De novo annotation of the immune-enriched transcriptome provides insights into immune system genes of Chinese sturgeon (Acipenser sinensis).
Identifieur interne : 000051 ( PubMed/Corpus ); précédent : 000050; suivant : 000052De novo annotation of the immune-enriched transcriptome provides insights into immune system genes of Chinese sturgeon (Acipenser sinensis).
Auteurs : Rong Zhu ; He-Jun Du ; Shun-Yi Li ; Ya-Dong Li ; Hong Ni ; Xue-Jing Yu ; Yan-Yan Yang ; Yu-Ding Fan ; Nan Jiang ; Ling-Bing Zeng ; Xing-Guo WangSource :
- Fish & shellfish immunology [ 1095-9947 ] ; 2016.
Abstract
Chinese sturgeon (Acipenser sinensis), one of the oldest extant actinopterygian fishes with very high evolutionary, economical and conservation interest, is considered to be one of the critically endangered aquatic animals in China. Up to date, the immune system of this species remains largely undetermined with little sequence information publicly available. Herein, the first comprehensive transcriptome of immune tissues for Chinese sturgeon was characterized using Illumina deep sequencing. Over 67 million high-quality reads were generated and de novo assembled into the final set of 91,739 unique sequences. The annotation pipeline revealed that 25,871 unigenes were successfully annotated in the public databases, of which only 2002 had significant match to the existing sequences for the genus Acipenser. Overall 22,827 unigenes were categorized into 52 GO terms, 12,742 were classified into 26 KOG categories, and 4968 were assigned to 339 KEGG pathways. A more detailed annotation search showed the presence of a notable representation of immune-related genes, which suggests that this non-teleost actinopterygian fish harbors the same intermediates as in the well known immune pathways from mammals and teleosts, such as pattern recognition receptor (PRR) signaling pathway, JAK-STAT signaling pathway, complement and coagulation pathway, T-cell receptor (TCR) and B-cell receptor (BCR) signaling pathways. Additional genetic marker discovery led to the retrieval of 20,056 simple sequence repeats (SSRs) and 327,140 single nucleotide polymorphisms (SNPs). This immune-enriched transcriptome of Chinese sturgeon represents a rich resource that adds to the currently nascent field of chondrostean fish immunogenetics and furthers the conservation and management of this valuable fish.
DOI: 10.1016/j.fsi.2016.06.051
PubMed: 27368537
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">De novo annotation of the immune-enriched transcriptome provides insights into immune system genes of Chinese sturgeon (Acipenser sinensis).</title><author><name sortKey="Zhu, Rong" sort="Zhu, Rong" uniqKey="Zhu R" first="Rong" last="Zhu">Rong Zhu</name><affiliation><nlm:affiliation>Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.</nlm:affiliation></affiliation></author><author><name sortKey="Du, He Jun" sort="Du, He Jun" uniqKey="Du H" first="He-Jun" last="Du">He-Jun Du</name><affiliation><nlm:affiliation>Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Institute of Chinese Sturgeon, China Three Gorges Corporation, Yichang, Hubei 443100, China.</nlm:affiliation></affiliation></author><author><name sortKey="Li, Shun Yi" sort="Li, Shun Yi" uniqKey="Li S" first="Shun-Yi" last="Li">Shun-Yi Li</name><affiliation><nlm:affiliation>Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.</nlm:affiliation></affiliation></author><author><name sortKey="Li, Ya Dong" sort="Li, Ya Dong" uniqKey="Li Y" first="Ya-Dong" last="Li">Ya-Dong Li</name><affiliation><nlm:affiliation>Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.</nlm:affiliation></affiliation></author><author><name sortKey="Ni, Hong" sort="Ni, Hong" uniqKey="Ni H" first="Hong" last="Ni">Hong Ni</name><affiliation><nlm:affiliation>Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.</nlm:affiliation></affiliation></author><author><name sortKey="Yu, Xue Jing" sort="Yu, Xue Jing" uniqKey="Yu X" first="Xue-Jing" last="Yu">Xue-Jing Yu</name><affiliation><nlm:affiliation>Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.</nlm:affiliation></affiliation></author><author><name sortKey="Yang, Yan Yan" sort="Yang, Yan Yan" uniqKey="Yang Y" first="Yan-Yan" last="Yang">Yan-Yan Yang</name><affiliation><nlm:affiliation>Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.</nlm:affiliation></affiliation></author><author><name sortKey="Fan, Yu Ding" sort="Fan, Yu Ding" uniqKey="Fan Y" first="Yu-Ding" last="Fan">Yu-Ding Fan</name><affiliation><nlm:affiliation>Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China.</nlm:affiliation></affiliation></author><author><name sortKey="Jiang, Nan" sort="Jiang, Nan" uniqKey="Jiang N" first="Nan" last="Jiang">Nan Jiang</name><affiliation><nlm:affiliation>Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zeng, Ling Bing" sort="Zeng, Ling Bing" uniqKey="Zeng L" first="Ling-Bing" last="Zeng">Ling-Bing Zeng</name><affiliation><nlm:affiliation>Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China. 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Electronic address: zlb@yfi.ac.cn.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Xing Guo" sort="Wang, Xing Guo" uniqKey="Wang X" first="Xing-Guo" last="Wang">Xing-Guo Wang</name><affiliation><nlm:affiliation>Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China. Electronic address: xgwang@hubu.edu.cn.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Fish & shellfish immunology</title><idno type="eISSN">1095-9947</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Chinese sturgeon (Acipenser sinensis), one of the oldest extant actinopterygian fishes with very high evolutionary, economical and conservation interest, is considered to be one of the critically endangered aquatic animals in China. Up to date, the immune system of this species remains largely undetermined with little sequence information publicly available. Herein, the first comprehensive transcriptome of immune tissues for Chinese sturgeon was characterized using Illumina deep sequencing. Over 67 million high-quality reads were generated and de novo assembled into the final set of 91,739 unique sequences. The annotation pipeline revealed that 25,871 unigenes were successfully annotated in the public databases, of which only 2002 had significant match to the existing sequences for the genus Acipenser. Overall 22,827 unigenes were categorized into 52 GO terms, 12,742 were classified into 26 KOG categories, and 4968 were assigned to 339 KEGG pathways. A more detailed annotation search showed the presence of a notable representation of immune-related genes, which suggests that this non-teleost actinopterygian fish harbors the same intermediates as in the well known immune pathways from mammals and teleosts, such as pattern recognition receptor (PRR) signaling pathway, JAK-STAT signaling pathway, complement and coagulation pathway, T-cell receptor (TCR) and B-cell receptor (BCR) signaling pathways. Additional genetic marker discovery led to the retrieval of 20,056 simple sequence repeats (SSRs) and 327,140 single nucleotide polymorphisms (SNPs). This immune-enriched transcriptome of Chinese sturgeon represents a rich resource that adds to the currently nascent field of chondrostean fish immunogenetics and furthers the conservation and management of this valuable fish.</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">27368537</PMID><DateCreated><Year>2016</Year><Month>08</Month><Day>01</Day></DateCreated><DateRevised><Year>2016</Year><Month>12</Month><Day>19</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1095-9947</ISSN><JournalIssue CitedMedium="Internet"><Volume>55</Volume><PubDate><Year>2016</Year><Month>Aug</Month></PubDate></JournalIssue><Title>Fish & shellfish immunology</Title><ISOAbbreviation>Fish Shellfish Immunol.</ISOAbbreviation></Journal><ArticleTitle>De novo annotation of the immune-enriched transcriptome provides insights into immune system genes of Chinese sturgeon (Acipenser sinensis).</ArticleTitle><Pagination><MedlinePgn>699-716</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.fsi.2016.06.051</ELocationID><ELocationID EIdType="pii" ValidYN="Y">S1050-4648(16)30412-0</ELocationID><Abstract><AbstractText>Chinese sturgeon (Acipenser sinensis), one of the oldest extant actinopterygian fishes with very high evolutionary, economical and conservation interest, is considered to be one of the critically endangered aquatic animals in China. Up to date, the immune system of this species remains largely undetermined with little sequence information publicly available. Herein, the first comprehensive transcriptome of immune tissues for Chinese sturgeon was characterized using Illumina deep sequencing. Over 67 million high-quality reads were generated and de novo assembled into the final set of 91,739 unique sequences. The annotation pipeline revealed that 25,871 unigenes were successfully annotated in the public databases, of which only 2002 had significant match to the existing sequences for the genus Acipenser. Overall 22,827 unigenes were categorized into 52 GO terms, 12,742 were classified into 26 KOG categories, and 4968 were assigned to 339 KEGG pathways. A more detailed annotation search showed the presence of a notable representation of immune-related genes, which suggests that this non-teleost actinopterygian fish harbors the same intermediates as in the well known immune pathways from mammals and teleosts, such as pattern recognition receptor (PRR) signaling pathway, JAK-STAT signaling pathway, complement and coagulation pathway, T-cell receptor (TCR) and B-cell receptor (BCR) signaling pathways. Additional genetic marker discovery led to the retrieval of 20,056 simple sequence repeats (SSRs) and 327,140 single nucleotide polymorphisms (SNPs). This immune-enriched transcriptome of Chinese sturgeon represents a rich resource that adds to the currently nascent field of chondrostean fish immunogenetics and furthers the conservation and management of this valuable fish.</AbstractText><CopyrightInformation>Copyright © 2016 Elsevier Ltd. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zhu</LastName><ForeName>Rong</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Du</LastName><ForeName>He-Jun</ForeName><Initials>HJ</Initials><AffiliationInfo><Affiliation>Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Institute of Chinese Sturgeon, China Three Gorges Corporation, Yichang, Hubei 443100, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Shun-Yi</ForeName><Initials>SY</Initials><AffiliationInfo><Affiliation>Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Ya-Dong</ForeName><Initials>YD</Initials><AffiliationInfo><Affiliation>Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ni</LastName><ForeName>Hong</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yu</LastName><ForeName>Xue-Jing</ForeName><Initials>XJ</Initials><AffiliationInfo><Affiliation>Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Yan-Yan</ForeName><Initials>YY</Initials><AffiliationInfo><Affiliation>Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fan</LastName><ForeName>Yu-Ding</ForeName><Initials>YD</Initials><AffiliationInfo><Affiliation>Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jiang</LastName><ForeName>Nan</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zeng</LastName><ForeName>Ling-Bing</ForeName><Initials>LB</Initials><AffiliationInfo><Affiliation>Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China. Electronic address: zlb@yfi.ac.cn.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Xing-Guo</ForeName><Initials>XG</Initials><AffiliationInfo><Affiliation>Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Sciences, Hubei University, Wuhan, Hubei 430062, China. Electronic address: xgwang@hubu.edu.cn.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>06</Month><Day>29</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Fish Shellfish Immunol</MedlineTA><NlmUniqueID>9505220</NlmUniqueID><ISSNLinking>1050-4648</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Chinese sturgeon (Acipenser sinensis)</Keyword><Keyword MajorTopicYN="N">De novo assembly</Keyword><Keyword MajorTopicYN="N">Immune-related gene</Keyword><Keyword MajorTopicYN="N">Microsatellites</Keyword><Keyword MajorTopicYN="N">Transcriptome</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>01</Month><Day>08</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2016</Year><Month>06</Month><Day>24</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2016</Year><Month>06</Month><Day>27</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>7</Month><Day>3</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>7</Month><Day>3</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>7</Month><Day>3</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">27368537</ArticleId><ArticleId IdType="pii">S1050-4648(16)30412-0</ArticleId><ArticleId IdType="doi">10.1016/j.fsi.2016.06.051</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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