Sequencing and De Novo Assembly of the Gonadal Transcriptome of the Endangered Chinese Sturgeon (Acipenser sinensis).
Identifieur interne : 000130 ( PubMed/Curation ); précédent : 000129; suivant : 000131Sequencing and De Novo Assembly of the Gonadal Transcriptome of the Endangered Chinese Sturgeon (Acipenser sinensis).
Auteurs : Huamei Yue [République populaire de Chine] ; Chuangju Li [République populaire de Chine] ; Hao Du [République populaire de Chine] ; Shuhuan Zhang [République populaire de Chine] ; Qiwei Wei [République populaire de Chine]Source :
- PloS one [ 1932-6203 ] ; 2015.
English descriptors
- KwdEn :
- MESH :
- genetics : Fishes, Transcriptome.
- Animals, Gene Library, Molecular Sequence Annotation.
Abstract
The Chinese sturgeon (Acipenser sinensis) is endangered through anthropogenic activities including over-fishing, damming, shipping, and pollution. Controlled reproduction has been adopted and successfully conducted for conservation. However, little information is available on the reproductive regulation of the species. In this study, we conducted de novo transcriptome assembly of the gonad tissue to create a comprehensive dataset for A. sinensis.
DOI: 10.1371/journal.pone.0127332
PubMed: 26030930
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Freshwater Fisheries Research Center, Chinese Academy of Fisheries Science, Wuxi 214081, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China; Freshwater Fisheries Research Center, Chinese Academy of Fisheries Science, Wuxi 214081</wicri:regionArea></affiliation></author><author><name sortKey="Li, Chuangju" sort="Li, Chuangju" uniqKey="Li C" first="Chuangju" last="Li">Chuangju Li</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China; Freshwater Fisheries Research Center, Chinese Academy of Fisheries Science, Wuxi 214081, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China; Freshwater Fisheries Research Center, Chinese Academy of Fisheries Science, Wuxi 214081</wicri:regionArea></affiliation></author><author><name sortKey="Du, Hao" sort="Du, Hao" uniqKey="Du H" first="Hao" last="Du">Hao Du</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China; Freshwater Fisheries Research Center, Chinese Academy of Fisheries Science, Wuxi 214081, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China; Freshwater Fisheries Research Center, Chinese Academy of Fisheries Science, Wuxi 214081</wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Shuhuan" sort="Zhang, Shuhuan" uniqKey="Zhang S" first="Shuhuan" last="Zhang">Shuhuan Zhang</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China; Freshwater Fisheries Research Center, Chinese Academy of Fisheries Science, Wuxi 214081, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China; Freshwater Fisheries Research Center, Chinese Academy of Fisheries Science, Wuxi 214081</wicri:regionArea></affiliation></author><author><name sortKey="Wei, Qiwei" sort="Wei, Qiwei" uniqKey="Wei Q" first="Qiwei" last="Wei">Qiwei Wei</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China; Freshwater Fisheries Research Center, Chinese Academy of Fisheries Science, Wuxi 214081, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China; Freshwater Fisheries Research Center, Chinese Academy of Fisheries Science, Wuxi 214081</wicri:regionArea></affiliation></author></analytic><series><title level="j">PloS one</title><idno type="eISSN">1932-6203</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Fishes (genetics)</term><term>Gene Library</term><term>Molecular Sequence Annotation</term><term>Transcriptome (genetics)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Fishes</term><term>Transcriptome</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Gene Library</term><term>Molecular Sequence Annotation</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The Chinese sturgeon (Acipenser sinensis) is endangered through anthropogenic activities including over-fishing, damming, shipping, and pollution. Controlled reproduction has been adopted and successfully conducted for conservation. However, little information is available on the reproductive regulation of the species. In this study, we conducted de novo transcriptome assembly of the gonad tissue to create a comprehensive dataset for A. sinensis.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26030930</PMID><DateCreated><Year>2015</Year><Month>06</Month><Day>02</Day></DateCreated><DateCompleted><Year>2016</Year><Month>03</Month><Day>04</Day></DateCompleted><DateRevised><Year>2015</Year><Month>06</Month><Day>10</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>10</Volume><Issue>6</Issue><PubDate><Year>2015</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS ONE</ISOAbbreviation></Journal><ArticleTitle>Sequencing and De Novo Assembly of the Gonadal Transcriptome of the Endangered Chinese Sturgeon (Acipenser sinensis).</ArticleTitle><Pagination><MedlinePgn>e0127332</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0127332</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">The Chinese sturgeon (Acipenser sinensis) is endangered through anthropogenic activities including over-fishing, damming, shipping, and pollution. Controlled reproduction has been adopted and successfully conducted for conservation. However, little information is available on the reproductive regulation of the species. In this study, we conducted de novo transcriptome assembly of the gonad tissue to create a comprehensive dataset for A. sinensis.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">The Illumina sequencing platform was adopted to obtain 47,333,701 and 47,229,705 high quality reads from testis and ovary cDNA libraries generated from three-year-old A. sinensis. We identified 86,027 unigenes of which 30,268 were annotated in the NCBI non-redundant protein database and 28,281 were annotated in the Swiss-prot database. Among the annotated unigenes, 26,152 and 7,734 unigenes, respectively, were assigned to gene ontology categories and clusters of orthologous groups. In addition, 12,557 unigenes were mapped to 231 pathways in the Kyoto Encyclopedia of Genes and Genomes Pathway database. A total of 1,896 unigenes, potentially differentially expressed between the two gonad types, were found, with 1,894 predicted to be up-regulated in ovary and only two in testis. Fifty-five potential gametogenesis-related genes were screened in the transcriptome and 34 genes with significant matches were found. Besides, more paralogs of 11 genes in three gene families (sox, apolipoprotein and cyclin) were found in A. sinensis compared to their orthologs in the diploid Danio rerio. In addition, 12,151 putative simple sequence repeats (SSRs) were detected.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">This study provides the first de novo transcriptome analysis currently available for A. sinensis. The transcriptomic data represents the fundamental resource for future research on the mechanism of early gametogenesis in sturgeons. The SSRs identified in this work will be valuable for assessment of genetic diversity of wild fish and genealogy management of cultured fish.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Yue</LastName><ForeName>Huamei</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China; Freshwater Fisheries Research Center, Chinese Academy of Fisheries Science, Wuxi 214081, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Chuangju</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China; Freshwater Fisheries Research Center, Chinese Academy of Fisheries Science, Wuxi 214081, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Du</LastName><ForeName>Hao</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China; Freshwater Fisheries Research Center, Chinese Academy of Fisheries Science, Wuxi 214081, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Shuhuan</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China; Freshwater Fisheries Research Center, Chinese Academy of Fisheries Science, Wuxi 214081, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wei</LastName><ForeName>Qiwei</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China; Freshwater Fisheries Research Center, Chinese Academy of Fisheries Science, Wuxi 214081, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2015</Year><Month>06</Month><Day>01</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS 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MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005399" MajorTopicYN="N">Fishes</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015723" MajorTopicYN="N">Gene Library</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058977" MajorTopicYN="N">Molecular Sequence Annotation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059467" MajorTopicYN="N">Transcriptome</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList><OtherID Source="NLM">PMC4452307</OtherID></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2014</Year><Month>02</Month><Day>11</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2015</Year><Month>04</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>6</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>6</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>3</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26030930</ArticleId><ArticleId IdType="doi">10.1371/journal.pone.0127332</ArticleId><ArticleId IdType="pii">PONE-D-14-01669</ArticleId><ArticleId IdType="pmc">PMC4452307</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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