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Poitrimol C, Thiébaut É, Daguin-Thiébaut C, Le Port AS, Ballenghien M, Tran Lu Y A, Jollivet D, Hourdez S, Matabos M. Contrasted phylogeographic patterns of hydrothermal vent gastropods along South West Pacific: Woodlark Basin, a possible contact zone and/or stepping-stone. PLoS One 2022; 17:e0275638. [PMID: 36197893 PMCID: PMC9534440 DOI: 10.1371/journal.pone.0275638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022] Open
Abstract
Understanding drivers of biodiversity patterns is essential to evaluate the potential impact of deep-sea mining on ecosystems resilience. While the South West Pacific forms an independent biogeographic province for hydrothermal vent fauna, different degrees of connectivity among basins were previously reported for a variety of species depending on their ability to disperse. In this study, we compared phylogeographic patterns of several vent gastropods across South West Pacific back-arc basins and the newly-discovered La Scala site on the Woodlark Ridge by analysing their genetic divergence using a barcoding approach. We focused on six genera of vent gastropods widely distributed in the region: Lepetodrilus, Symmetromphalus, Lamellomphalus, Shinkailepas, Desbruyeresia and Provanna. A wide-range sampling was conducted at different vent fields across the Futuna Volcanic Arc, the Manus, Woodlark, North Fiji, and Lau Basins, during the CHUBACARC cruise in 2019. The Cox1-based genetic structure of geographic populations was examined for each taxon to delineate putative cryptic species and assess potential barriers or contact zones between basins. Results showed contrasted phylogeographic patterns among species, even between closely related species. While some species are widely distributed across basins (i.e. Shinkailepas tollmanni, Desbruyeresia melanioides and Lamellomphalus) without evidence of strong barriers to gene flow, others are restricted to one (i.e. Shinkailepas tufari complex of cryptic species, Desbruyeresia cancellata and D. costata). Other species showed intermediate patterns of isolation with different lineages separating the Manus Basin from the Lau/North Fiji Basins (i.e. Lepetodrilus schrolli, Provanna and Symmetromphalus spp.). Individuals from the Woodlark Basin were either endemic to this area (though possibly representing intermediate OTUs between the Manus Basin and the other eastern basins populations) or, coming into contact from these basins, highlighting the stepping-stone role of the Woodlark Basin in the dispersal of the South West Pacific vent fauna. Results are discussed according to the dispersal ability of species and the geological history of the South West Pacific.
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Affiliation(s)
- Camille Poitrimol
- Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
- Biologie et Ecologie des Ecosystèmes marins Profonds, Ifremer, CNRS, UBO, Plouzané, France
- * E-mail:
| | - Éric Thiébaut
- Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Claire Daguin-Thiébaut
- Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Anne-Sophie Le Port
- Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Marion Ballenghien
- Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Adrien Tran Lu Y
- Institut des Sciences de l’Evolution de Montpellier, Université Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Didier Jollivet
- Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Stéphane Hourdez
- Laboratoire d’Ecogéochimie des Environnements Benthiques, Observatoire Océanologique de Banyuls, Sorbonne Université, CNRS, Banyuls-sur-Mer, France
| | - Marjolaine Matabos
- Biologie et Ecologie des Ecosystèmes marins Profonds, Ifremer, CNRS, UBO, Plouzané, France
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Guzinski J, Ruggeri P, Ballenghien M, Mauger S, Jacquemin B, Jollivet C, Coudret J, Jaugeon L, Destombe C, Valero M. Seascape Genomics of the Sugar Kelp Saccharina latissima along the North Eastern Atlantic Latitudinal Gradient. Genes (Basel) 2020; 11:E1503. [PMID: 33322137 PMCID: PMC7763533 DOI: 10.3390/genes11121503] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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] [Received: 11/07/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 12/23/2022] Open
Abstract
Temperature is one of the most important range-limiting factors for many seaweeds. Driven by the recent climatic changes, rapid northward shifts of species' distribution ranges can potentially modify the phylogeographic signature of Last Glacial Maximum. We explored this question in detail in the cold-tolerant kelp species Saccharina latissima, using microsatellites and double digest restriction site-associated DNA sequencing ( ddRAD-seq) derived single nucleotide polymorphisms (SNPs) to analyze the genetic diversity and structure in 11 sites spanning the entire European Atlantic latitudinal range of this species. In addition, we checked for statistical correlation between genetic marker allele frequencies and three environmental proxies (sea surface temperature, salinity, and water turbidity). Our findings revealed that genetic diversity was significantly higher for the northernmost locality (Spitsbergen) compared to the southern ones (Northern Iberia), which we discuss in light of the current state of knowledge on phylogeography of S. latissima and the potential influence of the recent climatic changes on the population structure of this species. Seven SNPs and 12 microsatellite alleles were found to be significantly associated with at least one of the three environmental variables. We speculate on the putative adaptive functions of the genes associated with the outlier markers and the importance of these markers for successful conservation and aquaculture strategies for S. latissima in this age of rapid global change.
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Affiliation(s)
- Jaromir Guzinski
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone KT15 3NB, Surrey, UK
| | - Paolo Ruggeri
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
- Xelect ltd, Horizon House, Abbey Walk, St Andrews KY16 9LB, Scotland, UK
| | - Marion Ballenghien
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
- UMR 7144, Adaptation et Diversité en Milieu Marin, CNRS, Sorbonne Université, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France
| | - Stephane Mauger
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
| | - Bertrand Jacquemin
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
- CEVA, 83 Presqu’île de Pen Lan, 22610 Pleubian, France
| | - Chloe Jollivet
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
- Ecole polytechnique de Lausanne (EPFL), SV-IBI UPOATES, Route cantonale, CH-1015 Lausanne, Switzerland
| | - Jerome Coudret
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
| | - Lucie Jaugeon
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
| | - Christophe Destombe
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
| | - Myriam Valero
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
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Guzinski J, Ballenghien M, Daguin‐Thiébaut C, Lévêque L, Viard F. Population genomics of the introduced and cultivated Pacific kelp Undaria pinnatifida: Marinas-not farms-drive regional connectivity and establishment in natural rocky reefs. Evol Appl 2018; 11:1582-1597. [PMID: 30344629 PMCID: PMC6183462 DOI: 10.1111/eva.12647] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/02/2018] [Accepted: 05/09/2018] [Indexed: 01/03/2023] Open
Abstract
Ports and farms are well-known primary introduction hot spots for marine non-indigenous species (NIS). The extent to which these anthropogenic habitats are sustainable sources of propagules and influence the evolution of NIS in natural habitats was examined in the edible seaweed Undaria pinnatifida, native to Asia and introduced to Europe in the 1970s. Following its deliberate introduction 40 years ago along the French coast of the English Channel, this kelp is now found in three contrasting habitat types: farms, marinas and natural rocky reefs. In the light of the continuous spread of this NIS, it is imperative to better understand the processes behind its sustainable establishment in the wild. In addition, developing effective management plans to curtail the spread of U. pinnatifida requires determining how the three types of populations interact with one another. In addition to an analysis using microsatellite markers, we developed, for the first time in a kelp, a ddRAD-sequencing technique to genotype 738 individuals sampled in 11 rocky reefs, 12 marinas, and two farms located along ca. 1,000 km of coastline. As expected, the RAD-seq panel showed more power than the microsatellite panel for identifying fine-grained patterns. However, both panels demonstrated habitat-specific properties of the study populations. In particular, farms displayed very low genetic diversity and no inbreeding conversely to populations in marinas and natural rocky reefs. In addition, strong, but chaotic regional genetic structure, was revealed, consistent with human-mediated dispersal (e.g., leisure boating). We also uncovered a tight relationship between populations in rocky reefs and those in nearby marinas, but not with nearby farms, suggesting spillover from marinas into the wild. At last, a temporal survey spanning 20 generations showed that wild populations are now self-sustaining, albeit there was no evidence for local adaptation to any of the three habitats. These findings highlight that limiting the spread of U. pinnatifida requires efficient management policies that also target marinas.
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Affiliation(s)
- Jaromir Guzinski
- Laboratory Adaptation and Diversity in Marine Environments (UMR 7144 CNRS SU)CNRSSorbonne UniversitéRoscoffFrance
- Laboratory Evolutionary Biology and Ecology of Algae (UMI 3614 CNRS SU)CNRSSorbonne UniversitéRoscoffFrance
| | - Marion Ballenghien
- Laboratory Adaptation and Diversity in Marine Environments (UMR 7144 CNRS SU)CNRSSorbonne UniversitéRoscoffFrance
| | - Claire Daguin‐Thiébaut
- Laboratory Adaptation and Diversity in Marine Environments (UMR 7144 CNRS SU)CNRSSorbonne UniversitéRoscoffFrance
| | - Laurent Lévêque
- Fédération de Recherche (FR 2424 CNRS SU)CNRSSorbonne UniversitéRoscoffFrance
| | - Frédérique Viard
- Laboratory Adaptation and Diversity in Marine Environments (UMR 7144 CNRS SU)CNRSSorbonne UniversitéRoscoffFrance
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Bernard M, Rousvoal S, Jacquemin B, Ballenghien M, Peters AF, Leblanc C. qPCR-based relative quantification of the brown algal endophyte Laminarionema elsbetiae in Saccharina latissima: variation and dynamics of host-endophyte interactions. J Appl Phycol 2018; 30:2901-2911. [PMID: 30416259 PMCID: PMC6208874 DOI: 10.1007/s10811-017-1367-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 12/06/2017] [Accepted: 12/06/2017] [Indexed: 05/11/2023]
Abstract
Morphological changes-such as dark spots, twisted stipes and deformed blades-have been observed in wild and cultivated Saccharina latissima. The putative cause for the disease symptoms is the filamentous endophytic brown alga Laminarionema elsbetiae, which is known to invade stipes and fronds of its hosts. Little is known about this interaction and its occurrence in the field, although former studies indicated high endophyte prevalence in kelp populations. Previous epidemiological studies on kelp endophytes were mainly based on the examination of microscopic sections, followed by time-consuming isolation and cultivation steps in order to identify the endophyte and a reliable method to quantify endophyte infections was missing. As a novel approach, we established and validated a qPCR assay for relative quantification of the endophyte L. elsbetiae within its host S. latissima, which allows to examine both, the prevalence of endophytic algae and the severity of infections. The assay was shown to be highly specific and suitable to reliably detect small amounts of endophyte DNA in the host. Using this method, we detected very high endophyte prevalence in the investigated kelp populations, up to 100% in young S. latissima sporophytes in Brittany during spring. Furthermore, our results suggest that Saccharina sporophytes are infected early in their life and that seasonality and environmental factors have a significant impact on infection rates. In the future, this approach could also be applied to study other host-endophyte pairs using specific primers.
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Affiliation(s)
- Miriam Bernard
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Universités, UPMC Univ. Paris 06, 29680 Roscoff, France
| | - Sylvie Rousvoal
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Universités, UPMC Univ. Paris 06, 29680 Roscoff, France
| | - Bertrand Jacquemin
- CNRS, UMI 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, Sorbonne Universités, UPMC Univ. Paris 06, 29680 Roscoff, France
- Present Address: CEVA, 22610 Pleubian, France
| | - Marion Ballenghien
- CNRS, UMI 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, Sorbonne Universités, UPMC Univ. Paris 06, 29680 Roscoff, France
| | | | - Catherine Leblanc
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Universités, UPMC Univ. Paris 06, 29680 Roscoff, France
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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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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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Dedeine F, Weinert LA, Bigot D, Josse T, Ballenghien M, Cahais V, Galtier N, Gayral P. Comparative Analysis of Transcriptomes from Secondary Reproductives of Three Reticulitermes Termite Species. PLoS One 2015; 10:e0145596. [PMID: 26698123 PMCID: PMC4689415 DOI: 10.1371/journal.pone.0145596] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 12/07/2015] [Indexed: 01/24/2023] Open
Abstract
Termites are eusocial insects related to cockroaches that feed on lignocellulose. These insects are key species in ecosystems since they recycle a large amount of nutrients but also are pests, exerting major economic impacts. Knowledge on the molecular pathways underlying reproduction, caste differentiation or lignocellulose digestion would largely benefit from additional transcriptomic data. This study focused on transcriptomes of secondary reproductive females (nymphoid neotenics). Thirteen transcriptomes were used: 10 of Reticulitermes flavipes and R. grassei sequenced from a previous study, and two transcriptomes of R. lucifugus sequenced for the present study. After transcriptome assembly and read mapping, we examined interspecific variations of genes expressed by termites or gut microorganisms. A total of 18,323 orthologous gene clusters were detected. Functional annotation and taxonomic assignment were performed on a total of 41,287 predicted contigs in the three termite species. Between the termite species studied, functional categories of genes were comparable. Gene ontology (GO) terms analysis allowed the discovery of 9 cellulases and a total of 79 contigs potentially involved in 11 enzymatic activities used in wood metabolism. Altogether, results of this study illustrate the strong potential for the use of comparative interspecific transcriptomes, representing a complete resource for future studies including differentially expressed genes between castes or SNP analysis for population genetics.
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Affiliation(s)
- Franck Dedeine
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS—Université François Rabelais, 37200, Tours, France
| | - Lucy A. Weinert
- Institut des Sciences de l’Evolution, UMR 5554, Université de Montpellier—CNRS—IRD—EPHE, Montpellier, France
| | - Diane Bigot
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS—Université François Rabelais, 37200, Tours, France
| | - Thibaut Josse
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS—Université François Rabelais, 37200, Tours, France
| | - Marion Ballenghien
- Institut des Sciences de l’Evolution, UMR 5554, Université de Montpellier—CNRS—IRD—EPHE, Montpellier, France
| | - Vincent Cahais
- Institut des Sciences de l’Evolution, UMR 5554, Université de Montpellier—CNRS—IRD—EPHE, Montpellier, France
| | - Nicolas Galtier
- Institut des Sciences de l’Evolution, UMR 5554, Université de Montpellier—CNRS—IRD—EPHE, Montpellier, 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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Burgarella C, Gayral P, Ballenghien M, Bernard A, David P, Jarne P, Correa A, Hurtrez-Boussès S, Escobar J, Galtier N, Glémin S. Molecular Evolution of Freshwater Snails with Contrasting Mating Systems. Mol Biol Evol 2015; 32:2403-16. [PMID: 25980005 DOI: 10.1093/molbev/msv121] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Because mating systems affect population genetics and ecology, they are expected to impact the molecular evolution of species. Self-fertilizing species experience reduced effective population size, recombination rates, and heterozygosity, which in turn should decrease the efficacy of natural selection, both adaptive and purifying, and the strength of meiotic drive processes such as GC-biased gene conversion. The empirical evidence is only partly congruent with these predictions, depending on the analyzed species, some, but not all, of the expected effects have been observed. One possible reason is that self-fertilization is an evolutionary dead-end, so that most current selfers recently evolved self-fertilization, and their genome has not yet been strongly impacted by selfing. Here, we investigate the molecular evolution of two groups of freshwater snails in which mating systems have likely been stable for several millions of years. Analyzing coding sequence polymorphism, divergence, and expression levels, we report a strongly reduced genetic diversity, decreased efficacy of purifying selection, slower rate of adaptive evolution, and weakened codon usage bias/GC-biased gene conversion in the selfer Galba compared with the outcrosser Physa, in full agreement with theoretical expectations. Our results demonstrate that self-fertilization, when effective in the long run, is a major driver of population genomic and molecular evolutionary processes. Despite the genomic effects of selfing, Galba truncatula seems to escape the demographic consequences of the genetic load. We suggest that the particular ecology of the species may buffer the negative consequences of selfing, shedding new light on the dead-end hypothesis.
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Affiliation(s)
- Concetta Burgarella
- Institut des Sciences de l'Evolution, UMR, CNRS 5554, Université Montpellier II, Montpellier, France
| | - Philippe Gayral
- Institut des Sciences de l'Evolution, UMR, CNRS 5554, Université Montpellier II, Montpellier, France
| | - Marion Ballenghien
- Institut des Sciences de l'Evolution, UMR, CNRS 5554, Université Montpellier II, Montpellier, France
| | - Aurélien Bernard
- Institut des Sciences de l'Evolution, UMR, CNRS 5554, Université Montpellier II, Montpellier, France
| | | | | | - Ana Correa
- MIVEGEC (Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution, Contrôle), UMR (UM1-UM2-CNRS 5290-IRD224), IRD, Montpellier, France
| | - Sylvie Hurtrez-Boussès
- MIVEGEC (Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution, Contrôle), UMR (UM1-UM2-CNRS 5290-IRD224), IRD, Montpellier, France
| | - Juan Escobar
- Institut des Sciences de l'Evolution, UMR, CNRS 5554, Université Montpellier II, Montpellier, France
| | - Nicolas Galtier
- Institut des Sciences de l'Evolution, UMR, CNRS 5554, Université Montpellier II, Montpellier, France
| | - Sylvain Glémin
- Institut des Sciences de l'Evolution, UMR, CNRS 5554, Université Montpellier II, Montpellier, France
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9
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Figuet E, Ballenghien M, Romiguier J, Galtier N. Biased gene conversion and GC-content evolution in the coding sequences of reptiles and vertebrates. Genome Biol Evol 2014; 7:240-50. [PMID: 25527834 PMCID: PMC4316630 DOI: 10.1093/gbe/evu277] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Mammalian and avian genomes are characterized by a substantial spatial heterogeneity of GC-content, which is often interpreted as reflecting the effect of local GC-biased gene conversion (gBGC), a meiotic repair bias that favors G and C over A and T alleles in high-recombining genomic regions. Surprisingly, the first fully sequenced nonavian sauropsid (i.e., reptile), the green anole Anolis carolinensis, revealed a highly homogeneous genomic GC-content landscape, suggesting the possibility that gBGC might not be at work in this lineage. Here, we analyze GC-content evolution at third-codon positions (GC3) in 44 vertebrates species, including eight newly sequenced transcriptomes, with a specific focus on nonavian sauropsids. We report that reptiles, including the green anole, have a genome-wide distribution of GC3 similar to that of mammals and birds, and we infer a strong GC3-heterogeneity to be already present in the tetrapod ancestor. We further show that the dynamic of coding sequence GC-content is largely governed by karyotypic features in vertebrates, notably in the green anole, in agreement with the gBGC hypothesis. The discrepancy between third-codon positions and noncoding DNA regarding GC-content dynamics in the green anole could not be explained by the activity of transposable elements or selection on codon usage. This analysis highlights the unique value of third-codon positions as an insertion/deletion-free marker of nucleotide substitution biases that ultimately affect the evolution of proteins.
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Affiliation(s)
- Emeric Figuet
- CNRS, Université Montpellier 2, UMR 5554, Institut des Sciences de l'Evolution de Montpellier, France
| | - Marion Ballenghien
- CNRS, Université Montpellier 2, UMR 5554, Institut des Sciences de l'Evolution de Montpellier, France
| | - Jonathan Romiguier
- CNRS, Université Montpellier 2, UMR 5554, Institut des Sciences de l'Evolution de Montpellier, France Department of Ecology and Evolution, Biophore, University of Lausanne, Switzerland
| | - Nicolas Galtier
- CNRS, Université Montpellier 2, UMR 5554, Institut des Sciences de l'Evolution de Montpellier, France
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10
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Romiguier J, Gayral P, Ballenghien M, Bernard A, Cahais V, Chenuil A, Chiari Y, Dernat R, Duret L, Faivre N, Loire E, Lourenco JM, Nabholz B, Roux C, Tsagkogeorga G, Weber AAT, Weinert LA, Belkhir K, Bierne N, Glémin S, Galtier N. Comparative population genomics in animals uncovers the determinants of genetic diversity. Nature 2014; 515:261-3. [DOI: 10.1038/nature13685] [Citation(s) in RCA: 405] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 07/17/2014] [Indexed: 02/07/2023]
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11
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Lapègue S, Harrang E, Heurtebise S, Flahauw E, Donnadieu C, Gayral P, Ballenghien M, Genestout L, Barbotte L, Mahla R, Haffray P, Klopp C. Development of SNP-genotyping arrays in two shellfish species. Mol Ecol Resour 2014; 14:820-30. [DOI: 10.1111/1755-0998.12230] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 12/26/2013] [Accepted: 01/08/2014] [Indexed: 11/30/2022]
Affiliation(s)
- S. Lapègue
- Ifremer; SG2M-LGPMM; Laboratoire de Génétique et Pathologie des Mollusques Marins; La Tremblade France
| | - E. Harrang
- Ifremer; SG2M-LGPMM; Laboratoire de Génétique et Pathologie des Mollusques Marins; La Tremblade France
| | - S. Heurtebise
- Ifremer; SG2M-LGPMM; Laboratoire de Génétique et Pathologie des Mollusques Marins; La Tremblade France
| | - E. Flahauw
- Ifremer; SG2M-LGPMM; Laboratoire de Génétique et Pathologie des Mollusques Marins; La Tremblade France
| | - C. Donnadieu
- INRA UMR444; Laboratoire de Génétique Cellulaire; Plateforme GeT-PlaGe Genotoul; Castanet-Tolosan France
| | - P. Gayral
- CNRS UMR 5554; Institut des Sciences de l'Evolution de Montpellier; Université Montpellier 2; Montpellier France
- CNRS UMR 7261; Institut de Recherche sur la Biologie de l'Insecte; Faculté des Sciences et Techniques; Université François Rabelais; Tours France
| | - M. Ballenghien
- CNRS UMR 5554; Institut des Sciences de l'Evolution de Montpellier; Université Montpellier 2; Montpellier France
| | - L. Genestout
- LABOGENA; Domaine de Vilvert; Jouy-en-Josas France
| | - L. Barbotte
- LABOGENA; Domaine de Vilvert; Jouy-en-Josas France
| | - R. Mahla
- LABOGENA; Domaine de Vilvert; Jouy-en-Josas France
| | - P. Haffray
- SYSAAF; Station LPGP/INRA; Campus de Beaulieu; 35042 Rennes France
| | - C. Klopp
- INRA; Sigenae; UR875 Biométrie et Intelligence Artificielle; Castanet-Tolosan France
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12
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Romiguier J, Lourenco J, Gayral P, Faivre N, Weinert LA, Ravel S, Ballenghien M, Cahais V, Bernard A, Loire E, Keller L, Galtier N. Population genomics of eusocial insects: the costs of a vertebrate-like effective population size. J Evol Biol 2014; 27:593-603. [DOI: 10.1111/jeb.12331] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 12/27/2013] [Accepted: 01/02/2014] [Indexed: 12/15/2022]
Affiliation(s)
- J. Romiguier
- Institut des Sciences de l'Evolution de Montpellier; Université Montpellier 2; CNRS UMR 5554; Montpellier France
| | - J. Lourenco
- Institut des Sciences de l'Evolution de Montpellier; Université Montpellier 2; CNRS UMR 5554; Montpellier France
| | - P. Gayral
- Institut des Sciences de l'Evolution de Montpellier; Université Montpellier 2; CNRS UMR 5554; Montpellier France
- Institut de Recherches sur la Biologie de l'Insecte; CNRS UMR 7261; Université François-Rabelais; Tours France
| | - N. Faivre
- Institut des Sciences de l'Evolution de Montpellier; Université Montpellier 2; CNRS UMR 5554; Montpellier France
| | - L. A. Weinert
- Institut des Sciences de l'Evolution de Montpellier; Université Montpellier 2; CNRS UMR 5554; Montpellier France
- Department of Veterinary Medicine; University of Cambridge; Cambridge UK
| | - S. Ravel
- Institut des Sciences de l'Evolution de Montpellier; Université Montpellier 2; CNRS UMR 5554; Montpellier France
| | - M. Ballenghien
- Institut des Sciences de l'Evolution de Montpellier; Université Montpellier 2; CNRS UMR 5554; Montpellier France
| | - V. Cahais
- Institut des Sciences de l'Evolution de Montpellier; Université Montpellier 2; CNRS UMR 5554; Montpellier France
| | - A. Bernard
- Institut des Sciences de l'Evolution de Montpellier; Université Montpellier 2; CNRS UMR 5554; Montpellier France
| | - E. Loire
- Institut des Sciences de l'Evolution de Montpellier; Université Montpellier 2; CNRS UMR 5554; Montpellier France
| | - L. Keller
- Department of Ecology and Evolution, Biophore; University of Lausanne; Lausanne Switzerland
| | - N. Galtier
- Institut des Sciences de l'Evolution de Montpellier; Université Montpellier 2; CNRS UMR 5554; Montpellier France
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13
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Riquet F, Daguin‐Thiébaut C, Ballenghien M, Bierne N, Viard F. Contrasting patterns of genome‐wide polymorphism in the native and invasive range of the marine molluscCrepidula fornicata. Mol Ecol 2013; 22:1003-18. [PMID: 23286428 DOI: 10.1111/mec.12161] [Citation(s) in RCA: 37] [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] [Received: 08/10/2012] [Revised: 10/15/2012] [Accepted: 10/29/2012] [Indexed: 01/03/2023]
Affiliation(s)
- Florentine Riquet
- UPMC Univ Paris 06 Team Diversity and Connectivity in Coastal Marine Landscapes UMR 7144 Station Biologique de Roscoff 29680 Roscoff France
- CNRS Laboratory Adaptation and Diversity in the Marine Environment UMR 7144 Station Biologique de Roscoff 29680 Roscoff France
| | - Claire Daguin‐Thiébaut
- UPMC Univ Paris 06 Team Diversity and Connectivity in Coastal Marine Landscapes UMR 7144 Station Biologique de Roscoff 29680 Roscoff France
- CNRS Laboratory Adaptation and Diversity in the Marine Environment UMR 7144 Station Biologique de Roscoff 29680 Roscoff France
| | - Marion Ballenghien
- UPMC Univ Paris 06 Team Diversity and Connectivity in Coastal Marine Landscapes UMR 7144 Station Biologique de Roscoff 29680 Roscoff France
- CNRS Laboratory Adaptation and Diversity in the Marine Environment UMR 7144 Station Biologique de Roscoff 29680 Roscoff France
- Université Montpellier 2 Place Eugène Bataillon 34095 Montpellier France
- CNRS Institut des Sciences de l'Evolution Laboratory Phylogénie et Evolution moléculaire UMR 5554 Université Montpellier 2 Place Eugène Bataillon 34095 Montpellier Cedex 05 France
| | - Nicolas Bierne
- Université Montpellier 2 Place Eugène Bataillon 34095 Montpellier France
- CNRS Institut des Sciences de l'Evolution UMR 5554 Station Méditerranéenne de l'Environnement Littoral, 2 rue des Chantiers 34200 Sète France
| | - Frédérique Viard
- UPMC Univ Paris 06 Team Diversity and Connectivity in Coastal Marine Landscapes UMR 7144 Station Biologique de Roscoff 29680 Roscoff France
- CNRS Laboratory Adaptation and Diversity in the Marine Environment UMR 7144 Station Biologique de Roscoff 29680 Roscoff France
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14
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Cahais V, Gayral P, Tsagkogeorga G, Melo-Ferreira J, Ballenghien M, Weinert L, Chiari Y, Belkhir K, Ranwez V, Galtier N. Reference-free transcriptome assembly in non-model animals from next-generation sequencing data. Mol Ecol Resour 2012. [PMID: 22540679 DOI: 10.1111/j.1755-0998.2012.03148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Next-generation sequencing (NGS) technologies offer the opportunity for population genomic study of non-model organisms sampled in the wild. The transcriptome is a convenient and popular target for such purposes. However, designing genetic markers from NGS transcriptome data requires assembling gene-coding sequences out of short reads. This is a complex task owing to gene duplications, genetic polymorphism, alternative splicing and transcription noise. Typical assembling programmes return thousands of predicted contigs, whose connection to the species true gene content is unclear, and from which SNP definition is uneasy. Here, the transcriptomes of five diverse non-model animal species (hare, turtle, ant, oyster and tunicate) were assembled from newly generated 454 and Illumina sequence reads. In two species for which a reference genome is available, a new procedure was introduced to annotate each predicted contig as either a full-length cDNA, fragment, chimera, allele, paralogue, genomic sequence or other, based on the number of, and overlap between, blast hits to the appropriate reference. Analyses showed that (i) the highest quality assemblies are obtained when 454 and Illumina data are combined, (ii) typical de novo assemblies include a majority of irrelevant cDNA predictions and (iii) assemblies can be appropriately cleaned by filtering contigs based on length and coverage. We conclude that robust, reference-free assembly of thousands of genes from transcriptomic NGS data is possible, opening promising perspectives for transcriptome-based population genomics in animals. A Galaxy pipeline implementing our best-performing assembling strategy is provided.
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Affiliation(s)
- V Cahais
- CNRS UMR 5554, Institut des Sciences de l'Evolution de Montpellier, Université Montpellier 2, Place E. Bataillon, 34095 Montpellier, France
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15
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Cahais V, Gayral P, Tsagkogeorga G, Melo-Ferreira J, Ballenghien M, Weinert L, Chiari Y, Belkhir K, Ranwez V, Galtier N. Reference-free transcriptome assembly in non-model animals from next-generation sequencing data. Mol Ecol Resour 2012; 12:834-45. [PMID: 22540679 DOI: 10.1111/j.1755-0998.2012.03148.x] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Next-generation sequencing (NGS) technologies offer the opportunity for population genomic study of non-model organisms sampled in the wild. The transcriptome is a convenient and popular target for such purposes. However, designing genetic markers from NGS transcriptome data requires assembling gene-coding sequences out of short reads. This is a complex task owing to gene duplications, genetic polymorphism, alternative splicing and transcription noise. Typical assembling programmes return thousands of predicted contigs, whose connection to the species true gene content is unclear, and from which SNP definition is uneasy. Here, the transcriptomes of five diverse non-model animal species (hare, turtle, ant, oyster and tunicate) were assembled from newly generated 454 and Illumina sequence reads. In two species for which a reference genome is available, a new procedure was introduced to annotate each predicted contig as either a full-length cDNA, fragment, chimera, allele, paralogue, genomic sequence or other, based on the number of, and overlap between, blast hits to the appropriate reference. Analyses showed that (i) the highest quality assemblies are obtained when 454 and Illumina data are combined, (ii) typical de novo assemblies include a majority of irrelevant cDNA predictions and (iii) assemblies can be appropriately cleaned by filtering contigs based on length and coverage. We conclude that robust, reference-free assembly of thousands of genes from transcriptomic NGS data is possible, opening promising perspectives for transcriptome-based population genomics in animals. A Galaxy pipeline implementing our best-performing assembling strategy is provided.
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Affiliation(s)
- V Cahais
- CNRS UMR 5554, Institut des Sciences de l'Evolution de Montpellier, Université Montpellier 2, Place E. Bataillon, 34095 Montpellier, France
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16
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Gayral P, Weinert L, Chiari Y, Tsagkogeorga G, Ballenghien M, Galtier N. Next-generation sequencing of transcriptomes: a guide to RNA isolation in nonmodel animals. Mol Ecol Resour 2011; 11:650-61. [PMID: 21481219 DOI: 10.1111/j.1755-0998.2011.03010.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Next Generation Sequencing technologies (NGS) are rapidly invading many evolutionary and ecological fields, such as phylogenomics, molecular evolution, population genomics and molecular ecology. Among the potential targets of NGS is transcriptome sequencing, a fast and relatively cheap way to generate massive amounts of coding sequence data, offering promising perspectives for the analysis of molecular diversity in the wild. A number of molecular ecology research groups therefore may switch from DNA-based to RNA-based typing in the near future. Sample preparation from natural populations, however, requires specific care and protocols when RNA is the target. Furthermore, NGS sequencing of transcriptome requires high amount of good-quality RNA. Here we present the results of RNA extraction experiments from various samples of 39 animal species caught in the wild. We compared tissue preparation and storage conditions, evaluated and improved standard RNA extraction protocols, and achieved RNA yield and quality suitable for NGS in all cases. We derive general guidelines for the production of ready-to-sequence RNA in nonmodel animals sampled in the field.
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Affiliation(s)
- Philippe Gayral
- Institut des Sciences de l'Evolution, CNRS UMR 5554, Université Montpellier 2, Place E Bataillon, 34095 Montpellier, France.
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