Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing
Identifieur interne : 000317 ( Main/Merge ); précédent : 000316; suivant : 000318Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing
Auteurs : R. Ogden [Royaume-Uni] ; K. Gharbi [Royaume-Uni] ; N. Mugue [Russie] ; J. Martinsohn [Italie] ; H. Senn [Royaume-Uni] ; J. W. Davey [Royaume-Uni] ; M. Pourkazemi [Iran] ; R. Mcewing [Royaume-Uni] ; C. Eland [Royaume-Uni] ; M. Vidotto [Italie] ; A. Sergeev [Russie] ; L. Congiu [Italie]Source :
- Molecular Ecology [ 0962-1083 ] ; 2013-06.
English descriptors
- KwdEn :
- MESH :
- chemical : Genetic Markers.
- classification : Fishes.
- genetics : Fishes, Polymorphism, Single Nucleotide.
- Animals, Base Sequence, Endangered Species, Genomics, Genotype, High-Throughput Nucleotide Sequencing, Microsatellite Repeats, Sequence Analysis, DNA.
Abstract
Caviar‐producing sturgeons belonging to the genus Acipenser are considered to be one of the most endangered species groups in the world. Continued overfishing in spite of increasing legislation, zero catch quotas and extensive aquaculture production have led to the collapse of wild stocks across Europe and Asia. The evolutionary relationships among Adriatic, Russian, Persian and Siberian sturgeons are complex because of past introgression events and remain poorly understood. Conservation management, traceability and enforcement suffer a lack of appropriate DNA markers for the genetic identification of sturgeon at the species, population and individual level. This study employed RAD sequencing to discover and characterize single nucleotide polymorphism (SNP) DNA markers for use in sturgeon conservation in these four tetraploid species over three biological levels, using a single sequencing lane. Four population meta‐samples and eight individual samples from one family were barcoded separately before sequencing. Analysis of 14.4 Gb of paired‐end RAD data focused on the identification of SNPs in the paired‐end contig, with subsequent in silico and empirical validation of candidate markers. Thousands of putatively informative markers were identified including, for the first time, SNPs that show population‐wide differentiation between Russian and Persian sturgeons, representing an important advance in our ability to manage these cryptic species. The results highlight the challenges of genotyping‐by‐sequencing in polyploid taxa, while establishing the potential genetic resources for developing a new range of caviar traceability and enforcement tools.
Url:
DOI: 10.1111/mec.12234
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Bassi 58/b 35121, Padova</wicri:regionArea><wicri:noRegion>Padova</wicri:noRegion></affiliation></author></analytic><monogr></monogr><series><title level="j">Molecular Ecology</title><title level="j" type="abbrev">Mol Ecol</title><idno type="ISSN">0962-1083</idno><idno type="eISSN">1365-294X</idno><imprint><publisher>Blackwell Publishing Ltd</publisher><date type="published" when="2013-06">2013-06</date><biblScope unit="volume">22</biblScope><biblScope unit="issue">11</biblScope><biblScope unit="page" from="3112">3112</biblScope><biblScope unit="page" to="3123">3123</biblScope></imprint><idno type="ISSN">0962-1083</idno></series><idno type="istex">9A3CD144570E803AB357D08BFA0825BEEFDE53CC</idno><idno type="DOI">10.1111/mec.12234</idno><idno type="ArticleID">MEC12234</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0962-1083</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Endangered Species</term><term>Fishes (classification)</term><term>Fishes (genetics)</term><term>Genetic Markers</term><term>Genomics</term><term>Genotype</term><term>High-Throughput Nucleotide Sequencing</term><term>Microsatellite Repeats</term><term>Polymorphism, Single Nucleotide (genetics)</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Genetic Markers</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Fishes</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Fishes</term><term>Polymorphism, Single Nucleotide</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Endangered Species</term><term>Genomics</term><term>Genotype</term><term>High-Throughput Nucleotide Sequencing</term><term>Microsatellite Repeats</term><term>Sequence Analysis, DNA</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract">Caviar‐producing sturgeons belonging to the genus Acipenser are considered to be one of the most endangered species groups in the world. Continued overfishing in spite of increasing legislation, zero catch quotas and extensive aquaculture production have led to the collapse of wild stocks across Europe and Asia. The evolutionary relationships among Adriatic, Russian, Persian and Siberian sturgeons are complex because of past introgression events and remain poorly understood. Conservation management, traceability and enforcement suffer a lack of appropriate DNA markers for the genetic identification of sturgeon at the species, population and individual level. This study employed RAD sequencing to discover and characterize single nucleotide polymorphism (SNP) DNA markers for use in sturgeon conservation in these four tetraploid species over three biological levels, using a single sequencing lane. Four population meta‐samples and eight individual samples from one family were barcoded separately before sequencing. Analysis of 14.4 Gb of paired‐end RAD data focused on the identification of SNPs in the paired‐end contig, with subsequent in silico and empirical validation of candidate markers. Thousands of putatively informative markers were identified including, for the first time, SNPs that show population‐wide differentiation between Russian and Persian sturgeons, representing an important advance in our ability to manage these cryptic species. The results highlight the challenges of genotyping‐by‐sequencing in polyploid taxa, while establishing the potential genetic resources for developing a new range of caviar traceability and enforcement tools.</div></front></TEI><double doi="10.1111/mec.12234"><ISTEX><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title xml:lang="en">Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing</title><author><name sortKey="Ogden, R" sort="Ogden, R" uniqKey="Ogden R" first="R." last="Ogden">R. Ogden</name></author><author><name sortKey="Gharbi, K" sort="Gharbi, K" uniqKey="Gharbi K" first="K." last="Gharbi">K. Gharbi</name></author><author><name sortKey="Mugue, N" sort="Mugue, N" uniqKey="Mugue N" first="N." last="Mugue">N. Mugue</name></author><author><name sortKey="Martinsohn, J" sort="Martinsohn, J" uniqKey="Martinsohn J" first="J." last="Martinsohn">J. Martinsohn</name></author><author><name sortKey="Senn, H" sort="Senn, H" uniqKey="Senn H" first="H." last="Senn">H. Senn</name></author><author><name sortKey="Davey, J W" sort="Davey, J W" uniqKey="Davey J" first="J. W." last="Davey">J. W. Davey</name></author><author><name sortKey="Pourkazemi, M" sort="Pourkazemi, M" uniqKey="Pourkazemi M" first="M." last="Pourkazemi">M. Pourkazemi</name></author><author><name sortKey="Mcewing, R" sort="Mcewing, R" uniqKey="Mcewing R" first="R." last="Mcewing">R. Mcewing</name></author><author><name sortKey="Eland, C" sort="Eland, C" uniqKey="Eland C" first="C." last="Eland">C. Eland</name></author><author><name sortKey="Vidotto, M" sort="Vidotto, M" uniqKey="Vidotto M" first="M." last="Vidotto">M. Vidotto</name></author><author><name sortKey="Sergeev, A" sort="Sergeev, A" uniqKey="Sergeev A" first="A." last="Sergeev">A. Sergeev</name></author><author><name sortKey="Congiu, L" sort="Congiu, L" uniqKey="Congiu L" first="L." last="Congiu">L. Congiu</name></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:9A3CD144570E803AB357D08BFA0825BEEFDE53CC</idno><date when="2013" year="2013">2013</date><idno type="doi">10.1111/mec.12234</idno><idno type="url">https://api.istex.fr/document/9A3CD144570E803AB357D08BFA0825BEEFDE53CC/fulltext/pdf</idno><idno type="wicri:Area/Istex/Corpus">001774</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">001774</idno><idno type="wicri:Area/Istex/Curation">001772</idno><idno type="wicri:Area/Istex/Checkpoint">000008</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Checkpoint">000008</idno><idno type="wicri:doubleKey">0962-1083:2013:Ogden R:sturgeon:conservation:genomics</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main" xml:lang="en">Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing</title><author><name sortKey="Ogden, R" sort="Ogden, R" uniqKey="Ogden R" first="R." last="Ogden">R. Ogden</name><affiliation wicri:level="3"><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>TRACE Wildlife Forensics Network, RZSS, EH12 6TS, Edinburgh</wicri:regionArea><placeName><settlement type="city">Édimbourg</settlement><region type="country">Écosse</region></placeName></affiliation><affiliation></affiliation></author><author><name sortKey="Gharbi, K" sort="Gharbi, K" uniqKey="Gharbi K" first="K." last="Gharbi">K. Gharbi</name><affiliation wicri:level="4"><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The GenePool, School of Biological Sciences, The University of Edinburgh, Edinburgh</wicri:regionArea><placeName><settlement type="city">Édimbourg</settlement><region type="country">Écosse</region></placeName><orgName type="university">Université d'Édimbourg</orgName></affiliation></author><author><name sortKey="Mugue, N" sort="Mugue, N" uniqKey="Mugue N" first="N." last="Mugue">N. 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Senn</name><affiliation wicri:level="3"><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>WildGenes Laboratory, Royal Zoological Society of Scotland, EH12 6TS, Edinburgh</wicri:regionArea><placeName><settlement type="city">Édimbourg</settlement><region type="country">Écosse</region></placeName></affiliation></author><author><name sortKey="Davey, J W" sort="Davey, J W" uniqKey="Davey J" first="J. W." last="Davey">J. W. Davey</name><affiliation wicri:level="4"><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, EH9 3JT, Edinburgh</wicri:regionArea><placeName><settlement type="city">Édimbourg</settlement><region type="country">Écosse</region></placeName><orgName type="university">Université d'Édimbourg</orgName></affiliation></author><author><name sortKey="Pourkazemi, M" sort="Pourkazemi, M" uniqKey="Pourkazemi M" first="M." last="Pourkazemi">M. Pourkazemi</name><affiliation wicri:level="1"><country xml:lang="fr">Iran</country><wicri:regionArea>Sturgeon International Research Institute, PO Box 41635‐3464, Rasht</wicri:regionArea><wicri:noRegion>Rasht</wicri:noRegion></affiliation></author><author><name sortKey="Mcewing, R" sort="Mcewing, R" uniqKey="Mcewing R" first="R." last="Mcewing">R. Mcewing</name><affiliation wicri:level="3"><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>TRACE Wildlife Forensics Network, RZSS, EH12 6TS, Edinburgh</wicri:regionArea><placeName><settlement type="city">Édimbourg</settlement><region type="country">Écosse</region></placeName></affiliation></author><author><name sortKey="Eland, C" sort="Eland, C" uniqKey="Eland C" first="C." last="Eland">C. Eland</name><affiliation wicri:level="4"><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The GenePool, School of Biological Sciences, The University of Edinburgh, Edinburgh</wicri:regionArea><placeName><settlement type="city">Édimbourg</settlement><region type="country">Écosse</region></placeName><orgName type="university">Université d'Édimbourg</orgName></affiliation></author><author><name sortKey="Vidotto, M" sort="Vidotto, M" uniqKey="Vidotto M" first="M." last="Vidotto">M. Vidotto</name><affiliation wicri:level="1"><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Biology, University of Padova, Via U. Bassi 58/b 35121, Padova</wicri:regionArea><wicri:noRegion>Padova</wicri:noRegion></affiliation></author><author><name sortKey="Sergeev, A" sort="Sergeev, A" uniqKey="Sergeev A" first="A." last="Sergeev">A. 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Bassi 58/b 35121, Padova</wicri:regionArea><wicri:noRegion>Padova</wicri:noRegion></affiliation></author></analytic><monogr></monogr><series><title level="j">Molecular Ecology</title><title level="j" type="abbrev">Mol Ecol</title><idno type="ISSN">0962-1083</idno><idno type="eISSN">1365-294X</idno><imprint><publisher>Blackwell Publishing Ltd</publisher><date type="published" when="2013-06">2013-06</date><biblScope unit="volume">22</biblScope><biblScope unit="issue">11</biblScope><biblScope unit="page" from="3112">3112</biblScope><biblScope unit="page" to="3123">3123</biblScope></imprint><idno type="ISSN">0962-1083</idno></series><idno type="istex">9A3CD144570E803AB357D08BFA0825BEEFDE53CC</idno><idno type="DOI">10.1111/mec.12234</idno><idno type="ArticleID">MEC12234</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0962-1083</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract">Caviar‐producing sturgeons belonging to the genus Acipenser are considered to be one of the most endangered species groups in the world. Continued overfishing in spite of increasing legislation, zero catch quotas and extensive aquaculture production have led to the collapse of wild stocks across Europe and Asia. The evolutionary relationships among Adriatic, Russian, Persian and Siberian sturgeons are complex because of past introgression events and remain poorly understood. Conservation management, traceability and enforcement suffer a lack of appropriate DNA markers for the genetic identification of sturgeon at the species, population and individual level. This study employed RAD sequencing to discover and characterize single nucleotide polymorphism (SNP) DNA markers for use in sturgeon conservation in these four tetraploid species over three biological levels, using a single sequencing lane. Four population meta‐samples and eight individual samples from one family were barcoded separately before sequencing. Analysis of 14.4 Gb of paired‐end RAD data focused on the identification of SNPs in the paired‐end contig, with subsequent in silico and empirical validation of candidate markers. Thousands of putatively informative markers were identified including, for the first time, SNPs that show population‐wide differentiation between Russian and Persian sturgeons, representing an important advance in our ability to manage these cryptic species. The results highlight the challenges of genotyping‐by‐sequencing in polyploid taxa, while establishing the potential genetic resources for developing a new range of caviar traceability and enforcement tools.</div></front></TEI></ISTEX><PubMed><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing.</title><author><name sortKey="Ogden, R" sort="Ogden, R" uniqKey="Ogden R" first="R" last="Ogden">R. Ogden</name><affiliation wicri:level="1"><nlm:affiliation>TRACE Wildlife Forensics Network, RZSS, Edinburgh, EH12 6TS, UK. rob.ogden@tracenetwork.org</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>TRACE Wildlife Forensics Network, RZSS, Edinburgh, EH12 6TS</wicri:regionArea><wicri:noRegion>EH12 6TS</wicri:noRegion></affiliation></author><author><name sortKey="Gharbi, K" sort="Gharbi, K" uniqKey="Gharbi K" first="K" last="Gharbi">K. Gharbi</name></author><author><name sortKey="Mugue, N" sort="Mugue, N" uniqKey="Mugue N" first="N" last="Mugue">N. Mugue</name></author><author><name sortKey="Martinsohn, J" sort="Martinsohn, J" uniqKey="Martinsohn J" first="J" last="Martinsohn">J. Martinsohn</name></author><author><name sortKey="Senn, H" sort="Senn, H" uniqKey="Senn H" first="H" last="Senn">H. Senn</name></author><author><name sortKey="Davey, J W" sort="Davey, J W" uniqKey="Davey J" first="J W" last="Davey">J W Davey</name></author><author><name sortKey="Pourkazemi, M" sort="Pourkazemi, M" uniqKey="Pourkazemi M" first="M" last="Pourkazemi">M. Pourkazemi</name></author><author><name sortKey="Mcewing, R" sort="Mcewing, R" uniqKey="Mcewing R" first="R" last="Mcewing">R. Mcewing</name></author><author><name sortKey="Eland, C" sort="Eland, C" uniqKey="Eland C" first="C" last="Eland">C. Eland</name></author><author><name sortKey="Vidotto, M" sort="Vidotto, M" uniqKey="Vidotto M" first="M" last="Vidotto">M. Vidotto</name></author><author><name sortKey="Sergeev, A" sort="Sergeev, A" uniqKey="Sergeev A" first="A" last="Sergeev">A. Sergeev</name></author><author><name sortKey="Congiu, L" sort="Congiu, L" uniqKey="Congiu L" first="L" last="Congiu">L. Congiu</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2013">2013</date><idno type="RBID">pubmed:23473098</idno><idno type="pmid">23473098</idno><idno type="doi">10.1111/mec.12234</idno><idno type="wicri:Area/PubMed/Corpus">000256</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000256</idno><idno type="wicri:Area/PubMed/Curation">000256</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000256</idno><idno type="wicri:Area/PubMed/Checkpoint">000256</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000256</idno><idno type="wicri:Area/Ncbi/Merge">000473</idno><idno type="wicri:Area/Ncbi/Curation">000473</idno><idno type="wicri:Area/Ncbi/Checkpoint">000473</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing.</title><author><name sortKey="Ogden, R" sort="Ogden, R" uniqKey="Ogden R" first="R" last="Ogden">R. Ogden</name><affiliation wicri:level="1"><nlm:affiliation>TRACE Wildlife Forensics Network, RZSS, Edinburgh, EH12 6TS, UK. rob.ogden@tracenetwork.org</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>TRACE Wildlife Forensics Network, RZSS, Edinburgh, EH12 6TS</wicri:regionArea><wicri:noRegion>EH12 6TS</wicri:noRegion></affiliation></author><author><name sortKey="Gharbi, K" sort="Gharbi, K" uniqKey="Gharbi K" first="K" last="Gharbi">K. Gharbi</name></author><author><name sortKey="Mugue, N" sort="Mugue, N" uniqKey="Mugue N" first="N" last="Mugue">N. Mugue</name></author><author><name sortKey="Martinsohn, J" sort="Martinsohn, J" uniqKey="Martinsohn J" first="J" last="Martinsohn">J. Martinsohn</name></author><author><name sortKey="Senn, H" sort="Senn, H" uniqKey="Senn H" first="H" last="Senn">H. Senn</name></author><author><name sortKey="Davey, J W" sort="Davey, J W" uniqKey="Davey J" first="J W" last="Davey">J W Davey</name></author><author><name sortKey="Pourkazemi, M" sort="Pourkazemi, M" uniqKey="Pourkazemi M" first="M" last="Pourkazemi">M. Pourkazemi</name></author><author><name sortKey="Mcewing, R" sort="Mcewing, R" uniqKey="Mcewing R" first="R" last="Mcewing">R. Mcewing</name></author><author><name sortKey="Eland, C" sort="Eland, C" uniqKey="Eland C" first="C" last="Eland">C. Eland</name></author><author><name sortKey="Vidotto, M" sort="Vidotto, M" uniqKey="Vidotto M" first="M" last="Vidotto">M. Vidotto</name></author><author><name sortKey="Sergeev, A" sort="Sergeev, A" uniqKey="Sergeev A" first="A" last="Sergeev">A. Sergeev</name></author><author><name sortKey="Congiu, L" sort="Congiu, L" uniqKey="Congiu L" first="L" last="Congiu">L. Congiu</name></author></analytic><series><title level="j">Molecular ecology</title><idno type="eISSN">1365-294X</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Endangered Species</term><term>Fishes (classification)</term><term>Fishes (genetics)</term><term>Genetic Markers</term><term>Genomics</term><term>Genotype</term><term>High-Throughput Nucleotide Sequencing</term><term>Microsatellite Repeats</term><term>Polymorphism, Single Nucleotide (genetics)</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Genetic Markers</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Fishes</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Fishes</term><term>Polymorphism, Single Nucleotide</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Endangered Species</term><term>Genomics</term><term>Genotype</term><term>High-Throughput Nucleotide Sequencing</term><term>Microsatellite Repeats</term><term>Sequence Analysis, DNA</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Caviar-producing sturgeons belonging to the genus Acipenser are considered to be one of the most endangered species groups in the world. Continued overfishing in spite of increasing legislation, zero catch quotas and extensive aquaculture production have led to the collapse of wild stocks across Europe and Asia. The evolutionary relationships among Adriatic, Russian, Persian and Siberian sturgeons are complex because of past introgression events and remain poorly understood. Conservation management, traceability and enforcement suffer a lack of appropriate DNA markers for the genetic identification of sturgeon at the species, population and individual level. This study employed RAD sequencing to discover and characterize single nucleotide polymorphism (SNP) DNA markers for use in sturgeon conservation in these four tetraploid species over three biological levels, using a single sequencing lane. Four population meta-samples and eight individual samples from one family were barcoded separately before sequencing. Analysis of 14.4 Gb of paired-end RAD data focused on the identification of SNPs in the paired-end contig, with subsequent in silico and empirical validation of candidate markers. Thousands of putatively informative markers were identified including, for the first time, SNPs that show population-wide differentiation between Russian and Persian sturgeons, representing an important advance in our ability to manage these cryptic species. The results highlight the challenges of genotyping-by-sequencing in polyploid taxa, while establishing the potential genetic resources for developing a new range of caviar traceability and enforcement tools.</div></front></TEI></PubMed></double></record>Pour manipuler ce document sous Unix (Dilib)
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