In-depth transcriptome analysis of Larimichthys polyactis, de novo assembly, functional annotation
Larimichthys polyactis (small yellow croaker) is a commercially important marine benthic fish, and is the main catching target of fisheries in China, Japan and Korea. Researches across different fields have progressed the understanding of this species; however, no genomics studies of this fish have...
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| Veröffentlicht in: | Marine genomics 2017-06, Vol.33, p.27-29 |
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| creator | Liu, Lian-Wei Sui, You-Zhen Zhu, Wen-Bin Guo, Ai Xu, Kai-Da Zhou, Yong-Dong |
| description | Larimichthys polyactis (small yellow croaker) is a commercially important marine benthic fish, and is the main catching target of fisheries in China, Japan and Korea. Researches across different fields have progressed the understanding of this species; however, no genomics studies of this fish have been reported so far. In this study, we performed de novo transcriptome sequencing of eight cDNA libraries from brain, gill, heart, intestine, liver, muscle, ovary, and testis tissues of L. polyactis. A total of 182,227,948 paired-end reads (>200bp) were generated, from which 134,439 transcripts were assembled. These transcripts yielded a total of 93,990 non-redundant transcripts (unigenes) that were assigned functional annotations based on BlastX searches (E-value |
| doi_str_mv | 10.1016/j.margen.2017.02.002 |
| format | Article |
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Researches across different fields have progressed the understanding of this species; however, no genomics studies of this fish have been reported so far. In this study, we performed de novo transcriptome sequencing of eight cDNA libraries from brain, gill, heart, intestine, liver, muscle, ovary, and testis tissues of L. polyactis. A total of 182,227,948 paired-end reads (>200bp) were generated, from which 134,439 transcripts were assembled. These transcripts yielded a total of 93,990 non-redundant transcripts (unigenes) that were assigned functional annotations based on BlastX searches (E-value<1×10−5) against the following databases: NCBI NR, Swiss-Prot, TrEMBL, CDD, Pfam, and COG. In addition, 12,539 simple sequence repeats (SSRs) were identified. Our study provides a valuable resource of L. polyactis transcriptomic data that are expected to be useful for gene expression and functional studies of L. polyactis.</description><identifier>ISSN: 1874-7787</identifier><identifier>EISSN: 1876-7478</identifier><identifier>DOI: 10.1016/j.margen.2017.02.002</identifier><identifier>PMID: 28258924</identifier><language>eng</language><publisher>Netherlands: Elsevier B.V</publisher><subject>Animals ; China ; Female ; Functional annotation ; Gene Expression Profiling ; Gene Library ; Illumina HiSeq 2500 ; Larimichthys polyactis ; Male ; Microsatellite Repeats ; Molecular Sequence Annotation ; Perciformes - genetics ; Transcriptome</subject><ispartof>Marine genomics, 2017-06, Vol.33, p.27-29</ispartof><rights>2017 Elsevier B.V.</rights><rights>Copyright © 2017 Elsevier B.V. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c362t-489159181702e004ed5fd94649a4af1b0e3d2c3ad04516d06ecd80a62f410b9f3</citedby><cites>FETCH-LOGICAL-c362t-489159181702e004ed5fd94649a4af1b0e3d2c3ad04516d06ecd80a62f410b9f3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.margen.2017.02.002$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3548,27922,27923,45993</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28258924$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Liu, Lian-Wei</creatorcontrib><creatorcontrib>Sui, You-Zhen</creatorcontrib><creatorcontrib>Zhu, Wen-Bin</creatorcontrib><creatorcontrib>Guo, Ai</creatorcontrib><creatorcontrib>Xu, Kai-Da</creatorcontrib><creatorcontrib>Zhou, Yong-Dong</creatorcontrib><title>In-depth transcriptome analysis of Larimichthys polyactis, de novo assembly, functional annotation</title><title>Marine genomics</title><addtitle>Mar Genomics</addtitle><description>Larimichthys polyactis (small yellow croaker) is a commercially important marine benthic fish, and is the main catching target of fisheries in China, Japan and Korea. Researches across different fields have progressed the understanding of this species; however, no genomics studies of this fish have been reported so far. In this study, we performed de novo transcriptome sequencing of eight cDNA libraries from brain, gill, heart, intestine, liver, muscle, ovary, and testis tissues of L. polyactis. A total of 182,227,948 paired-end reads (>200bp) were generated, from which 134,439 transcripts were assembled. These transcripts yielded a total of 93,990 non-redundant transcripts (unigenes) that were assigned functional annotations based on BlastX searches (E-value<1×10−5) against the following databases: NCBI NR, Swiss-Prot, TrEMBL, CDD, Pfam, and COG. In addition, 12,539 simple sequence repeats (SSRs) were identified. Our study provides a valuable resource of L. polyactis transcriptomic data that are expected to be useful for gene expression and functional studies of L. polyactis.</description><subject>Animals</subject><subject>China</subject><subject>Female</subject><subject>Functional annotation</subject><subject>Gene Expression Profiling</subject><subject>Gene Library</subject><subject>Illumina HiSeq 2500</subject><subject>Larimichthys polyactis</subject><subject>Male</subject><subject>Microsatellite Repeats</subject><subject>Molecular Sequence Annotation</subject><subject>Perciformes - genetics</subject><subject>Transcriptome</subject><issn>1874-7787</issn><issn>1876-7478</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kE9v1DAQxSMEoqXwDRDykUMTxo7Xdi5IqOJPpZW4wNly7AnrVWIH21sp375etnDkNDOa9-Zpfk3zlkJHgYoPx24x6ReGjgGVHbAOgD1rrqmSopVcqud_et5KqeRV8yrnI4BgUsHL5ooptlMD49fNeB9ah2s5kJJMyDb5tcQFiQlm3rLPJE5kb5JfvD2Uw5bJGufN2OLzLXFIQnyIxOSMyzhvt2Q6hbqK1VsPhFjMeXjdvJjMnPHNU71pfn75_OPuW7v__vX-7tO-tb1gpeVqoLuBKiqBIQBHt5vcwAUfDDcTHQF7x2xvHPAdFQ4EWqfACDZxCuMw9TfN-8vdNcXfJ8xFLz5bnGcTMJ6yPtPgXPQ9q1J-kdoUc0446bW-aNKmKegzXX3UF7r6TFcD05Vutb17SjiNC7p_pr84q-DjRYD1zwePSWfrMVh0PqEt2kX__4RHZMCOYQ</recordid><startdate>201706</startdate><enddate>201706</enddate><creator>Liu, Lian-Wei</creator><creator>Sui, You-Zhen</creator><creator>Zhu, Wen-Bin</creator><creator>Guo, Ai</creator><creator>Xu, Kai-Da</creator><creator>Zhou, Yong-Dong</creator><general>Elsevier B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>201706</creationdate><title>In-depth transcriptome analysis of Larimichthys polyactis, de novo assembly, functional annotation</title><author>Liu, Lian-Wei ; Sui, You-Zhen ; Zhu, Wen-Bin ; Guo, Ai ; Xu, Kai-Da ; Zhou, Yong-Dong</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c362t-489159181702e004ed5fd94649a4af1b0e3d2c3ad04516d06ecd80a62f410b9f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Animals</topic><topic>China</topic><topic>Female</topic><topic>Functional annotation</topic><topic>Gene Expression Profiling</topic><topic>Gene Library</topic><topic>Illumina HiSeq 2500</topic><topic>Larimichthys polyactis</topic><topic>Male</topic><topic>Microsatellite Repeats</topic><topic>Molecular Sequence Annotation</topic><topic>Perciformes - genetics</topic><topic>Transcriptome</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Liu, Lian-Wei</creatorcontrib><creatorcontrib>Sui, You-Zhen</creatorcontrib><creatorcontrib>Zhu, Wen-Bin</creatorcontrib><creatorcontrib>Guo, Ai</creatorcontrib><creatorcontrib>Xu, Kai-Da</creatorcontrib><creatorcontrib>Zhou, Yong-Dong</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Marine genomics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Liu, Lian-Wei</au><au>Sui, You-Zhen</au><au>Zhu, Wen-Bin</au><au>Guo, Ai</au><au>Xu, Kai-Da</au><au>Zhou, Yong-Dong</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>In-depth transcriptome analysis of Larimichthys polyactis, de novo assembly, functional annotation</atitle><jtitle>Marine genomics</jtitle><addtitle>Mar Genomics</addtitle><date>2017-06</date><risdate>2017</risdate><volume>33</volume><spage>27</spage><epage>29</epage><pages>27-29</pages><issn>1874-7787</issn><eissn>1876-7478</eissn><abstract>Larimichthys polyactis (small yellow croaker) is a commercially important marine benthic fish, and is the main catching target of fisheries in China, Japan and Korea. Researches across different fields have progressed the understanding of this species; however, no genomics studies of this fish have been reported so far. In this study, we performed de novo transcriptome sequencing of eight cDNA libraries from brain, gill, heart, intestine, liver, muscle, ovary, and testis tissues of L. polyactis. A total of 182,227,948 paired-end reads (>200bp) were generated, from which 134,439 transcripts were assembled. These transcripts yielded a total of 93,990 non-redundant transcripts (unigenes) that were assigned functional annotations based on BlastX searches (E-value<1×10−5) against the following databases: NCBI NR, Swiss-Prot, TrEMBL, CDD, Pfam, and COG. In addition, 12,539 simple sequence repeats (SSRs) were identified. Our study provides a valuable resource of L. polyactis transcriptomic data that are expected to be useful for gene expression and functional studies of L. polyactis.</abstract><cop>Netherlands</cop><pub>Elsevier B.V</pub><pmid>28258924</pmid><doi>10.1016/j.margen.2017.02.002</doi><tpages>3</tpages></addata></record> |
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| identifier | ISSN: 1874-7787 |
| ispartof | Marine genomics, 2017-06, Vol.33, p.27-29 |
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| language | eng |
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| source | MEDLINE; ScienceDirect Journals (5 years ago - present) |
| subjects | Animals China Female Functional annotation Gene Expression Profiling Gene Library Illumina HiSeq 2500 Larimichthys polyactis Male Microsatellite Repeats Molecular Sequence Annotation Perciformes - genetics Transcriptome |
| title | In-depth transcriptome analysis of Larimichthys polyactis, de novo assembly, functional annotation |
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