Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing.
Identifieur interne : 000256 ( PubMed/Curation ); précédent : 000255; suivant : 000257Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing.
Auteurs : R. Ogden [Royaume-Uni] ; K. Gharbi ; N. Mugue ; J. Martinsohn ; H. Senn ; J W Davey ; M. Pourkazemi ; R. Mcewing ; C. Eland ; M. Vidotto ; A. Sergeev ; L. CongiuSource :
- Molecular ecology [ 1365-294X ] ; 2013.
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.
DOI: 10.1111/mec.12234
PubMed: 23473098
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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. 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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></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><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23473098</PMID><DateCreated><Year>2013</Year><Month>05</Month><Day>30</Day></DateCreated><DateCompleted><Year>2014</Year><Month>01</Month><Day>08</Day></DateCompleted><DateRevised><Year>2016</Year><Month>11</Month><Day>22</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1365-294X</ISSN><JournalIssue CitedMedium="Internet"><Volume>22</Volume><Issue>11</Issue><PubDate><Year>2013</Year><Month>Jun</Month></PubDate></JournalIssue><Title>Molecular ecology</Title><ISOAbbreviation>Mol. Ecol.</ISOAbbreviation></Journal><ArticleTitle>Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing.</ArticleTitle><Pagination><MedlinePgn>3112-23</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/mec.12234</ELocationID><Abstract><AbstractText>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.</AbstractText><CopyrightInformation>© 2013 John Wiley & Sons Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ogden</LastName><ForeName>R</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>TRACE Wildlife Forensics Network, RZSS, Edinburgh, EH12 6TS, UK. rob.ogden@tracenetwork.org</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gharbi</LastName><ForeName>K</ForeName><Initials>K</Initials></Author><Author ValidYN="Y"><LastName>Mugue</LastName><ForeName>N</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Martinsohn</LastName><ForeName>J</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Senn</LastName><ForeName>H</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Davey</LastName><ForeName>J W</ForeName><Initials>JW</Initials></Author><Author ValidYN="Y"><LastName>Pourkazemi</LastName><ForeName>M</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>McEwing</LastName><ForeName>R</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Eland</LastName><ForeName>C</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Vidotto</LastName><ForeName>M</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Sergeev</LastName><ForeName>A</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Congiu</LastName><ForeName>L</ForeName><Initials>L</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>MR/K001744/1</GrantID><Agency>Medical Research Council</Agency><Country>United Kingdom</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2013</Year><Month>03</Month><Day>08</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Mol Ecol</MedlineTA><NlmUniqueID>9214478</NlmUniqueID><ISSNLinking>0962-1083</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005819">Genetic Markers</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D056727" MajorTopicYN="N">Endangered Species</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005399" MajorTopicYN="N">Fishes</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005819" MajorTopicYN="N">Genetic Markers</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="N">Genomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018895" MajorTopicYN="N">Microsatellite Repeats</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2012</Year><Month>06</Month><Day>29</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2012</Year><Month>12</Month><Day>11</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2012</Year><Month>12</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2013</Year><Month>3</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2013</Year><Month>3</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2014</Year><Month>1</Month><Day>9</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">23473098</ArticleId><ArticleId IdType="doi">10.1111/mec.12234</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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