RNA-sequencing of the sturgeon Acipenser baeri provides insights into expression dynamics of morphogenic differentiation and developmental regulatory genes in early versus late developmental stages.
Identifieur interne : 000039 ( PubMed/Checkpoint ); précédent : 000038; suivant : 000040RNA-sequencing of the sturgeon Acipenser baeri provides insights into expression dynamics of morphogenic differentiation and developmental regulatory genes in early versus late developmental stages.
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 :
- BMC genomics [ 1471-2164 ] ; 2016.
Abstract
Acipenser baeri, one of the critically endangered animals on the verge of extinction, is a key species for evolutionary, developmental, physiology and conservation studies and a standout amongst the most important food products worldwide. Though the transcriptome of the early development of A. baeri has been published recently, the transcriptome changes occurring in the transition from embryonic to late stages are still unknown. The aim of this work was to analyze the transcriptomes of embryonic and post-embryonic stages of A. baeri and identify differentially expressed genes (DEGs) and their expression patterns using mRNA collected from specimens at big yolk plug, wide neural plate and 64 day old sturgeon developmental stages for RNA-Seq.
DOI: 10.1186/s12864-016-2839-3
PubMed: 27502271
Affiliations:
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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, 200090, 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, 200090</wicri:regionArea><wicri:noRegion>200090</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Fengying" sort="Zhang, Fengying" uniqKey="Zhang F" first="Fengying" last="Zhang">Fengying Zhang</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Shanghai, 200090, 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, 200090</wicri:regionArea><wicri:noRegion>200090</wicri:noRegion></affiliation></author><author><name sortKey="Lin, Yu" sort="Lin, Yu" uniqKey="Lin Y" first="Yu" last="Lin">Yu Lin</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Shanghai, 200090, 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, 200090</wicri:regionArea><wicri:noRegion>200090</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, 200090, China. malingbo@vip.sina.com.</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, 200090</wicri:regionArea><wicri:noRegion>200090</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</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">Acipenser baeri, one of the critically endangered animals on the verge of extinction, is a key species for evolutionary, developmental, physiology and conservation studies and a standout amongst the most important food products worldwide. Though the transcriptome of the early development of A. baeri has been published recently, the transcriptome changes occurring in the transition from embryonic to late stages are still unknown. The aim of this work was to analyze the transcriptomes of embryonic and post-embryonic stages of A. baeri and identify differentially expressed genes (DEGs) and their expression patterns using mRNA collected from specimens at big yolk plug, wide neural plate and 64 day old sturgeon developmental stages for RNA-Seq.</div></front></TEI><pubmed><MedlineCitation Status="In-Data-Review" Owner="NLM"><PMID Version="1">27502271</PMID><DateCreated><Year>2016</Year><Month>08</Month><Day>09</Day></DateCreated><DateRevised><Year>2016</Year><Month>08</Month><Day>12</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>17</Volume><PubDate><Year>2016</Year><Month>Aug</Month><Day>08</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>RNA-sequencing of the sturgeon Acipenser baeri provides insights into expression dynamics of morphogenic differentiation and developmental regulatory genes in early versus late developmental stages.</ArticleTitle><Pagination><MedlinePgn>564</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12864-016-2839-3</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Acipenser baeri, one of the critically endangered animals on the verge of extinction, is a key species for evolutionary, developmental, physiology and conservation studies and a standout amongst the most important food products worldwide. Though the transcriptome of the early development of A. baeri has been published recently, the transcriptome changes occurring in the transition from embryonic to late stages are still unknown. The aim of this work was to analyze the transcriptomes of embryonic and post-embryonic stages of A. baeri and identify differentially expressed genes (DEGs) and their expression patterns using mRNA collected from specimens at big yolk plug, wide neural plate and 64 day old sturgeon developmental stages for RNA-Seq.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">The paired-end sequencing of the transcriptome of samples of A. baeri collected at two early (big yolk plug (T1, 32 h after fertilization) and wide neural plate formation (T2, 45 h after fertilization)) and one late (T22, 64 day old sturgeon) developmental stages using Illumina Hiseq2000 platform generated 64039846, 64635214 and 75293762 clean paired-end reads for T1, T2 and T22, respectively. After quality control, the sequencing reads were de novo assembled to generate a set of 149,265 unigenes with N50 value of 1277 bp. Functional annotation indicated that a substantial number of these unigenes had significant similarity with proteins in public databases. Differential expression profiling allowed the identification of 2789, 12,819 and 10,824 DEGs from the respective T1 vs. T2, T1 vs. T22 and T2 vs. T22 comparisons. High correlation of DEGs' features was recorded among early stages while significant divergences were observed when comparing the late stage with early stages. GO and KEGG enrichment analyses revealed the biological processes, cellular component, molecular functions and metabolic pathways associated with identified DEGs. The qRT-PCR performed for candidate genes in specimens confirmed the validity of the RNA-seq data.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">This study presents, for the first time, an extensive overview of RNA-Seq based characterization of the early and post-embryonic developmental transcriptomes of A. baeri and provided 149,265 gene sequences that will be potentially valuable for future molecular and genetic studies in A. baeri.</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, 200090, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>East China Sea fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, 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, 200090, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>East China Sea fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, 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, 200090, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>East China Sea fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, 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, 200090, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>East China Sea fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, 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, 200090, China. malingbo@vip.sina.com.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>East China Sea fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, China. malingbo@vip.sina.com.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>08</Month><Day>08</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><OtherID Source="NLM">PMC4977659</OtherID><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Acipenser baeri</Keyword><Keyword MajorTopicYN="N">Development</Keyword><Keyword MajorTopicYN="N">Differentially expressed genes</Keyword><Keyword MajorTopicYN="N">Embryonic stages</Keyword><Keyword MajorTopicYN="N">Late stages</Keyword><Keyword MajorTopicYN="N">Transcriptome sequencing</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>12</Month><Day>17</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2016</Year><Month>06</Month><Day>15</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>8</Month><Day>10</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>8</Month><Day>10</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>8</Month><Day>10</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">27502271</ArticleId><ArticleId IdType="doi">10.1186/s12864-016-2839-3</ArticleId><ArticleId IdType="pii">10.1186/s12864-016-2839-3</ArticleId><ArticleId IdType="pmc">PMC4977659</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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