Transcriptome Sequencing, De Novo Assembly and Differential Gene Expression Analysis of the Early Development of Acipenser baeri.
Identifieur interne : 000653 ( Ncbi/Merge ); précédent : 000652; suivant : 000654Transcriptome Sequencing, De Novo Assembly and Differential Gene Expression Analysis of the Early Development of Acipenser baeri.
Auteurs : Wei Song [République populaire de Chine] ; Keji Jiang [République populaire de Chine] ; Fengying Zhang [République populaire de Chine] ; Yu Lin [République populaire de Chine] ; Lingbo Ma [République populaire de Chine]Source :
- PloS one [ 1932-6203 ] ; 2015.
English descriptors
- KwdEn :
- MESH :
- embryology : Fishes.
- genetics : Fishes.
- methods : Computational Biology.
- Animals, Cluster Analysis, Gene Expression Profiling, Gene Expression Regulation, Developmental, High-Throughput Nucleotide Sequencing, Molecular Sequence Annotation, Transcriptome.
Abstract
The molecular mechanisms that drive the development of the endangered fossil fish species Acipenser baeri are difficult to study due to the lack of genomic data. Recent advances in sequencing technologies and the reducing cost of sequencing offer exclusive opportunities for exploring important molecular mechanisms underlying specific biological processes. This manuscript describes the large scale sequencing and analyses of mRNA from Acipenser baeri collected at five development time points using the Illumina Hiseq2000 platform. The sequencing reads were de novo assembled and clustered into 278167 unigenes, of which 57346 (20.62%) had 45837 known homologues proteins in Uniprot protein databases while 11509 proteins matched with at least one sequence of assembled unigenes. The remaining 79.38% of unigenes could stand for non-coding unigenes or unigenes specific to A. baeri. A number of 43062 unigenes were annotated into functional categories via Gene Ontology (GO) annotation whereas 29526 unigenes were associated with 329 pathways by mapping to KEGG database. Subsequently, 3479 differentially expressed genes were scanned within developmental stages and clustered into 50 gene expression profiles. Genes preferentially expressed at each stage were also identified. Through GO and KEGG pathway enrichment analysis, relevant physiological variations during the early development of A. baeri could be better cognized. Accordingly, the present study gives insights into the transcriptome profile of the early development of A. baeri, and the information contained in this large scale transcriptome will provide substantial references for A. baeri developmental biology and promote its aquaculture research.
DOI: 10.1371/journal.pone.0137450
PubMed: 26359664
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East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Shanghai, China; East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai</wicri:regionArea><wicri:noRegion>Shanghai</wicri:noRegion></affiliation></author><author><name sortKey="Jiang, Keji" sort="Jiang, Keji" uniqKey="Jiang K" first="Keji" last="Jiang">Keji Jiang</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Shanghai, China; East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Shanghai, China; 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East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Shanghai, China; East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai</wicri:regionArea><wicri:noRegion>Shanghai</wicri:noRegion></affiliation></author><author><name sortKey="Ma, Lingbo" sort="Ma, Lingbo" uniqKey="Ma L" first="Lingbo" last="Ma">Lingbo Ma</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Shanghai, China; East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Shanghai, China; East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai</wicri:regionArea><wicri:noRegion>Shanghai</wicri:noRegion></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>Cluster Analysis</term><term>Computational Biology (methods)</term><term>Fishes (embryology)</term><term>Fishes (genetics)</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Developmental</term><term>High-Throughput Nucleotide Sequencing</term><term>Molecular Sequence Annotation</term><term>Transcriptome</term></keywords><keywords scheme="MESH" qualifier="embryology" xml:lang="en"><term>Fishes</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Fishes</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Cluster Analysis</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Developmental</term><term>High-Throughput Nucleotide Sequencing</term><term>Molecular Sequence Annotation</term><term>Transcriptome</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The molecular mechanisms that drive the development of the endangered fossil fish species Acipenser baeri are difficult to study due to the lack of genomic data. Recent advances in sequencing technologies and the reducing cost of sequencing offer exclusive opportunities for exploring important molecular mechanisms underlying specific biological processes. This manuscript describes the large scale sequencing and analyses of mRNA from Acipenser baeri collected at five development time points using the Illumina Hiseq2000 platform. The sequencing reads were de novo assembled and clustered into 278167 unigenes, of which 57346 (20.62%) had 45837 known homologues proteins in Uniprot protein databases while 11509 proteins matched with at least one sequence of assembled unigenes. The remaining 79.38% of unigenes could stand for non-coding unigenes or unigenes specific to A. baeri. A number of 43062 unigenes were annotated into functional categories via Gene Ontology (GO) annotation whereas 29526 unigenes were associated with 329 pathways by mapping to KEGG database. Subsequently, 3479 differentially expressed genes were scanned within developmental stages and clustered into 50 gene expression profiles. Genes preferentially expressed at each stage were also identified. Through GO and KEGG pathway enrichment analysis, relevant physiological variations during the early development of A. baeri could be better cognized. Accordingly, the present study gives insights into the transcriptome profile of the early development of A. baeri, and the information contained in this large scale transcriptome will provide substantial references for A. baeri developmental biology and promote its aquaculture research.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26359664</PMID><DateCreated><Year>2015</Year><Month>09</Month><Day>12</Day></DateCreated><DateCompleted><Year>2016</Year><Month>05</Month><Day>31</Day></DateCompleted><DateRevised><Year>2015</Year><Month>09</Month><Day>19</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>10</Volume><Issue>9</Issue><PubDate><Year>2015</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS ONE</ISOAbbreviation></Journal><ArticleTitle>Transcriptome Sequencing, De Novo Assembly and Differential Gene Expression Analysis of the Early Development of Acipenser baeri.</ArticleTitle><Pagination><MedlinePgn>e0137450</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0137450</ELocationID><Abstract><AbstractText>The molecular mechanisms that drive the development of the endangered fossil fish species Acipenser baeri are difficult to study due to the lack of genomic data. Recent advances in sequencing technologies and the reducing cost of sequencing offer exclusive opportunities for exploring important molecular mechanisms underlying specific biological processes. This manuscript describes the large scale sequencing and analyses of mRNA from Acipenser baeri collected at five development time points using the Illumina Hiseq2000 platform. The sequencing reads were de novo assembled and clustered into 278167 unigenes, of which 57346 (20.62%) had 45837 known homologues proteins in Uniprot protein databases while 11509 proteins matched with at least one sequence of assembled unigenes. The remaining 79.38% of unigenes could stand for non-coding unigenes or unigenes specific to A. baeri. A number of 43062 unigenes were annotated into functional categories via Gene Ontology (GO) annotation whereas 29526 unigenes were associated with 329 pathways by mapping to KEGG database. Subsequently, 3479 differentially expressed genes were scanned within developmental stages and clustered into 50 gene expression profiles. Genes preferentially expressed at each stage were also identified. Through GO and KEGG pathway enrichment analysis, relevant physiological variations during the early development of A. baeri could be better cognized. Accordingly, the present study gives insights into the transcriptome profile of the early development of A. baeri, and the information contained in this large scale transcriptome will provide substantial references for A. baeri developmental biology and promote its aquaculture research.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Song</LastName><ForeName>Wei</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Shanghai, China; East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jiang</LastName><ForeName>Keji</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Shanghai, China; East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Fengying</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Shanghai, China; East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lin</LastName><ForeName>Yu</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Shanghai, China; East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ma</LastName><ForeName>Lingbo</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Shanghai, China; East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 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>09</Month><Day>11</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS One</MedlineTA><NlmUniqueID>101285081</NlmUniqueID><ISSNLinking>1932-6203</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections 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2010 Jul;138(7):745-56</RefSource><PMID Version="1">20386959</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Genome Biol. 2010;11(10):R106</RefSource><PMID Version="1">20979621</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>BMC Dev Biol. 2011;11:30</RefSource><PMID Version="1">21609443</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>BMC Bioinformatics. 2011;12:323</RefSource><PMID Version="1">21816040</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>BMC Genomics. 2013;14:407</RefSource><PMID Version="1">23773438</PMID></CommentsCorrections></CommentsCorrectionsList><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016000" MajorTopicYN="N">Cluster Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="Y">Computational Biology</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005399" MajorTopicYN="N">Fishes</DescriptorName><QualifierName UI="Q000196" MajorTopicYN="Y">embryology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018507" MajorTopicYN="Y">Gene Expression Regulation, Developmental</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="Y">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058977" MajorTopicYN="Y">Molecular Sequence Annotation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059467" MajorTopicYN="Y">Transcriptome</DescriptorName></MeshHeading></MeshHeadingList><OtherID Source="NLM">PMC4567377</OtherID></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>04</Month><Day>19</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2015</Year><Month>08</Month><Day>17</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>9</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>9</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>6</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26359664</ArticleId><ArticleId IdType="doi">10.1371/journal.pone.0137450</ArticleId><ArticleId IdType="pii">PONE-D-15-16507</ArticleId><ArticleId IdType="pmc">PMC4567377</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Song, Wei" sort="Song, Wei" uniqKey="Song W" first="Wei" last="Song">Wei Song</name></noRegion><name sortKey="Jiang, Keji" sort="Jiang, Keji" uniqKey="Jiang K" first="Keji" last="Jiang">Keji Jiang</name><name sortKey="Lin, Yu" sort="Lin, Yu" uniqKey="Lin Y" first="Yu" last="Lin">Yu Lin</name><name sortKey="Ma, Lingbo" sort="Ma, Lingbo" uniqKey="Ma L" first="Lingbo" last="Ma">Lingbo Ma</name><name sortKey="Zhang, Fengying" sort="Zhang, Fengying" uniqKey="Zhang F" first="Fengying" last="Zhang">Fengying Zhang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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