: Transcriptomic analysis sheds light on different activity patterns of three amphipod species under long-term cold exposure. Mol Ecol 2021; 30:5735-5751. [PMID: 34480774 DOI: 10.1111/mec.16164] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 08/31/2021] [Indexed: 12/27/2022]
Abstract
Species of littoral freshwater environments in regions with continental climate experience pronounced seasonal temperature changes. Coping with long cold winters and hot summers requires specific physiological and behavioural adaptations. Endemic amphipods of Lake Baikal, Eulimnogammarus verrucosus and Eulimnogammarus cyaneus, show high metabolic activity throughout the year; E. verrucosus even reproduces in winter. In contrast, the widespread Holarctic amphipod Gammarus lacustris overwinters in torpor. This study investigated the transcriptomic hallmarks of E. verrucosus, E. cyaneus and G. lacustris exposed to low water temperatures. Amphipods were exposed to 1.5°C and 12°C (corresponding to the mean winter and summer water temperatures, respectively, in the Baikal littoral) for one month. At 1.5°C, G. lacustris showed upregulation of ribosome biogenesis and mRNA processing genes, as well as downregulation of genes related to growth, reproduction and locomotor activity, indicating enhanced energy allocation to somatic maintenance. Our results suggest that the mitogen-activated protein kinase (MAPK) signalling pathway is involved in the preparation for hibernation; downregulation of the actin cytoskeleton pathway genes could relate to the observed low locomotor activity of G. lacustris at 1.5°C. The differences between the transcriptomes of E. verrucosus and E. cyaneus from the 1.5°C and 12°C exposures were considerably smaller than for G. lacustris. In E. verrucosus, cold-exposure triggered reproductive activity was indicated by upregulation of respective genes, whereas in E. cyaneus, genes related to mitochondria functioning were upregulated, indicating cold compensation in this species. Our data elucidate the molecular characteristics behind the different adaptations of amphipod species from the Lake Baikal area to winter conditions.
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Affiliation(s)
- Polina Lipaeva
- Department of Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Kseniya Vereshchagina
- Institute of Biology, Irkutsk State University, Irkutsk, Russia.,Baikal Research Centre, Irkutsk, Russia
| | - Polina Drozdova
- Institute of Biology, Irkutsk State University, Irkutsk, Russia.,Baikal Research Centre, Irkutsk, Russia
| | - Lena Jakob
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | | | - Magnus Lucassen
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Daria Bedulina
- Institute of Biology, Irkutsk State University, Irkutsk, Russia.,Baikal Research Centre, Irkutsk, Russia
| | - Maxim Timofeyev
- Institute of Biology, Irkutsk State University, Irkutsk, Russia.,Baikal Research Centre, Irkutsk, Russia
| | - Peter Stadler
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, Universität Leipzig, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Department of Theoretical Chemistry, University of Vienna, Vienna, Austria.,Facultad de Ciencias, Universidad National de Colombia, Bogotá, Colombia.,Santa Fe Institute, Santa Fe, New Mexico, USA
| | - Till Luckenbach
- Department of Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
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Zafeiropoulos H, Gioti A, Ninidakis S, Potirakis A, Paragkamian S, Angelova N, Antoniou A, Danis T, Kaitetzidou E, Kasapidis P, Kristoffersen JB, Papadogiannis V, Pavloudi C, Ha QV, Lagnel J, Pattakos N, Perantinos G, Sidirokastritis D, Vavilis P, Kotoulas G, Manousaki T, Sarropoulou E, Tsigenopoulos CS, Arvanitidis C, Magoulas A, Pafilis E. 0s and 1s in marine molecular research: a regional HPC perspective. Gigascience 2021; 10:6353916. [PMID: 34405237 PMCID: PMC8371273 DOI: 10.1093/gigascience/giab053] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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] [Received: 04/07/2021] [Revised: 07/07/2021] [Accepted: 07/20/2021] [Indexed: 01/23/2023] Open
Abstract
High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade's experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility's future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned.
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Affiliation(s)
- Haris Zafeiropoulos
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece.,Department of Biology, University of Crete, Voutes University Campus, P.O. Box 2208, 70013, Heraklion, Crete, Greece
| | - Anastasia Gioti
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Stelios Ninidakis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Antonis Potirakis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Savvas Paragkamian
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece.,Department of Biology, University of Crete, Voutes University Campus, P.O. Box 2208, 70013, Heraklion, Crete, Greece
| | - Nelina Angelova
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Aglaia Antoniou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Theodoros Danis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece.,School of Medicine, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Eliza Kaitetzidou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Panagiotis Kasapidis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Jon Bent Kristoffersen
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Vasileios Papadogiannis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Christina Pavloudi
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Quoc Viet Ha
- Bull SAS, Rue du Gros Caillou, 78340 Les Clayes-sous-Bois, France
| | - Jacques Lagnel
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Centre de Recherche Provence-Alpes-Côte d'Azur, Domaine Saint Maurice, CS60094, 84143 Montfavet Cedex, France
| | - Nikos Pattakos
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Giorgos Perantinos
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Dimitris Sidirokastritis
- Hellenic Centre for Marine Research, Network Operation Center, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Panagiotis Vavilis
- Hellenic Centre for Marine Research, Network Operation Center, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Georgios Kotoulas
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Tereza Manousaki
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Elena Sarropoulou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Costas S Tsigenopoulos
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Christos Arvanitidis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece.,LifeWatch European Research Infrastructure Consortium, Sector II-III Plaza de España, 41071, Seville, Spain
| | - Antonios Magoulas
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Evangelos Pafilis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece
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8
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Muyle A, Martin H, Zemp N, Mollion M, Gallina S, Tavares R, Silva A, Bataillon T, Widmer A, Glémin S, Touzet P, Marais GAB. Dioecy Is Associated with High Genetic Diversity and Adaptation Rates in the Plant Genus Silene. Mol Biol Evol 2021; 38:805-818. [PMID: 32926156 PMCID: PMC7947750 DOI: 10.1093/molbev/msaa229] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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] [Indexed: 12/20/2022] Open
Abstract
About 15,000 angiosperm species (∼6%) have separate sexes, a phenomenon known as dioecy. Why dioecious taxa are so rare is still an open question. Early work reported lower species richness in dioecious compared with nondioecious sister clades, raising the hypothesis that dioecy may be an evolutionary dead-end. This hypothesis has been recently challenged by macroevolutionary analyses that detected no or even positive effect of dioecy on diversification. However, the possible genetic consequences of dioecy at the population level, which could drive the long-term fate of dioecious lineages, have not been tested so far. Here, we used a population genomics approach in the Silene genus to look for possible effects of dioecy, especially for potential evidence of evolutionary handicaps of dioecy underlying the dead-end hypothesis. We collected individual-based RNA-seq data from several populations in 13 closely related species with different sexual systems: seven dioecious, three hermaphroditic, and three gynodioecious species. We show that dioecy is associated with increased genetic diversity, as well as higher selection efficacy both against deleterious mutations and for beneficial mutations. The results hold after controlling for phylogenetic inertia, differences in species census population sizes and geographic ranges. We conclude that dioecious Silene species neither show signs of increased mutational load nor genetic evidence for extinction risk. We discuss these observations in the light of the possible demographic differences between dioecious and self-compatible hermaphroditic species and how this could be related to alternatives to the dead-end hypothesis to explain the rarity of dioecy.
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Affiliation(s)
- Aline Muyle
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA
| | - Hélène Martin
- University of Lille, CNRS, UMR 8198—Evo-Eco-Paleo, F-59000 Lille, France
- Département de Biologie, Institut de Biologie Integrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Niklaus Zemp
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Genetic Diversity Centre (GDC), ETH Zurich, Zurich, Switzerland
| | - Maéva Mollion
- Bioinformatics Research Centre, Aarhus University, Aarhus C, Denmark
| | - Sophie Gallina
- University of Lille, CNRS, UMR 8198—Evo-Eco-Paleo, F-59000 Lille, France
| | - Raquel Tavares
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
| | - Alexandre Silva
- Centro de Interpretação da Serra da Estrela (CISE), Seia, Portugal
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus C, Denmark
| | - Alex Widmer
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Sylvain Glémin
- CNRS, ECOBIO [(Ecosystèmes, Biodiversité, Évolution)]—UMR 6553, University of Rennes, Rennes, France
- Department of Ecology and Genetics, Evolutionary Biology Center and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Pascal Touzet
- University of Lille, CNRS, UMR 8198—Evo-Eco-Paleo, F-59000 Lille, France
| | - Gabriel A B Marais
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
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9
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Abstract
RNA editing of adenosines to inosines contributes to a wide range of biological processes by regulating gene expression post-transcriptionally. To understand the effect, accurate mapping of inosines is necessary. The most conventional method to identify an editing site is to compare the cDNA sequence with its corresponding genomic sequence. However, this method has a high false discovery rate because guanosine signals, due to experimental errors or noise in the obtained sequences, contaminate genuine inosine signals detected as guanosine. To ensure high accuracy, we developed the Inosine Chemical Erasing (ICE) method to accurately and biochemically identify inosines in RNA strands utilizing inosine cyanoethylation and reverse transcription-PCR. Furthermore, we applied this technique to next-generation sequencing technology, called ICE-seq, to conduct an unbiased genome-wide screening of A-to-I editing sites in the transcriptome.
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10
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Zheng X, Zhang L, Jiang W, Abasubong KP, Zhang C, Zhang D, Li X, Jiang G, Chi C, Liu W. Effects of dietary icariin supplementation on the ovary development-related transcriptome of Chinese mitten crab (Eriocheir sinensis). Comp Biochem Physiol Part D Genomics Proteomics 2020; 37:100756. [PMID: 33197858 DOI: 10.1016/j.cbd.2020.100756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 12/11/2022]
Abstract
The Chinese mitten crab (Eriocheir sinensis) is an economically important aquaculture species in China, with distinct differences in ovarian maturation status between crabs fed with natural diets and artificial diets during the listing period, thus, leading to selling price differentiation. Our previous study showed that dietary supplementation with 100 mg/kg icariin can effectively promote ovarian development of E. sinensis. However, the internal molecular mechanism has not yet been elucidated because of a lack of comprehensive genome sequence information. We compared the ovary transcriptomes of E. sinensis fed with two diets containing 0 and 100 mg/kg ICA using the BGISEQ-500 platform. This yielded 12.54 Gb clean bases and 54,794 unigenes, 13,832 of which were found to be differentially expressed after icariin exposure. Twenty pathways closely related to gonadal development were selected through KEGG analysis. Seven differentially expressed genes relevant to vitellogenesis and oocyte maturation (serine/threonine-protein kinase mos-like, Eg2, cytoplasmic polyadenylation element-binding protein, cyclin B, vitellogenin 1, cathepsin D, and juvenile hormone esterase-like carboxylesterase 1) were validated by qRT-PCR, and four proteins (MEK1/2, ERK1/2, Cyclin B and Cdc2) associated with the progesterone mediated oocyte maturation pathway (i.e., MAPK/MPF pathway) were analyzed by western-blot. The results showed that icariin could promote the synthesis, processing and deposition of vitellogenin in oocytes, and that it also has the potential to promote oocyte maturation (resumption of Meiosis I) by altering the expression of the relevant genes and proteins.
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Affiliation(s)
- Xiaochuan Zheng
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, National Experimental Teaching Center for Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing 210095, Jiangsu Province, People's Republic of China
| | - Ling Zhang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, National Experimental Teaching Center for Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing 210095, Jiangsu Province, People's Republic of China
| | - Weibo Jiang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, National Experimental Teaching Center for Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing 210095, Jiangsu Province, People's Republic of China
| | - Kenneth P Abasubong
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, National Experimental Teaching Center for Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing 210095, Jiangsu Province, People's Republic of China
| | - Caiyan Zhang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, National Experimental Teaching Center for Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing 210095, Jiangsu Province, People's Republic of China
| | - Dingdong Zhang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, National Experimental Teaching Center for Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing 210095, Jiangsu Province, People's Republic of China
| | - Xiangfei Li
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, National Experimental Teaching Center for Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing 210095, Jiangsu Province, People's Republic of China
| | - Guangzhen Jiang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, National Experimental Teaching Center for Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing 210095, Jiangsu Province, People's Republic of China
| | - Cheng Chi
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, National Experimental Teaching Center for Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing 210095, Jiangsu Province, People's Republic of China
| | - Wenbin Liu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, National Experimental Teaching Center for Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing 210095, Jiangsu Province, People's Republic of China.
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11
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Cai ML, Zhang QL, Zhang JJ, Ding WQ, Huang HY, Peng CL. Comparative physiological and transcriptomic analyses of photosynthesis in Sphagneticola calendulacea (L.) Pruski and Sphagneticola trilobata (L.) Pruski. Sci Rep 2020; 10:17810. [PMID: 33082378 PMCID: PMC7576218 DOI: 10.1038/s41598-020-74289-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 01/06/2020] [Accepted: 09/24/2020] [Indexed: 11/09/2022] Open
Abstract
Sphagneticola trilobata (L.) Pruski is one of the fast-growing malignant weeds in South China. It has severely influenced local biodiversity and native plant habitat. Photosynthesis is the material basis of plant growth and development. However, there are few reports on the photosynthetic transcriptome of S. trilobata. In this study, S. trilobata had a relatively large leaf area and biomass. The gas exchange parameters per unit area of leaves, including net photosynthetic capacity (Pn), intercellular CO2 (Ci), stomatal conductance (Gs), transpiration rate (Tr), water use efficiency (WUE), photosynthetic pigment and Rubisco protein content were higher than those of the native plant Sphagneticola calendulacea (L.) Pruski. On this basis, the differences in photosynthesis pathways between the two Sphagneticola species were analyzed by using the Illumina HiSeq platform. The sequencing results for S. trilobata and S. calendulacea revealed 159,366 and 177,069 unigenes, respectively. Functional annotation revealed 119,350 and 150,846 non-redundant protein database annotations (Nr), 96,637 and 115,711 Swiss-Prot annotations, 49,159 and 60,116 Kyoto Encyclopedia of Genes and Genomes annotations (KEGG), and 83,712 and 97,957 Gene Ontology annotations (GO) in S. trilobata and S. calendulacea, respectively. Additionally, our analysis showed that the expression of key protease genes involved in the photosynthesis pathway, particularly CP43, CP47, PsbA and PetC, had high expression levels in leaves of S. trilobata in comparison to native species. Physiological and transcriptomic analyses suggest the high expression of photosynthetic genes ensures the high photosynthetic capacity of leaves, which is one of the inherent advantages underlying the successful invasion by S. trilobata.
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Affiliation(s)
- Min-Ling Cai
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Qi-Lei Zhang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Jun-Jie Zhang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Wen-Qiao Ding
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Hong-Ying Huang
- College of Chemistry & Biology and Environmental Engineering, Xiangnan University, Chenzhou, 423043, Hunan, People's Republic of China.
| | - Chang-Lian Peng
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China.
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12
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Puglia GD, Prjibelski AD, Vitale D, Bushmanova E, Schmid KJ, Raccuia SA. Hybrid transcriptome sequencing approach improved assembly and gene annotation in Cynara cardunculus (L.). BMC Genomics 2020; 21:317. [PMID: 32819282 PMCID: PMC7441626 DOI: 10.1186/s12864-020-6670-5] [Citation(s) in RCA: 12] [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] [Received: 05/31/2019] [Accepted: 03/13/2020] [Indexed: 12/11/2022] Open
Abstract
Background The investigation of transcriptome profiles using short reads in non-model organisms, which lack of well-annotated genomes, is limited by partial gene reconstruction and isoform detection. In contrast, long-reads sequencing techniques revealed their potential to generate complete transcript assemblies even when a reference genome is lacking. Cynara cardunculus var. altilis (DC) (cultivated cardoon) is a perennial hardy crop adapted to dry environments with many industrial and nutraceutical applications due to the richness of secondary metabolites mostly produced in flower heads. The investigation of this species benefited from the recent release of a draft genome, but the transcriptome profile during the capitula formation still remains unexplored. In the present study we show a transcriptome analysis of vegetative and inflorescence organs of cultivated cardoon through a novel hybrid RNA-seq assembly approach utilizing both long and short RNA-seq reads. Results The inclusion of a single Nanopore flow-cell output in a hybrid sequencing approach determined an increase of 15% complete assembled genes and 18% transcript isoforms respect to short reads alone. Among 25,463 assembled unigenes, we identified 578 new genes and updated 13,039 gene models, 11,169 of which were alternatively spliced isoforms. During capitulum development, 3424 genes were differentially expressed and approximately two-thirds were identified as transcription factors including bHLH, MYB, NAC, C2H2 and MADS-box which were highly expressed especially after capitulum opening. We also show the expression dynamics of key genes involved in the production of valuable secondary metabolites of which capitulum is rich such as phenylpropanoids, flavonoids and sesquiterpene lactones. Most of their biosynthetic genes were strongly transcribed in the flower heads with alternative isoforms exhibiting differentially expression levels across the tissues. Conclusions This novel hybrid sequencing approach allowed to improve the transcriptome assembly, to update more than half of annotated genes and to identify many novel genes and different alternatively spliced isoforms. This study provides new insights on the flowering cycle in an Asteraceae plant, a valuable resource for plant biology and breeding in Cynara and an effective method for improving gene annotation.
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Affiliation(s)
- Giuseppe D Puglia
- Institute for Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Fruwirthstrasse 21, 70599, Stuttgart, Germany. .,Consiglio Nazionale delle Ricerche, Istituto per i Sistemi Agricoli e Forestali del Mediterraneo (CNR-ISAFOM) U.O.S. Catania, Via Empedocle, 58, 95128, Catania, Italy.
| | - Andrey D Prjibelski
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Domenico Vitale
- Consiglio Nazionale delle Ricerche, Istituto per i Sistemi Agricoli e Forestali del Mediterraneo (CNR-ISAFOM) U.O.S. Catania, Via Empedocle, 58, 95128, Catania, Italy
| | - Elena Bushmanova
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Karl J Schmid
- Institute for Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Fruwirthstrasse 21, 70599, Stuttgart, Germany.
| | - Salvatore A Raccuia
- Consiglio Nazionale delle Ricerche, Istituto per i Sistemi Agricoli e Forestali del Mediterraneo (CNR-ISAFOM) U.O.S. Catania, Via Empedocle, 58, 95128, Catania, Italy
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13
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Rousselle M, Simion P, Tilak MK, Figuet E, Nabholz B, Galtier N. Is adaptation limited by mutation? A timescale-dependent effect of genetic diversity on the adaptive substitution rate in animals. PLoS Genet 2020; 16:e1008668. [PMID: 32251427 PMCID: PMC7162527 DOI: 10.1371/journal.pgen.1008668] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [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: 12/18/2019] [Revised: 04/16/2020] [Accepted: 02/14/2020] [Indexed: 12/16/2022] Open
Abstract
Whether adaptation is limited by the beneficial mutation supply is a long-standing question of evolutionary genetics, which is more generally related to the determination of the adaptive substitution rate and its relationship with species effective population size (Ne) and genetic diversity. Empirical evidence reported so far is equivocal, with some but not all studies supporting a higher adaptive substitution rate in large-Ne than in small-Ne species. We gathered coding sequence polymorphism data and estimated the adaptive amino-acid substitution rate ωa, in 50 species from ten distant groups of animals with markedly different population mutation rate θ. We reveal the existence of a complex, timescale dependent relationship between species adaptive substitution rate and genetic diversity. We find a positive relationship between ωa and θ among closely related species, indicating that adaptation is indeed limited by the mutation supply, but this was only true in relatively low-θ taxa. In contrast, we uncover no significant correlation between ωa and θ at a larger taxonomic scale, suggesting that the proportion of beneficial mutations scales negatively with species' long-term Ne.
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Affiliation(s)
| | - Paul Simion
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
- LEGE, Department of Biology, University of Namur, Namur, Belgium
| | - Marie-Ka Tilak
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Emeric Figuet
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Benoit Nabholz
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Nicolas Galtier
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
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14
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González-Aravena M, Kenny NJ, Osorio M, Font A, Riesgo A, Cárdenas CA. Warm temperatures, cool sponges: the effect of increased temperatures on the Antarctic sponge Isodictya sp. PeerJ 2019; 7:e8088. [PMID: 31824760 PMCID: PMC6896943 DOI: 10.7717/peerj.8088] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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] [Received: 08/12/2019] [Accepted: 10/23/2019] [Indexed: 12/31/2022] Open
Abstract
Although the cellular and molecular responses to exposure to relatively high temperatures (acute thermal stress or heat shock) have been studied previously, only sparse empirical evidence of how it affects cold-water species is available. As climate change becomes more pronounced in areas such as the Western Antarctic Peninsula, both long-term and occasional acute temperature rises will impact species found there, and it has become crucial to understand the capacity of these species to respond to such thermal stress. Here, we use the Antarctic sponge Isodictya sp. to investigate how sessile organisms (particularly Porifera) can adjust to acute short-term heat stress, by exposing this species to 3 and 5 °C for 4 h, corresponding to predicted temperatures under high-end 2080 IPCC-SRES scenarios. Assembling a de novo reference transcriptome (90,188 contigs, >93.7% metazoan BUSCO genes) we have begun to discern the molecular response employed by Isodictya to adjust to heat exposure. Our initial analyses suggest that TGF-β, ubiquitin and hedgehog cascades are involved, alongside other genes. However, the degree and type of response changed little from 3 to 5 °C in the time frame examined, suggesting that even moderate rises in temperature could cause stress at the limits of this organism’s capacity. Given the importance of sponges to Antarctic ecosystems, our findings are vital for discerning the consequences of short-term increases in Antarctic ocean temperature on these and other species.
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Affiliation(s)
| | - Nathan J Kenny
- Life Sciences, The Natural History Museum, London, London, UK.,Life Sciences, Oxford Brookes University, Oxford, UK
| | - Magdalena Osorio
- Departamento Científico, Instituto Antártico Chileno, Puntas Arenas, Chile
| | - Alejandro Font
- Departamento Científico, Instituto Antártico Chileno, Puntas Arenas, Chile
| | - Ana Riesgo
- Life Sciences, The Natural History Museum, London, London, UK
| | - César A Cárdenas
- Departamento Científico, Instituto Antártico Chileno, Puntas Arenas, Chile
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15
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Vilperte V, Lucaciu CR, Halbwirth H, Boehm R, Rattei T, Debener T. Hybrid de novo transcriptome assembly of poinsettia (Euphorbia pulcherrima Willd. Ex Klotsch) bracts. BMC Genomics 2019; 20:900. [PMID: 31775622 PMCID: PMC6882326 DOI: 10.1186/s12864-019-6247-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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] [Received: 07/01/2019] [Accepted: 10/30/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Poinsettia is a popular and important ornamental crop, mostly during the Christmas season. Its bract coloration ranges from pink/red to creamy/white shades. Despite its ornamental value, there is a lack of knowledge about the genetics and molecular biology of poinsettia, especially on the mechanisms of color formation. We performed an RNA-Seq analysis in order to shed light on the transcriptome of poinsettia bracts. Moreover, we analyzed the transcriptome differences of red- and white-bracted poinsettia varieties during bract development and coloration. For the assembly of a bract transcriptome, two paired-end cDNA libraries from a red and white poinsettia pair were sequenced with the Illumina technology, and one library from a red-bracted variety was used for PacBio sequencing. Both short and long reads were assembled using a hybrid de novo strategy. Samples of red- and white-bracted poinsettias were sequenced and comparatively analyzed in three color developmental stages in order to understand the mechanisms of color formation and accumulation in the species. RESULTS The final transcriptome contains 288,524 contigs, with 33% showing confident protein annotation against the TAIR10 database. The BUSCO pipeline, which is based on near-universal orthologous gene groups, was applied to assess the transcriptome completeness. From a total of 1440 BUSCO groups searched, 77% were categorized as complete (41% as single-copy and 36% as duplicated), 10% as fragmented and 13% as missing BUSCOs. The gene expression comparison between red and white varieties of poinsettia showed a differential regulation of the flavonoid biosynthesis pathway only at particular stages of bract development. An initial impairment of the flavonoid pathway early in the color accumulation process for the white poinsettia variety was observed, but these differences were no longer present in the subsequent stages of bract development. Nonetheless, GSTF11 and UGT79B10 showed a lower expression in the last stage of bract development for the white variety and, therefore, are potential candidates for further studies on poinsettia coloration. CONCLUSIONS In summary, this transcriptome analysis provides a valuable foundation for further studies on poinsettia, such as plant breeding and genetics, and highlights crucial information on the molecular mechanism of color formation.
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Affiliation(s)
- Vinicius Vilperte
- Institute of Plant Genetics, Leibniz Universität Hannover, 30419, Hannover, Germany.,Klemm + Sohn GmbH & Co., 70379, Stuttgart, KG, Germany
| | - Calin Rares Lucaciu
- Department of Microbiology and Ecosystem Science, University of Vienna, 1090, Vienna, Austria
| | - Heidi Halbwirth
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, 1060, Vienna, Austria
| | - Robert Boehm
- Klemm + Sohn GmbH & Co., 70379, Stuttgart, KG, Germany
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, University of Vienna, 1090, Vienna, Austria.
| | - Thomas Debener
- Institute of Plant Genetics, Leibniz Universität Hannover, 30419, Hannover, Germany.
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16
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Armstrong EK, Miller AD, Mondon JA, Greenfield PA, Stephenson SA, Tan MH, Gan HM, Hook SE. De Novo assembly and characterisation of the greentail prawn (Metapenaeus bennettae) hepatopancreas transcriptome – identification of stress response and detoxification transcripts. Mar Genomics 2019; 47:100677. [DOI: 10.1016/j.margen.2019.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/15/2019] [Accepted: 04/05/2019] [Indexed: 11/19/2022]
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17
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Medina-Santos R, Guerra-Duarte C, de Almeida Lima S, Costal-Oliveira F, Alves de Aquino P, Oliveira do Carmo A, Ferreyra CB, Gonzalez-Kozlova EE, Kalapothakis E, Chávez-Olórtegui C. Diversity of astacin-like metalloproteases identified by transcriptomic analysis in Peruvian Loxosceles laeta spider venom and in vitro activity characterization. Biochimie 2019; 167:81-92. [PMID: 31476328 DOI: 10.1016/j.biochi.2019.08.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 04/17/2019] [Accepted: 08/28/2019] [Indexed: 11/25/2022]
Abstract
Loxosceles spiders are found in almost all countries of South America. In Peru, Loxosceles laeta species is the main responsible for the accidents caused by poisonous animals, being known as "killer spiders", due to the large number of fatal accidents observed. Astacin-like metalloproteases, named LALPs (Loxosceles astacin-like metalloproteases) are highly expressed in Loxosceles spiders venom gland. These proteases may be involved in hemorrhage and venom spreading, being relevant to the envenoming proccess. Thus, the aim of this work was to analyze Peruvian L. laeta venom gland transcripts using bioinformatics tools, focusing on LALPs. A cDNA library from Peruvian L. laeta venom glands was constructed and sequenced by MiSeq (Illumina) sequencer. After assembly, the resulting sequences were annotated, seeking out for similarity with previously described LALPs. Nine possible LALPs isoforms from Peruvian L. laeta venom were identified and the results were validated by in silico and in vitro experiments. This study contributes to a better understanding of the molecular diversity of Loxosceles venom and provide insights about the action of LALPs.
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Affiliation(s)
- Raíssa Medina-Santos
- Biochemistry and Immunology Department, Federal University of Minas Gerais, Brazil; Genetic, Ecology and Evolution Department, Federal University of Minas Gerais, Brazil
| | | | | | | | | | | | - César Bonilla Ferreyra
- Univesidad Nacional Mayor de San Marcos, Facultad de Odontología, Lima, Peru; Instituto Nacional de Salud, Lima, Peru
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18
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Kang YJ, Yang DC, Kong L, Hou M, Meng YQ, Wei L, Gao G. CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features. Nucleic Acids Res 2019; 45:W12-W16. [PMID: 28521017 PMCID: PMC5793834 DOI: 10.1093/nar/gkx428] [Citation(s) in RCA: 750] [Impact Index Per Article: 150.0] [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: 03/01/2017] [Accepted: 05/03/2017] [Indexed: 12/19/2022] Open
Abstract
With advances in next-generation sequencing technologies, numerous novel transcripts in a large number of organisms have been identified. With the goal of fast, accurate assessment of the coding ability of RNA transcripts, we upgraded the coding potential calculator CPC1 to CPC2. CPC2 runs ∼1000 times faster than CPC1 and exhibits superior accuracy compared with CPC1, especially for long non-coding transcripts. Moreover, the model of CPC2 is species-neutral, making it feasible for ever-growing non-model organism transcriptomes. A mobile-friendly web server, as well as a downloadable standalone package, is freely available at http://cpc2.cbi.pku.edu.cn.
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Affiliation(s)
- Yu-Jian Kang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China
| | - De-Chang Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China
| | - Lei Kong
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China
| | - Mei Hou
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China
| | - Yu-Qi Meng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China
| | - Liping Wei
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China
| | - Ge Gao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China
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Arslan M, Devisetty UK, Porsch M, Große I, Müller JA, Michalski SG. RNA-Seq analysis of soft rush (Juncus effusus): transcriptome sequencing, de novo assembly, annotation, and polymorphism identification. BMC Genomics 2019; 20:489. [PMID: 31195970 PMCID: PMC6567414 DOI: 10.1186/s12864-019-5886-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 07/23/2018] [Accepted: 06/05/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Juncus effusus L. (family: Juncaceae; order: Poales) is a helophytic rush growing in temperate damp or wet terrestrial habitats and is of almost cosmopolitan distribution. The species has been studied intensively with respect to its interaction with co-occurring plants as well as microbes being involved in major biogeochemical cycles. J. effusus has biotechnological value as component of Constructed Wetlands where the plant has been employed in phytoremediation of contaminated water. Its genome has not been sequenced. RESULTS In this study we carried out functional annotation and polymorphism analysis of de novo assembled RNA-Seq data from 18 genotypes using 249 million paired-end Illumina HiSeq reads and 2.8 million 454 Titanium reads. The assembly comprised 158,591 contigs with a mean contig length of 780 bp. The assembly was annotated using the dammit! annotation pipeline, which queries the databases OrthoDB, Pfam-A, Rfam, and runs BUSCO (Benchmarking Single-Copy Ortholog genes). In total, 111,567 contigs (70.3%) were annotated with functional descriptions, assigned gene ontology terms, and conserved protein domains, which resulted in 30,932 non-redundant gene sequences. Results of BUSCO and KEGG pathway analyses were similar for J. effusus as for the well-studied members of the Poales, Oryza sativa and Sorghum bicolor. A total of 566,433 polymorphisms were identified in transcribed regions with an average frequency of 1 polymorphism in every 171 bases. CONCLUSIONS The transcriptome assembly was of high quality and genome coverage was sufficient for global analyses. This annotated knowledge resource can be utilized for future gene expression analysis, genomic feature comparisons, genotyping, primer design, and functional genomics in J. effusus.
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Affiliation(s)
- Muhammad Arslan
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstr, 15, Leipzig, Germany.,Institute for Biology V (Environmental Research), RWTH Aachen University, Templergraben 55, 52062, Aachen, Germany
| | | | - Martin Porsch
- Institute of Computer Science, Martin-Luther-University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120, Halle (Saale), Germany.,Core Facility Deep Sequencing, Martin-Luther-University Halle-Wittenberg, Magdeburger Str. 2, 06112, Halle (Saale), Germany
| | - Ivo Große
- Institute of Computer Science, Martin-Luther-University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120, Halle (Saale), Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
| | - Jochen A Müller
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstr, 15, Leipzig, Germany.
| | - Stefan G Michalski
- Department of Community Ecology, Helmholtz Centre for Environmental Research - UFZ, Theodor-Lieser-Str. 4, 06120, Halle (Saale), Germany
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20
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Alié A, Hiebert LS, Simion P, Scelzo M, Prünster MM, Lotito S, Delsuc F, Douzery EJP, Dantec C, Lemaire P, Darras S, Kawamura K, Brown FD, Tiozzo S. Convergent Acquisition of Nonembryonic Development in Styelid Ascidians. Mol Biol Evol 2019; 35:1728-1743. [PMID: 29660002 PMCID: PMC5995219 DOI: 10.1093/molbev/msy068] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [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] [Indexed: 01/04/2023] Open
Abstract
Asexual propagation and whole body regeneration are forms of nonembryonic development (NED) widespread across animal phyla and central in life history and evolutionary diversification of metazoans. Whereas it is challenging to reconstruct the gains or losses of NED at large phylogenetic scale, comparative studies could benefit from being conducted at more restricted taxonomic scale, in groups for which phylogenetic relationships are well established. The ascidian family of Styelidae encompasses strictly sexually reproducing solitary forms as well as colonial species that combine sexual reproduction with different forms of NED. To date, the phylogenetic relationships between colonial and solitary styelids remain controversial and so is the pattern of NED evolution. In this study, we built an original pipeline to combine eight genomes with 18 de novo assembled transcriptomes and constructed data sets of unambiguously orthologous genes. Using a phylogenomic super-matrix of 4,908 genes from these 26 tunicates we provided a robust phylogeny of this family of chordates, which supports two convergent acquisitions of NED. This result prompted us to further describe the budding process in the species Polyandrocarpa zorritensis, leading to the discovery of a novel mechanism of asexual development. Whereas the pipeline and the data sets produced can be used for further phylogenetic reconstructions in tunicates, the phylogeny provided here sets an evolutionary framework for future experimental studies on the emergence and disappearance of complex characters such as asexual propagation and whole body regeneration.
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Affiliation(s)
- Alexandre Alié
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06230 Paris, France
| | - Laurel Sky Hiebert
- Departamento de Zoologia - Instituto Biociências, Universidade de São Paulo, São Paulo, Brazil.,Centro de Biologia Marinha (CEBIMar), Universidade de São Paulo, São Paulo, Brazil
| | - Paul Simion
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Marta Scelzo
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06230 Paris, France
| | - Maria Mandela Prünster
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06230 Paris, France
| | - Sonia Lotito
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06230 Paris, France
| | - Frédéric Delsuc
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | | | | | | | - Sébastien Darras
- Sorbonne Université, CNRS, Biologie Int[1]egrative des Organismes Marins (BIOM),Observatoire Oc[1]eanologique, Banyuls/Mer, 06230 Paris, France
| | - Kazuo Kawamura
- Laboratory of Cellular and Molecular Biotechnology, Faculty of Science, Kochi University, Kochi, Japan
| | - Federico D Brown
- Departamento de Zoologia - Instituto Biociências, Universidade de São Paulo, São Paulo, Brazil.,Centro de Biologia Marinha (CEBIMar), Universidade de São Paulo, São Paulo, Brazil.,Instituto Nacional de Ciência e Tecnologia em Estudos Interdisciplinares e Transdisciplinares em Ecologia e Evolução (IN-TREE), Salvador, Brazil
| | - Stefano Tiozzo
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06230 Paris, France
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21
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Rousselle M, Laverré A, Figuet E, Nabholz B, Galtier N. Influence of Recombination and GC-biased Gene Conversion on the Adaptive and Nonadaptive Substitution Rate in Mammals versus Birds. Mol Biol Evol 2019; 36:458-471. [PMID: 30590692 PMCID: PMC6389324 DOI: 10.1093/molbev/msy243] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [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] [Indexed: 12/22/2022] Open
Abstract
Recombination is expected to affect functional sequence evolution in several ways. On the one hand, recombination is thought to improve the efficiency of multilocus selection by dissipating linkage disequilibrium. On the other hand, natural selection can be counteracted by recombination-associated transmission distorters such as GC-biased gene conversion (gBGC), which tends to promote G and C alleles irrespective of their fitness effect in high-recombining regions. It has been suggested that gBGC might impact coding sequence evolution in vertebrates, and particularly the ratio of nonsynonymous to synonymous substitution rates (dN/dS). However, distinctive gBGC patterns have been reported in mammals and birds, maybe reflecting the documented contrasts in evolutionary dynamics of recombination rate between these two taxa. Here, we explore how recombination and gBGC affect coding sequence evolution in mammals and birds by analyzing proteome-wide data in six species of Galloanserae (fowls) and six species of catarrhine primates. We estimated the dN/dS ratio and rates of adaptive and nonadaptive evolution in bins of genes of increasing recombination rate, separately analyzing AT → GC, GC → AT, and G ↔ C/A ↔ T mutations. We show that in both taxa, recombination and gBGC entail a decrease in dN/dS. Our analysis indicates that recombination enhances the efficiency of purifying selection by lowering Hill-Robertson effects, whereas gBGC leads to an overestimation of the adaptive rate of AT → GC mutations. Finally, we report a mutagenic effect of recombination, which is independent of gBGC.
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Affiliation(s)
| | - Alexandre Laverré
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Emeric Figuet
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Benoit Nabholz
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Nicolas Galtier
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
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22
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Abstract
Conservation genomics aims to preserve the viability of populations and the biodiversity of living organisms. Invertebrate organisms represent 95% of animal biodiversity; however, few genomic resources currently exist for the group. The subset of marine invertebrates includes the most ancient metazoan lineages and possesses codes for unique gene products and possible keys to adaptation. The benefits of supporting invertebrate conservation genomics research (e.g., likely discovery of novel genes, protein regulatory mechanisms, genomic innovations, and transposable elements) outweigh the various hurdles (rare, small, or polymorphic starting materials). Here we review best conservation genomics practices in the laboratory and in silico when applied to marine invertebrates and also showcase unique features in several case studies of acroporid corals, crown-of-thorns starfish, apple snails, and abalone. Marine conservation genomics should also address how diversity can lead to unique marine innovations, the impact of deleterious variation, and how genomic monitoring and profiling could positively affect broader conservation goals (e.g., value of baseline data for in situ/ex situ genomic stocks).
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Affiliation(s)
- Jose V Lopez
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, Florida 33004, USA;
| | - Bishoy Kamel
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, New Mexico 87131, USA;
| | - Mónica Medina
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA; ,
| | - Timothy Collins
- Department of Biological Sciences, Florida International University, Miami, Florida 33199, USA;
| | - Iliana B Baums
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA; ,
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23
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Mollion M, Ehlers BK, Figuet E, Santoni S, Lenormand T, Maurice S, Galtier N, Bataillon T. Patterns of Genome-Wide Nucleotide Diversity in the Gynodioecious Plant Thymus vulgaris Are Compatible with Recent Sweeps of Cytoplasmic Genes. Genome Biol Evol 2018; 10:239-248. [PMID: 29272394 PMCID: PMC5815141 DOI: 10.1093/gbe/evx272] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2017] [Indexed: 12/14/2022] Open
Abstract
Gynodioecy is a sexual dimorphism where females coexist with hermaphrodite individuals. In most cases, this dimorphism involves the interaction of cytoplasmic male sterility (CMS) genes and nuclear restorer genes. Two scenarios can account for how these interactions maintain gynodioecy. Either CMS genes recurrently enter populations at low frequency via mutation or migration and go to fixation unimpeded (successive sweeps), or CMS genes maintain polymorphism over evolutionary time through interactions with a nuclear restorer allele (balanced polymorphism). To distinguish between these scenarios, we used transcriptome sequencing in gynodioecious Thymus vulgaris and surveyed genome-wide diversity in 18 naturally occurring individuals sampled from populations at a local geographic scale. We contrast the amount and patterns of nucleotide diversity in the nuclear and cytoplasmic genome, and find ample diversity at the nuclear level (π = 0.019 at synonymous sites) but reduced genetic diversity and an excess of rare polymorphisms in the cytoplasmic genome relative to the nuclear genome. Our finding is incompatible with the maintenance of gynodioecy via scenarios invoking long-term balancing selection, and instead suggests the recent fixation of CMS lineages in the populations studied.
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Affiliation(s)
- Maeva Mollion
- Bioinformatics Research Center, Aarhus University, C.F. Møllers Alle 8, Building 1110, 8000 Aarhus C, Denmark
| | - Bodil K Ehlers
- Department of Bioscience, Aarhus University, Vejlsøvej 25, 8600 Silkeborg, Denmark
| | - Emeric Figuet
- Institut des Sciences de l'Evolution, UMR5554 - Université de Montpellier - CNRS - IRD - EPHE, Place E. Bataillon - CC64, 34095 Montpellier, France
| | - Sylvain Santoni
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), CNRS, 1919, route de Mende 34293 Montpellier, France
| | - Thomas Lenormand
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, 1919, route de Mende 34293 Montpellier, France
| | - Sandrine Maurice
- Institut des Sciences de l'Evolution, UMR5554 - Université de Montpellier - CNRS - IRD - EPHE, Place E. Bataillon - CC64, 34095 Montpellier, France
| | - Nicolas Galtier
- Institut des Sciences de l'Evolution, UMR5554 - Université de Montpellier - CNRS - IRD - EPHE, Place E. Bataillon - CC64, 34095 Montpellier, France
| | - Thomas Bataillon
- Bioinformatics Research Center, Aarhus University, C.F. Møllers Alle 8, Building 1110, 8000 Aarhus C, Denmark
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24
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Gervais O, Renault T, Arzul I. Molecular and cellular characterization of apoptosis in flat oyster a key mechanisms at the heart of host-parasite interactions. Sci Rep 2018; 8:12494. [PMID: 30131502 DOI: 10.1038/s41598-018-29776-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/14/2018] [Indexed: 01/09/2023] Open
Abstract
Bonamia ostreae has been associated with the decline of flat oyster Ostrea edulis populations in some European countries. This obligatory intracellular parasite persists and multiplies into hemocytes. Previous in vitro experiments showed that apoptosis is activated in hemocytes between 1 h and 4 h of contact with the parasite. The flat oyster uses the apoptosis pathway to defend against B. ostreae. However, the parasite might be also able to modulate this response in order to survive in its host. In order to investigate this hypothesis the apoptotic response of the host was evaluated using flow cytometry, transmission electron microscopy and by measuring the response of genes involved in the apoptotic pathway after 4 h. In parallel, the parasite response was investigated by measuring the expression of B. ostreae genes involved in different biological functions including cell cycle and cell death. Obtained results allow describing molecular apoptotic pathways in O. edulis and confirm that apoptosis is early activated in hemocytes after a contact with B. ostreae. Interestingly, at cellular and molecular levels this process appeared downregulated after 44 h of contact. Concurrently, parasite gene expression appeared reduced suggesting that the parasite could inhibit its own metabolism to escape the immune response.
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25
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Fraïsse C, Roux C, Gagnaire PA, Romiguier J, Faivre N, Welch JJ, Bierne N. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: the effects of sequencing techniques and sampling strategies. PeerJ 2018; 6:e5198. [PMID: 30083438 PMCID: PMC6071616 DOI: 10.7717/peerj.5198] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [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] [Received: 02/01/2018] [Accepted: 06/19/2018] [Indexed: 01/25/2023] Open
Abstract
Genome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymous mutations computed either from exome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the jSFS, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e., periodic connectivity) and across genes (i.e., genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding jSFS, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed.
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Affiliation(s)
- Christelle Fraïsse
- Institut des Sciences de l’Evolution UMR5554, University Montpellier, CNRS, IRD, EPHE, Montpellier, France
- Department of Genetics, University of Cambridge, Cambridge, UK
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Camille Roux
- Université de Lille, Unité Evo-Eco-Paléo (EEP), UMR 8198, Villeneuve d’Ascq, France
| | - Pierre-Alexandre Gagnaire
- Institut des Sciences de l’Evolution UMR5554, University Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Jonathan Romiguier
- Institut des Sciences de l’Evolution UMR5554, University Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Nicolas Faivre
- Institut des Sciences de l’Evolution UMR5554, University Montpellier, CNRS, IRD, EPHE, Montpellier, France
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - John J. Welch
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Nicolas Bierne
- Institut des Sciences de l’Evolution UMR5554, University Montpellier, CNRS, IRD, EPHE, Montpellier, France
- Department of Genetics, University of Cambridge, Cambridge, UK
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26
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Holding ML, Margres MJ, Mason AJ, Parkinson CL, Rokyta DR. Evaluating the Performance of De Novo Assembly Methods for Venom-Gland Transcriptomics. Toxins (Basel) 2018; 10:E249. [PMID: 29921759 DOI: 10.3390/toxins10060249] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/14/2018] [Accepted: 06/15/2018] [Indexed: 11/17/2022] Open
Abstract
Venom-gland transcriptomics is a key tool in the study of the evolution, ecology, function, and pharmacology of animal venoms. In particular, gene-expression variation and coding sequences gained through transcriptomics provide key information for explaining functional venom variation over both ecological and evolutionary timescales. The accuracy and usefulness of inferences made through transcriptomics, however, is limited by the accuracy of the transcriptome assembly, which is a bioinformatic problem with several possible solutions. Several methods have been employed to assemble venom-gland transcriptomes, with the Trinity assembler being the most commonly applied among them. Although previous evidence of variation in performance among assembly software exists, particularly regarding recovery of difficult-to-assemble multigene families such as snake venom metalloproteinases, much work to date still employs a single assembly method. We evaluated the performance of several commonly used de novo assembly methods for the recovery of both nontoxin transcripts and complete, high-quality venom-gene transcripts across eleven snake and four scorpion transcriptomes. We varied k-mer sizes used by some assemblers to evaluate the impact of k-mer length on transcript recovery. We showed that the recovery of nontoxin transcripts and toxin transcripts is best accomplished through different assembly software, with SDT at smaller k-mer lengths and Trinity being best for nontoxin recovery and a combination of SeqMan NGen and a seed-and-extend approach implemented in Extender as the best means of recovering a complete set of toxin transcripts. In particular, Extender was the only means tested capable of assembling multiple isoforms of the diverse snake venom metalloproteinase family, while traditional approaches such as Trinity recovered at most one metalloproteinase transcript. Our work demonstrated that traditional metrics of assembly performance are not predictive of performance in the recovery of complete and high quality toxin genes. Instead, effective venom-gland transcriptomic studies should combine and quality-filter the results of several assemblers with varying algorithmic strategies.
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27
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Abstract
There have been a number of recent insights in the area of genomic imprinting, the phenomenon whereby one of two autosomal alleles is selected for expression based on the parent of origin. This is due in part to a proliferation of new techniques for interrogating the genome that are leading researchers working on organisms other than mouse and human, where imprinting has been most studied, to become interested in looking for potential imprinting effects. Here, we recap what is known about the importance of imprints for growth and body size, as well as the main types of locus control. Interestingly, work from a number of labs has now shown that maintenance of the imprint post implantation appears to be a more crucial step than previously appreciated. We ask whether imprints can be reprogrammed somatically, how many loci there are and how conserved imprinted regions are in other species. Finally, we survey some of the methods available for examining DNA methylation genome-wide and look to the future of this burgeoning field.
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Affiliation(s)
- Sarah-Jayne Mackin
- Genomic Medicine Research GroupSchool of Biomedical Sciences, Ulster University, Northern Ireland, UK
| | - Avinash Thakur
- Genomic Medicine Research GroupSchool of Biomedical Sciences, Ulster University, Northern Ireland, UK
| | - Colum P Walsh
- Genomic Medicine Research GroupSchool of Biomedical Sciences, Ulster University, Northern Ireland, UK
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28
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Affiliation(s)
- Hannah Weigand
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
| | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße, Essen, Germany
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29
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Deng Y, Gu J, Yan Z, Wang M, Ma C, Zhang J, Jiang G, Ge M, Xu S, Xu Z, Xiao L. De novo transcriptomic analysis of the venomous glands from the scorpion Heterometrus spinifer revealed unique and extremely high diversity of the venom peptides. Toxicon 2018; 143:1-19. [DOI: 10.1016/j.toxicon.2017.12.051] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 12/22/2017] [Accepted: 12/25/2017] [Indexed: 02/07/2023]
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30
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Zheng Y, Wu W, Hu G, Zhao Z, Meng S, Fan L, Song C, Qiu L, Chen J. Hepatic transcriptome analysis of juvenile GIFT tilapia (Oreochromis niloticus), fed diets supplemented with different concentrations of resveratrol. Ecotoxicol Environ Saf 2018; 147:447-454. [PMID: 28892663 DOI: 10.1016/j.ecoenv.2017.08.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 04/25/2017] [Revised: 08/01/2017] [Accepted: 08/02/2017] [Indexed: 06/07/2023]
Abstract
The GIFT (Genetically Improved Farmed Tilapia) tilapia, Oreochromis niloticus, is cultured widely for the production of freshwater fish in China. Streptococcosis, which is related to pathogenic infections, occurs frequently in juvenile and adult female GIFT individuals. Resveratrol (RES) has been used in feed to control these infections in freshwater tilapia. To address the effects of RES on tilapia, we used high-throughput RNA sequencing technology (RNA-Seq, HiSeq. 2500) to explore the global transcriptomic response and specific involvement of hepatic mRNA of juvenile O. niloticus fed with diets containing different concentrations of (0, 0.025, 0.05, and 0.1g/kg) RES. A total of > 24,513,018 clean reads were generated and then assembled into 23,244 unigenes. The unigenes were annotated by comparing them against non-redundant protein sequence (Nr), non-redundant nucleotide (Nt), Swiss-Prot, Pfam, Gene Ontology database (GO), Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, and 12,578 unigenes were annotated to the GO database. A total of 1444 (0.025g/kg RES), 1526 (0.05g/kg RES), and 3135 (0.1g/kg RES) genes were detected as significant differentially expressed genes (DEGs), when compared with the controls. A total of 6 (0.025 vs 0.05g/kg RES), 19 (0.025 vs 0.1g/kg RES), and 124 (0.05 vs 0.1g/kg RES) genes were detected as significant DEGs. Six genes, including dnah7x1, sox4, fam46a, hsp90a, ddit4, and nmrk2, were associated with an immune response. These findings provide information on the innate immunity of GIFT and might contribute to the development of strategies for the effective management of diseases and long-term sustainability of O. niloticus culture.
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Affiliation(s)
- Yao Zheng
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Environment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors(Wuxi), Ministry of Agriculture, Wuxi, Jiangsu 214081, PR China
| | - Wei Wu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Environment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors(Wuxi), Ministry of Agriculture, Wuxi, Jiangsu 214081, PR China
| | - Gengdong Hu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Environment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors(Wuxi), Ministry of Agriculture, Wuxi, Jiangsu 214081, PR China
| | - Zhixiang Zhao
- Wuxi Fishery College, Nanjing Agricultural University, Wuxi, Jiangsu 214081, PR China
| | - Shunlong Meng
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Environment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors(Wuxi), Ministry of Agriculture, Wuxi, Jiangsu 214081, PR China
| | - Limin Fan
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Environment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors(Wuxi), Ministry of Agriculture, Wuxi, Jiangsu 214081, PR China
| | - Chao Song
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Environment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors(Wuxi), Ministry of Agriculture, Wuxi, Jiangsu 214081, PR China
| | - Liping Qiu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Environment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors(Wuxi), Ministry of Agriculture, Wuxi, Jiangsu 214081, PR China
| | - Jiazhang Chen
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Fishery Eco-Environment Monitoring Center of Lower Reaches of Yangtze River, Ministry of Agriculture/Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Environmental Factors(Wuxi), Ministry of Agriculture, Wuxi, Jiangsu 214081, PR China; Wuxi Fishery College, Nanjing Agricultural University, Wuxi, Jiangsu 214081, PR China; Key Laboratory of Control of Quality and Safety for Aquatic Products, Ministry of Agriculture, PR China.
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Bigot D, Atyame CM, Weill M, Justy F, Herniou EA, Gayral P. Discovery of Culex pipiens associated tunisia virus: a new ssRNA(+) virus representing a new insect associated virus family. Virus Evol 2018; 4:vex040. [PMID: 29340209 PMCID: PMC5763275 DOI: 10.1093/ve/vex040] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
In the global context of arboviral emergence, deep sequencing unlocks the discovery of new mosquito-borne viruses. Mosquitoes of the species Culex pipiens, C. torrentium, and C. hortensis were sampled from 22 locations worldwide for transcriptomic analyses. A virus discovery pipeline was used to analyze the dataset of 0.7 billion reads comprising 22 individual transcriptomes. Two closely related 6.8 kb viral genomes were identified in C. pipiens and named as Culex pipiens associated tunisia virus (CpATV) strains Ayed and Jedaida. The CpATV genome contained four ORFs. ORF1 possessed helicase and RNA-dependent RNA polymerase (RdRp) domains related to new viral sequences recently found mainly in dipterans. ORF2 and 4 contained a capsid protein domain showing strong homology with Virgaviridae plant viruses. ORF3 displayed similarities with eukaryotic Rhoptry domain and a merozoite surface protein (MSP7) domain only found in mosquito-transmitted Plasmodium, suggesting possible interactions between CpATV and vertebrate cells. Estimation of a strong purifying selection exerted on each ORFs and the presence of a polymorphism maintained in the coding region of ORF3 suggested that both CpATV sequences are genuine functional viruses. CpATV is part of an entirely new and highly diversified group of viruses recently found in insects, and that bears the genomic hallmarks of a new viral family.
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Affiliation(s)
- Diane Bigot
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université François-Rabelais, 37200 Tours, France
| | - Célestine M Atyame
- Institut des Sciences de l'Evolution, UMR 5554, Université Montpellier–CNRS–IRD–EPHE, Montpellier, France
| | - Mylène Weill
- Institut des Sciences de l'Evolution, UMR 5554, Université Montpellier–CNRS–IRD–EPHE, Montpellier, France
| | - Fabienne Justy
- Institut des Sciences de l'Evolution, UMR 5554, Université Montpellier–CNRS–IRD–EPHE, Montpellier, France
| | - Elisabeth A Herniou
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université François-Rabelais, 37200 Tours, France
| | - Philippe Gayral
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université François-Rabelais, 37200 Tours, France
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Tong GX, Xu W, Zhang YQ, Zhang QY, Yin JS, Kuang YY. De novo assembly and characterization of the Hucho taimen transcriptome. Ecol Evol 2017; 8:1271-1285. [PMID: 29375797 PMCID: PMC5773338 DOI: 10.1002/ece3.3735] [Citation(s) in RCA: 7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/22/2017] [Accepted: 11/27/2017] [Indexed: 11/10/2022] Open
Abstract
Taimen (Hucho taimen) is an important ecological and economic species that is classified as vulnerable by the IUCN Red List of Threatened Species; however, limited genomic information is available on this species. RNA‐Seq is a useful tool for obtaining genetic information and developing genetic markers for nonmodel species in addition to its application in gene expression profiling. In this study, we performed a comprehensive RNA‐Seq analysis of taimen. We obtained 157 M clean reads (14.7 Gb) and used them to de novo assemble a high‐quality transcriptome with a N50 size of 1,060 bp. In the assembly, 82% of the transcripts were annotated using several databases, and 14,666 of the transcripts contained a full open reading frame. The assembly covered 75% of the transcripts of Atlantic salmon and 57.3% of the protein‐coding genes of rainbow trout. To learn about the genome evolution, we performed a systematic comparative analysis across 11 teleosts including eight salmonids and found 313 unique gene families in taimen. Using Atlantic salmon and rainbow trout transcriptomes as the background, we identified 250 positive selection transcripts. The pathway enrichment analysis revealed a unique characteristic of taimen: It possesses more immune‐related genes than Atlantic salmon and rainbow trout; moreover, some genes have undergone strong positive selection. We also developed a pipeline for identifying microsatellite marker genotypes in samples and successfully identified 24 polymorphic microsatellite markers for taimen. These data and tools are useful for studying conservation genetics, phylogenetics, evolution among salmonids, and selective breeding for threatened taimen.
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Affiliation(s)
- Guang-Xiang Tong
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences Daoli District, Harbin Heilongjiang Province China
| | - Wei Xu
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences Daoli District, Harbin Heilongjiang Province China
| | - Yong-Quan Zhang
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences Daoli District, Harbin Heilongjiang Province China
| | - Qing-Yu Zhang
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences Daoli District, Harbin Heilongjiang Province China
| | - Jia-Sheng Yin
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences Daoli District, Harbin Heilongjiang Province China
| | - You-Yi Kuang
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences Daoli District, Harbin Heilongjiang Province China
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Koglin S, Trense D, Wink M, Sauer-Gürth H, Tietze DT. Characterization of a de novo assembled transcriptome of the Common Blackbird ( Turdus merula). PeerJ 2017; 5:e4045. [PMID: 29255646 PMCID: PMC5732540 DOI: 10.7717/peerj.4045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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] [Received: 08/04/2017] [Accepted: 10/26/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND In recent years, next generation high throughput sequencing technologies have proven to be useful tools for investigations concerning the genomics or transcriptomics also of non-model species. Consequently, ornithologists have adopted these technologies and the respective bioinformatics tools to survey the genomes and transcriptomes of a few avian non-model species. The Common Blackbird is one of the most common bird species living in European cities, which has successfully colonized urban areas and for which no reference genome or transcriptome is publicly available. However, to target questions like genome wide gene expression analysis, a reference genome or transcriptome is needed. METHODS Therefore, in this study two Common Blackbirds were sacrificed, their mRNA was isolated and analyzed by RNA-Seq to de novo assemble a transcriptome and characterize it. Illumina reads (125 bp paired-end) and a Velvet/Oases pipeline led to 162,158 transcripts. For the annotation (using Blast+), an unfiltered protein database was used. SNPs were identified using SAMtools and BCFtools. Furthermore, mRNA from three single tissues (brain, heart and liver) of the same two Common Blackbirds were sequenced by Illumina (75 bp single-end reads). The draft transcriptome and the three single tissues were compared by their BLAST hits with the package VennDiagram in R. RESULTS Following the annotation against protein databases, we found evidence for 15,580 genes in the transcriptome (all well characterized hits after annotation). On 18% of the assembled transcripts, 144,742 SNPs were identified which are, consequently, 0.09% of all nucleotides in the assembled transcriptome. In the transcriptome and in the single tissues (brain, heart and liver), 10,182 shared genes were found. DISCUSSION Using a next-generation technology and bioinformatics tools, we made a first step towards the genomic investigation of the Common Blackbird. The de novo assembled transcriptome is usable for downstream analyses such as differential gene expression analysis and SNP identification. This study shows the importance of the approach to sequence single tissues to understand functions of tissues, proteins and the phenotype.
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Affiliation(s)
- Sven Koglin
- Institute for Pharmacy and Molecular Biotechnology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Daronja Trense
- Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
| | - Michael Wink
- Institute for Pharmacy and Molecular Biotechnology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Hedwig Sauer-Gürth
- Institute for Pharmacy and Molecular Biotechnology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Dieter Thomas Tietze
- Institute for Pharmacy and Molecular Biotechnology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
- Current affiliation: Natural History Museum Basel, Basel, Switzerland
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Bigot D, Dalmon A, Roy B, Hou C, Germain M, Romary M, Deng S, Diao Q, Weinert LA, Cook JM, Herniou EA, Gayral P. The discovery of Halictivirus resolves the Sinaivirus phylogeny. J Gen Virol 2017; 98:2864-2875. [DOI: 10.1099/jgv.0.000957] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Diane Bigot
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université de Tours, 37200 Tours, France
| | - Anne Dalmon
- INRA UR 406 Abeilles et environnement, Centre de recherche Provence-Alpes-Côte d'Azur, Site Agroparc, Domaine St Paul 228, Route de l'aérodrome CS40509 84914 Avignon, France
| | - Bronwen Roy
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Chunsheng Hou
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Beijing 100093, PR China
| | - Michèle Germain
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université de Tours, 37200 Tours, France
| | - Manon Romary
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université de Tours, 37200 Tours, France
| | - Shuai Deng
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Beijing 100093, PR China
| | - Qingyun Diao
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Beijing 100093, PR China
| | - Lucy A. Weinert
- Institut des Sciences de l'Evolution UMR5554, Université Montpellier–CNRS–IRD–EPHE, Montpellier, France
- Present address: Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
| | - James M. Cook
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Elisabeth A. Herniou
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université de Tours, 37200 Tours, France
| | - Philippe Gayral
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université de Tours, 37200 Tours, France
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Ungaro A, Pech N, Martin JF, McCairns RJS, Mévy JP, Chappaz R, Gilles A. Challenges and advances for transcriptome assembly in non-model species. PLoS One 2017; 12:e0185020. [PMID: 28931057 DOI: 10.1371/journal.pone.0185020] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 09/04/2017] [Indexed: 12/28/2022] Open
Abstract
Analyses of high-throughput transcriptome sequences of non-model organisms are based on two main approaches: de novo assembly and genome-guided assembly using mapping to assign reads prior to assembly. Given the limits of mapping reads to a reference when it is highly divergent, as is frequently the case for non-model species, we evaluate whether using blastn would outperform mapping methods for read assignment in such situations (>15% divergence). We demonstrate its high performance by using simulated reads of lengths corresponding to those generated by the most common sequencing platforms, and over a realistic range of genetic divergence (0% to 30% divergence). Here we focus on gene identification and not on resolving the whole set of transcripts (i.e. the complete transcriptome). For simulated datasets, the transcriptome-guided assembly based on blastn recovers 94.8% of genes irrespective of read length at 0% divergence; however, assignment rate of reads is negatively correlated with both increasing divergence level and reducing read lengths. Nevertheless, we still observe 92.6% of recovered genes at 30% divergence irrespective of read length. This analysis also produces a categorization of genes relative to their assignment, and suggests guidelines for data processing prior to analyses of comparative transcriptomics and gene expression to minimize potential inferential bias associated with incorrect transcript assignment. We also compare the performances of de novo assembly alone vs in combination with a transcriptome-guided assembly based on blastn both via simulation and empirically, using data from a cyprinid fish species and from an oak species. For any simulated scenario, the transcriptome-guided assembly using blastn outperforms the de novo approach alone, including when the divergence level is beyond the reach of traditional mapping methods. Combining de novo assembly and a related reference transcriptome for read assignment also addresses the bias/error in contigs caused by the dependence on a related reference alone. Empirical data corroborate these findings when assembling transcriptomes from the two non-model organisms: Parachondrostoma toxostoma (fish) and Quercus pubescens (plant). For the fish species, out of the 31,944 genes known from D. rerio, the guided and de novo assemblies recover respectively 20,605 and 20,032 genes but the performance of the guided assembly approach is much higher for both the contiguity and completeness metrics. For the oak, out of the 29,971 genes known from Vitis vinifera, the transcriptome-guided and de novo assemblies display similar performance, but the new guided approach detects 16,326 genes where the de novo assembly only detects 9,385 genes.
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Ballenghien M, Faivre N, Galtier N. Patterns of cross-contamination in a multispecies population genomic project: detection, quantification, impact, and solutions. BMC Biol 2017; 15:25. [PMID: 28356154 DOI: 10.1186/s12915-017-0366-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/13/2017] [Indexed: 01/06/2023] Open
Abstract
Background Contamination is a well-known but often neglected problem in molecular biology. Here, we investigated the prevalence of cross-contamination among 446 samples from 116 distinct species of animals, which were processed in the same laboratory and subjected to subcontracted transcriptome sequencing. Results Using cytochrome oxidase 1 as a barcode, we identified a minimum of 782 events of between-species contamination, with approximately 80% of our samples being affected. An analysis of laboratory metadata revealed a strong effect of the sequencing center: nearly all the detected events of between-species contamination involved species that were sent the same day to the same company. We introduce new methods to address the amount of within-species, between-individual contamination, and to correct for this problem when calling genotypes from base read counts. Conclusions We report evidence for pervasive within-species contamination in this data set, and show that classical population genomic statistics, such as synonymous diversity, the ratio of non-synonymous to synonymous diversity, inbreeding coefficient FIT, and Tajima’s D, are sensitive to this problem to various extents. Control analyses suggest that our published results are probably robust to the problem of contamination. Recommendations on how to prevent or avoid contamination in large-scale population genomics/molecular ecology are provided based on this analysis. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0366-6) contains supplementary material, which is available to authorized users.
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Sales G, Deagle BE, Calura E, Martini P, Biscontin A, De Pittà C, Kawaguchi S, Romualdi C, Meyer B, Costa R, Jarman S. KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba). PLoS One 2017; 12:e0171908. [PMID: 28187156 PMCID: PMC5302830 DOI: 10.1371/journal.pone.0171908] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/27/2017] [Indexed: 12/18/2022] Open
Abstract
Antarctic krill (Euphausia superba) is a key species in the Southern Ocean with an estimated biomass between 100 and 500 million tonnes. Changes in krill population viability would have catastrophic effect on the Antarctic ecosystem. One looming threat due to elevated levels of anthropogenic atmospheric carbon dioxide (CO2) is ocean acidification (lowering of sea water pH by CO2 dissolving into the oceans). The genetics of Antarctic krill has long been of scientific interest for both for the analysis of population structure and analysis of functional genetics. However, the genetic resources available for the species are relatively modest. We have developed the most advanced genetic database on Euphausia superba, KrillDB, which includes comprehensive data sets of former and present transcriptome projects. In particular, we have built a de novo transcriptome assembly using more than 360 million Illumina sequence reads generated from larval krill including individuals subjected to different CO2 levels. The database gives access to: 1) the full list of assembled genes and transcripts; 2) their level of similarity to transcripts and proteins from other species; 3) the predicted protein domains contained within each transcript; 4) their predicted GO terms; 5) the level of expression of each transcript in the different larval stages and CO2 treatments. All references to external entities (sequences, domains, GO terms) are equipped with a link to the appropriate source database. Moreover, the software implements a full-text search engine that makes it possible to submit free-form queries. KrillDB represents the first large-scale attempt at classifying and annotating the full krill transcriptome. For this reason, we believe it will constitute a cornerstone of future approaches devoted to physiological and molecular study of this key species in the Southern Ocean food web.
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Affiliation(s)
- Gabriele Sales
- Department of Biology, University of Padova, Padova, Italy
| | - Bruce E. Deagle
- Australian Antarctic Division, Kingston, Tasmania, Australia
| | - Enrica Calura
- Department of Biology, University of Padova, Padova, Italy
| | - Paolo Martini
- Department of Biology, University of Padova, Padova, Italy
| | | | | | - So Kawaguchi
- Australian Antarctic Division, Kingston, Tasmania, Australia
| | | | - Bettina Meyer
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
- * E-mail: (BM); (RC); (SJ)
| | - Rodolfo Costa
- Department of Biology, University of Padova, Padova, Italy
- * E-mail: (BM); (RC); (SJ)
| | - Simon Jarman
- Australian Antarctic Division, Kingston, Tasmania, Australia
- * E-mail: (BM); (RC); (SJ)
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Weber AAT, Abi-Rached L, Galtier N, Bernard A, Montoya-Burgos JI, Chenuil A. Positive selection on sperm ion channels in a brooding brittle star: consequence of life-history traits evolution. Mol Ecol 2017; 26:3744-3759. [PMID: 28099777 DOI: 10.1111/mec.14024] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [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: 10/11/2016] [Revised: 01/04/2017] [Accepted: 01/09/2017] [Indexed: 01/12/2023]
Abstract
Closely related species are key models to investigate mechanisms leading to reproductive isolation and early stages of diversification, also at the genomic level. The brittle star cryptic species complex Ophioderma longicauda encompasses the sympatric broadcast-spawning species C3 and the internal brooding species C5. Here, we used de novo transcriptome sequencing and assembly in two closely related species displaying contrasting reproductive modes to compare their genetic diversity and to investigate the role of natural selection in reproductive isolation. We reconstructed 20 146 and 22 123 genes for C3 and C5, respectively, and characterized a set of 12 229 orthologs. Genetic diversity was 1.5-2 times higher in C3 compared to C5, confirming that species with low parental investment display higher levels of genetic diversity. Forty-eight genes were the targets of positive diversifying selection during the evolution of the two species. Notably, two genes (NHE and TetraKCNG) are sperm-specific ion channels involved in sperm motility. Ancestral sequence reconstructions show that natural selection targeted the two genes in the brooding species. This may result from an adaptation to the novel environmental conditions surrounding sperm in the brooding species, either directly affecting sperm or via an increase in male/female conflict. This phenomenon could have promoted prezygotic reproductive isolation between C3 and C5. Finally, the sperm receptors to egg chemoattractants differed between C3 and C5 in the ligand-binding region. We propose that mechanisms of species-specific gamete recognition in brittle stars occur during sperm chemotaxis (sperm attraction towards the eggs), contrary to other marine invertebrates where prezygotic barriers to interspecific hybridization typically occur before sperm-egg fusion.
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Affiliation(s)
- A A-T Weber
- Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE) - CNRS - IRD - UAPV, Aix-Marseille Université, Station Marine d'Endoume, Chemin de la Batterie des Lions, 13007, Marseille, France.,Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - L Abi-Rached
- Equipe ATIP, URMITE UM 63 CNRS 7278 IRD 198 Inserm U1095, IHU Méditerranée Infection, Aix-Marseille Université, Marseille, France
| | - N Galtier
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, IRD, EPHE, Université de Montpellier, Place E. Bataillon, 34095, Montpellier, France
| | - A Bernard
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, IRD, EPHE, Université de Montpellier, Place E. Bataillon, 34095, Montpellier, France
| | - J I Montoya-Burgos
- Department of Genetics and Evolution, University of Geneva, 4, Bvd d'Yvoy, 1205, Geneva, Switzerland
| | - A Chenuil
- Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE) - CNRS - IRD - UAPV, Aix-Marseille Université, Station Marine d'Endoume, Chemin de la Batterie des Lions, 13007, Marseille, France
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Marques JP, Farelo L, Vilela J, Vanderpool D, Alves PC, Good JM, Boursot P, Melo-Ferreira J. Range expansion underlies historical introgressive hybridization in the Iberian hare. Sci Rep 2017; 7:40788. [PMID: 28120863 DOI: 10.1038/srep40788] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/09/2016] [Indexed: 12/27/2022] Open
Abstract
Introgressive hybridization is an important and widespread evolutionary process, but the relative roles of neutral demography and natural selection in promoting massive introgression are difficult to assess and an important matter of debate. Hares from the Iberian Peninsula provide an appropriate system to study this question. In its northern range, the Iberian hare, Lepus granatensis, shows a northwards gradient of increasing mitochondrial DNA (mtDNA) introgression from the arctic/boreal L. timidus, which it presumably replaced after the last glacial maximum. Here, we asked whether a south-north expansion wave of L. granatensis into L. timidus territory could underlie mtDNA introgression, and whether nuclear genes interacting with mitochondria (“mitonuc” genes) were affected. We extended previous RNA-sequencing and produced a comprehensive annotated transcriptome assembly for L. granatensis. We then genotyped 100 discovered nuclear SNPs in 317 specimens spanning the species range. The distribution of allele frequencies across populations suggests a northwards range expansion, particularly in the region of mtDNA introgression. We found no correlation between variants at 39 mitonuc genes and mtDNA introgression frequency. Whether the nuclear and mitochondrial genomes coevolved will need a thorough investigation of the hundreds of mitonuc genes, but range expansion and species replacement likely promoted massive mtDNA introgression.
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Koehbach J, Clark RJ. Unveiling the diversity of cyclotides by combining peptidome and transcriptome analysis. Biopolymers 2016; 106:774-783. [DOI: 10.1002/bip.22858] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/05/2016] [Accepted: 04/11/2016] [Indexed: 01/11/2023]
Affiliation(s)
- Johannes Koehbach
- School of Biomedical Sciences; The University of Queensland; 4072 St. Lucia QLD Australia
| | - Richard J. Clark
- School of Biomedical Sciences; The University of Queensland; 4072 St. Lucia QLD Australia
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Abstract
Marine sponges are important members of coral reef ecosystems. Thus, their responses to changes in ocean chemistry and environmental conditions, particularly to higher seawater temperatures, will have potential impacts on the future of these reefs. To better understand the sponge thermal stress response, we investigated gene expression dynamics in the shallow water sponge, Haliclona tubifera (order Haplosclerida, class Demospongiae), subjected to elevated temperature. Using high-throughput transcriptome sequencing, we show that these conditions result in the activation of various processes that interact to maintain cellular homeostasis. Short-term thermal stress resulted in the induction of heat shock proteins, antioxidants, and genes involved in signal transduction and innate immunity pathways. Prolonged exposure to thermal stress affected the expression of genes involved in cellular damage repair, apoptosis, signaling and transcription. Interestingly, exposure to sublethal temperatures may improve the ability of the sponge to mitigate cellular damage under more extreme stress conditions. These insights into the potential mechanisms of adaptation and resilience of sponges contribute to a better understanding of sponge conservation status and the prediction of ecosystem trajectories under future climate conditions.
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Affiliation(s)
- Christine Guzman
- Marine Science Institute, College of Science, University of the Philippines, Diliman, Quezon City, Philippines
| | - Cecilia Conaco
- Marine Science Institute, College of Science, University of the Philippines, Diliman, Quezon City, Philippines
- * E-mail:
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Rousselle M, Faivre N, Ballenghien M, Galtier N, Nabholz B. Hemizygosity Enhances Purifying Selection: Lack of Fast-Z Evolution in Two Satyrine Butterflies. Genome Biol Evol 2016; 8:3108-3119. [PMID: 27590089 PMCID: PMC5174731 DOI: 10.1093/gbe/evw214] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [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: 12/14/2022] Open
Abstract
The fixation probability of a recessive beneficial mutation is increased on the X or Z chromosome, relative to autosomes, because recessive alleles carried by X or Z are exposed to selection in the heterogametic sex. This leads to an increased dN/dS ratio on sex chromosomes relative to autosomes, a pattern called the “fast-X” or “fast-Z” effect. Besides positive selection, the strength of genetic drift and the efficacy of purifying selection, which affect the rate of molecular evolution, might differ between sex chromosomes and autosomes. Disentangling the complex effects of these distinct forces requires the genome-wide analysis of polymorphism, divergence and gene expression data in a variety of taxa. Here we study the influence of hemizygosity of the Z chromosome in Maniola jurtina and Pyronia tithonus, two species of butterflies (Lepidoptera, Nymphalidae, Satyrinae). Using transcriptome data, we compare the strength of positive and negative selection between Z and autosomes accounting for sex-specific gene expression. We show that M. jurtina and P. tithonus do not experience a faster, but rather a slightly slower evolutionary rate on the Z than on autosomes. Our analysis failed to detect a significant difference in adaptive evolutionary rate between Z and autosomes, but comparison of male-biased, unbiased and female-biased Z-linked genes revealed an increased efficacy of purifying selection against recessive deleterious mutations in female-biased Z-linked genes. This probably contributes to the lack of fast-Z evolution of satyrines. We suggest that the effect of hemizygosity on the fate of recessive deleterious mutations should be taken into account when interpreting patterns of molecular evolution in sex chromosomes vs. autosomes.
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Affiliation(s)
- Marjolaine Rousselle
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Place E. Bataillon, Montpellier, France
| | - Nicolas Faivre
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Place E. Bataillon, Montpellier, France
| | - Marion Ballenghien
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Place E. Bataillon, Montpellier, France
| | - Nicolas Galtier
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Place E. Bataillon, Montpellier, France
| | - Benoit Nabholz
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Place E. Bataillon, Montpellier, France
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43
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Sarah G, Homa F, Pointet S, Contreras S, Sabot F, Nabholz B, Santoni S, Sauné L, Ardisson M, Chantret N, Sauvage C, Tregear J, Jourda C, Pot D, Vigouroux Y, Chair H, Scarcelli N, Billot C, Yahiaoui N, Bacilieri R, Khadari B, Boccara M, Barnaud A, Péros JP, Labouisse JP, Pham JL, David J, Glémin S, Ruiz M. A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives. Mol Ecol Resour 2016; 17:565-580. [PMID: 27487989 DOI: 10.1111/1755-0998.12587] [Citation(s) in RCA: 38] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 06/29/2016] [Accepted: 07/06/2016] [Indexed: 12/20/2022]
Abstract
We produced a unique large data set of reference transcriptomes to obtain new knowledge about the evolution of plant genomes and crop domestication. For this purpose, we validated a RNA-Seq data assembly protocol to perform comparative population genomics. For the validation, we assessed and compared the quality of de novo Illumina short-read assemblies using data from two crops for which an annotated reference genome was available, namely grapevine and sorghum. We used the same protocol for the release of 26 new transcriptomes of crop plants and wild relatives, including still understudied crops such as yam, pearl millet and fonio. The species list has a wide taxonomic representation with the inclusion of 15 monocots and 11 eudicots. All contigs were annotated using BLAST, prot4EST and Blast2GO. A strong originality of the data set is that each crop is associated with close relative species, which will permit whole-genome comparative evolutionary studies between crops and their wild-related species. This large resource will thus serve research communities working on both crops and model organisms. All the data are available at http://arcad-bioinformatics.southgreen.fr/.
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Affiliation(s)
| | - Felix Homa
- CIRAD, UMR AGAP, Avenue Agropolis, F-34398, Montpellier, France
| | | | | | | | - Benoit Nabholz
- Institut des Sciences de l'Evolution-Montpellier, UMR CNRS-UM2 5554, University Montpellier II, Montpellier, France
| | | | - Laure Sauné
- INRA, UMR AGAP, F-34060, Montpellier, France
| | | | | | - Christopher Sauvage
- INRA, UR1052, GAFL, 67 allée des Chênes Domaine Saint Maurice- CS60094, 84143, Montfavet Cedex, France
| | | | - Cyril Jourda
- CIRAD, UMR AGAP, Avenue Agropolis, F-34398, Montpellier, France
| | - David Pot
- CIRAD, UMR AGAP, Avenue Agropolis, F-34398, Montpellier, France
| | | | - Hana Chair
- CIRAD, UMR AGAP, Avenue Agropolis, F-34398, Montpellier, France
| | | | - Claire Billot
- CIRAD, UMR AGAP, Avenue Agropolis, F-34398, Montpellier, France
| | - Nabila Yahiaoui
- CIRAD, UMR AGAP, Avenue Agropolis, F-34398, Montpellier, France
| | | | | | - Michel Boccara
- CIRAD/CRC, UMR AGAP, UWI, St Augustine, Trinidad and Tobago
| | | | | | | | | | - Jacques David
- Montpellier SupAgro, UMR AGAP, F-34060, Montpellier, France
| | - Sylvain Glémin
- Institut des Sciences de l'Evolution-Montpellier, UMR CNRS-UM2 5554, University Montpellier II, Montpellier, France
| | - Manuel Ruiz
- CIRAD, UMR AGAP, Avenue Agropolis, F-34398, Montpellier, France.,CIAT, Recta Cali Palmira km 17, Cali, Colombia
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Muyle A, Käfer J, Zemp N, Mousset S, Picard F, Marais GA. SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms. Genome Biol Evol 2016; 8:2530-43. [PMID: 27492231 PMCID: PMC5010906 DOI: 10.1093/gbe/evw172] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [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: 12/13/2022] Open
Abstract
We propose a probabilistic framework to infer autosomal and sex-linked genes from RNA-seq data of a cross for any sex chromosome type (XY, ZW, and UV). Sex chromosomes (especially the non-recombining and repeat-dense Y, W, U, and V) are notoriously difficult to sequence. Strategies have been developed to obtain partially assembled sex chromosome sequences. Most of them remain difficult to apply to numerous non-model organisms, either because they require a reference genome, or because they are designed for evolutionarily old systems. Sequencing a cross (parents and progeny) by RNA-seq to study the segregation of alleles and infer sex-linked genes is a cost-efficient strategy, which also provides expression level estimates. However, the lack of a proper statistical framework has limited a broader application of this approach. Tests on empirical Silene data show that our method identifies 20-35% more sex-linked genes than existing pipelines, while making reliable inferences for downstream analyses. Approximately 12 individuals are needed for optimal results based on simulations. For species with an unknown sex-determination system, the method can assess the presence and type (XY vs. ZW) of sex chromosomes through a model comparison strategy. The method is particularly well optimized for sex chromosomes of young or intermediate age, which are expected in thousands of yet unstudied lineages. Any organisms, including non-model ones for which nothing is known a priori, that can be bred in the lab, are suitable for our method. SEX-DETector and its implementation in a Galaxy workflow are made freely available.
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Affiliation(s)
- Aline Muyle
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
| | - Jos Käfer
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
| | - Niklaus Zemp
- Institute of Integrative Biology (IBZ), ETH Zurich, Zürich, Switzerland
| | - Sylvain Mousset
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
| | - Franck Picard
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
| | - Gabriel Ab Marais
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
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Szulkin M, Gagnaire PA, Bierne N, Charmantier A. Population genomic footprints of fine-scale differentiation between habitats in Mediterranean blue tits. Mol Ecol 2016; 25:542-58. [PMID: 26800038 DOI: 10.1111/mec.13486] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [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: 02/25/2015] [Revised: 11/13/2015] [Accepted: 11/17/2015] [Indexed: 12/20/2022]
Abstract
Linking population genetic variation to the spatial heterogeneity of the environment is of fundamental interest to evolutionary biology and ecology, in particular when phenotypic differences between populations are observed at biologically small spatial scales. Here, we applied restriction-site associated DNA sequencing (RAD-Seq) to test whether phenotypically differentiated populations of wild blue tits (Cyanistes caeruleus) breeding in a highly heterogeneous environment exhibit genetic structure related to habitat type. Using 12 106 SNPs in 197 individuals from deciduous and evergreen oak woodlands, we applied complementary population genomic analyses, which revealed that genetic variation is influenced by both geographical distance and habitat type. A fine-scale genetic differentiation supported by genome- and transcriptome-wide analyses was found within Corsica, between two adjacent habitats where blue tits exhibit marked differences in breeding time while nesting < 6 km apart. Using redundancy analysis (RDA), we show that genomic variation remains associated with habitat type when controlling for spatial and temporal effects. Finally, our results suggest that the observed patterns of genomic differentiation were not driven by a small proportion of highly differentiated loci, but rather emerged through a process such as habitat choice, which reduces gene flow between habitats across the entire genome. The pattern of genomic isolation-by-environment closely matches differentiation observed at the phenotypic level, thereby offering significant potential for future inference of phenotype-genotype associations in a heterogeneous environment.
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Affiliation(s)
- M Szulkin
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 Campus CNRS, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
| | - P-A Gagnaire
- Université Montpellier 2, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France.,ISEM - CNRS, UMR 5554, SMEL, 2 rue des Chantiers, 34200, Sète, France
| | - N Bierne
- Université Montpellier 2, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France.,ISEM - CNRS, UMR 5554, SMEL, 2 rue des Chantiers, 34200, Sète, France
| | - A Charmantier
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 Campus CNRS, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
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46
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Amoutzias GD, Giannoulis T, Moutou KA, Psarra AMG, Stamatis C, Tsipourlianos A, Mamuris Z. SNP Identification through Transcriptome Analysis of the European Brown Hare (Lepus europaeus): Cellular Energetics and Mother's Curse. PLoS One 2016; 11:e0159939. [PMID: 27459096 PMCID: PMC4961287 DOI: 10.1371/journal.pone.0159939] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [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: 02/04/2016] [Accepted: 07/11/2016] [Indexed: 12/30/2022] Open
Abstract
The European brown hare (Lepus europaeus, Pallas 1778) is an important small game species in Europe. Due to its size and position in the food chain, as well as its life history, phenotypic variation and the relatively recent speciation events, brown hare plays an important role in the structure of various ecosystems and has emerged as an important species for population management and evolutionary studies. In order to identify informative SNPs for such studies, heart and liver tissues of three samples from the European lineage and a three-sample pool from the Anatolian lineage were subjected to RNA-Sequencing analysis. This effort resulted in 9496 well-assembled protein-coding sequences with close homology to human. After applying very stringent filtering criteria, 66185 polymorphic sites were identified in 7665 genes/cds and 2050 of those polymorphic sites are potentially capable of distinguishing the European from the Anatolian lineage. From these distinguishing mutations we focused on those in genes that are involved in cellular energy production, namely the glycolysis, Krebs cycle and the OXPHOS machinery. A selected set of SNPs was also validated by Sanger sequencing. By simulating the three European individuals as one pool, no substantial informative-SNP identification was lost, making it a cost-efficient approach. To our knowledge this is the first attempt to correlate the differentiation in both nuclear and mitochondrial genome between the two different lineages of L. europaeus with the observed spatial partitioning of the lineages of the species, proposing a possible mechanism that is maintaining the reproductive isolation of the lineages.
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Affiliation(s)
- Grigoris D. Amoutzias
- Department of Biochemistry and Biotechnology, University of Thessaly, 41221, Larissa, Greece
| | - Themistoklis Giannoulis
- Department of Biochemistry and Biotechnology, University of Thessaly, 41221, Larissa, Greece
| | - Katerina A. Moutou
- Department of Biochemistry and Biotechnology, University of Thessaly, 41221, Larissa, Greece
| | - Anna-Maria G. Psarra
- Department of Biochemistry and Biotechnology, University of Thessaly, 41221, Larissa, Greece
| | - Costas Stamatis
- Department of Biochemistry and Biotechnology, University of Thessaly, 41221, Larissa, Greece
| | - Andreas Tsipourlianos
- Department of Biochemistry and Biotechnology, University of Thessaly, 41221, Larissa, Greece
| | - Zissis Mamuris
- Department of Biochemistry and Biotechnology, University of Thessaly, 41221, Larissa, Greece
- * E-mail:
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47
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Ament-Velásquez SL, Figuet E, Ballenghien M, Zattara EE, Norenburg JL, Fernández-Álvarez FA, Bierne J, Bierne N, Galtier N. Population genomics of sexual and asexual lineages in fissiparous ribbon worms (Lineus, Nemertea): hybridization, polyploidy and the Meselson effect. Mol Ecol 2016; 25:3356-69. [DOI: 10.1111/mec.13717] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 04/18/2016] [Accepted: 05/02/2016] [Indexed: 12/28/2022]
Affiliation(s)
- S. L. Ament-Velásquez
- Institute of Evolutionary Sciences; University Montpellier; CNRS, IRD, EPHE; Place Eugène Bataillon; 34095 Montpellier France
- Department of Organismal Biology; Systematic Biology; Uppsala University; PO Box 256 SE-751 05 Uppsala Sweden
| | - E. Figuet
- Institute of Evolutionary Sciences; University Montpellier; CNRS, IRD, EPHE; Place Eugène Bataillon; 34095 Montpellier France
| | - M. Ballenghien
- Institute of Evolutionary Sciences; University Montpellier; CNRS, IRD, EPHE; Place Eugène Bataillon; 34095 Montpellier France
| | - E. E. Zattara
- Department of Biology; Indiana University; 107 S Indiana Ave Bloomington IN 47405 USA
- Department of Invertebrate Zoology; National Museum of Natural History; Smithsonian Institution; 10th St. & Constitution Ave. NW Washington DC 20560 USA
| | - J. L. Norenburg
- Department of Invertebrate Zoology; National Museum of Natural History; Smithsonian Institution; 10th St. & Constitution Ave. NW Washington DC 20560 USA
| | | | - J. Bierne
- Laboratoire de Biologie Cellulaire et Moléculaire; Université de Reims Champagne-Ardenne; 9 Boulevard de la Paix 51100 Reims France
| | - N. Bierne
- Institute of Evolutionary Sciences; University Montpellier; CNRS, IRD, EPHE; Place Eugène Bataillon; 34095 Montpellier France
| | - N. Galtier
- Institute of Evolutionary Sciences; University Montpellier; CNRS, IRD, EPHE; Place Eugène Bataillon; 34095 Montpellier France
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48
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Nürnberger B, Lohse K, Fijarczyk A, Szymura JM, Blaxter ML. Para-allopatry in hybridizing fire-bellied toads (Bombina bombina and B. variegata): Inference from transcriptome-wide coalescence analyses. Evolution 2016; 70:1803-18. [PMID: 27282112 PMCID: PMC5129456 DOI: 10.1111/evo.12978] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [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] [Received: 10/27/2015] [Revised: 05/18/2016] [Accepted: 05/27/2016] [Indexed: 12/26/2022]
Abstract
Ancient origins, profound ecological divergence, and extensive hybridization make the fire‐bellied toads Bombina bombina and B. variegata (Anura: Bombinatoridae) an intriguing test case of ecological speciation. Previous modeling has proposed that the narrow Bombina hybrid zones represent strong barriers to neutral introgression. We test this prediction by inferring the rate of gene exchange between pure populations on either side of the intensively studied Kraków transect. We developed a method to extract high confidence sets of orthologous genes from de novo transcriptome assemblies, fitted a range of divergence models to these data and assessed their relative support with analytic likelihood calculations. There was clear evidence for postdivergence gene flow, but, as expected, no perceptible signal of recent introgression via the nearby hybrid zone. The analysis of two additional Bombina taxa (B. v. scabra and B. orientalis) validated our parameter estimates against a larger set of prior expectations. Despite substantial cumulative introgression over millions of years, adaptive divergence of the hybridizing taxa is essentially unaffected by their lack of reproductive isolation. Extended distribution ranges also buffer them against small‐scale environmental perturbations that have been shown to reverse the speciation process in other, more recent ecotypes.
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Affiliation(s)
- Beate Nürnberger
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, EH9 3FL, United Kingdom. .,Current Address: Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
| | - Konrad Lohse
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, EH9 3FL, United Kingdom
| | - Anna Fijarczyk
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, EH9 3FL, United Kingdom.,Department of Comparative Anatomy, Institute of Zoology, Jagiellonian University, Gronostajowa 9, 30-387, Kraków, Poland.,Current Address: Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Jacek M Szymura
- Department of Comparative Anatomy, Institute of Zoology, Jagiellonian University, Gronostajowa 9, 30-387, Kraków, Poland
| | - Mark L Blaxter
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, EH9 3FL, United Kingdom
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49
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Bataillon T, Galtier N, Bernard A, Cryer N, Faivre N, Santoni S, Severac D, Mikkelsen TN, Larsen KS, Beier C, Sørensen JG, Holmstrup M, Ehlers BK. A replicated climate change field experiment reveals rapid evolutionary response in an ecologically important soil invertebrate. Glob Chang Biol 2016; 22:2370-2379. [PMID: 27109012 PMCID: PMC5021122 DOI: 10.1111/gcb.13293] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 01/15/2016] [Accepted: 02/17/2016] [Indexed: 06/05/2023]
Abstract
Whether species can respond evolutionarily to current climate change is crucial for the persistence of many species. Yet, very few studies have examined genetic responses to climate change in manipulated experiments carried out in natural field conditions. We examined the evolutionary response to climate change in a common annelid worm using a controlled replicated experiment where climatic conditions were manipulated in a natural setting. Analyzing the transcribed genome of 15 local populations, we found that about 12% of the genetic polymorphisms exhibit differences in allele frequencies associated to changes in soil temperature and soil moisture. This shows an evolutionary response to realistic climate change happening over short-time scale, and calls for incorporating evolution into models predicting future response of species to climate change. It also shows that designed climate change experiments coupled with genome sequencing offer great potential to test for the occurrence (or lack) of an evolutionary response.
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Affiliation(s)
- Thomas Bataillon
- Bioinformatics Research Center (BiRC)Aarhus UniversityC.F. Møllers Allé 8, Building 11108000Aarhus CDenmark
| | - Nicolas Galtier
- CNRS UMR 5554Institut des Sciences de l'Evolution de MontpellierUniversité Montpellier 234095 Montpellier Cedex 05France
| | - Aurelien Bernard
- CNRS UMR 5554Institut des Sciences de l'Evolution de MontpellierUniversité Montpellier 234095 Montpellier Cedex 05France
| | - Nicolai Cryer
- Bioinformatics Research Center (BiRC)Aarhus UniversityC.F. Møllers Allé 8, Building 11108000Aarhus CDenmark
| | - Nicolas Faivre
- CNRS UMR 5554Institut des Sciences de l'Evolution de MontpellierUniversité Montpellier 234095 Montpellier Cedex 05France
| | | | - Dany Severac
- c/o Institut de Génomique FonctionnelleMGX‐Montpellier GenomiX34094 Montpellier Cedex 05France
| | - Teis N. Mikkelsen
- Department of Chemical and Biochemical EngineeringEcosystems CentreTechnical University of Denmark2800Kgs. LyngbyDenmark
| | - Klaus S. Larsen
- Department for Geosciences and Natural Resource ManagementUniversity of CopenhagenRolighedsvej 23DK‐1958FrederiksbergDenmark
| | - Claus Beier
- Department for Geosciences and Natural Resource ManagementUniversity of CopenhagenRolighedsvej 23DK‐1958FrederiksbergDenmark
- Centre for Catchments and Urban Water ResearchNorwegian Institute for Water Research (NIVA)Gaustadalléen 210349OsloNorway
| | - Jesper G. Sørensen
- Department of BioscienceAarhus UniversityNy Munkegade 1168000Aarhus CDenmark
| | - Martin Holmstrup
- Department of BioscienceAarhus UniversityVejlsøvej 258600SilkeborgDenmark
| | - Bodil K. Ehlers
- Department of BioscienceAarhus UniversityVejlsøvej 258600SilkeborgDenmark
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50
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Cannarsa E, Zampicinini G, Friard O, Santovito A, Cervella P. De novo transcriptome sequencing of a non-model polychaete species. Mar Genomics 2016; 29:31-4. [PMID: 27337998 DOI: 10.1016/j.margen.2016.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 05/26/2016] [Accepted: 06/07/2016] [Indexed: 11/23/2022]
Abstract
Transcriptome sequencing is a useful method for studying gene-sequences data, especially in non-model organisms whose genomic sequences are yet to be determined. Indeed, even without any genome reference, transcripts can be assembled de novo to produce a genome-scale transcription map. Here we describe a de novo transcriptome assembly for the polychaete worm Ophryotrocha diadema, generated from 454-sequencing (Roche GS-FLX Titanium Sequencing). We describe the sequencing, the assembly and functional annotation of EST sequences, and the level of transcriptome coverage provided by our sequence data. The sequences we assembled represent a wide depiction of expressed genes from throughout the lifespan of O. diadema. We found gene sequences to be part of a broad range of functions (i.e. biological and metabolic processes, immune system, reproductive processes, development and growth, signalling and response to stimuli) and we therefore built the first transcriptomic reference for Ophryotrocha polychaete worms. These results encourage us to focus our investigation on many aspects of O. diadema and to extend our research to co-generic species.
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