Transcriptome analysis of the mud crab (Scylla paramamosain) by 454 deep sequencing: assembly, annotation, and marker discovery
In this study, we reported the characterization of the first transcriptome of the mud crab (Scylla paramamosain). Pooled cDNAs of four tissue types from twelve wild individuals were sequenced using the Roche 454 FLX platform. Analysis performed included de novo assembly of transcriptome sequences, f...
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| creator | Ma, Hongyu Ma, Chunyan Li, Shujuan Jiang, Wei Li, Xincang Liu, Yuexing Ma, Lingbo |
| description | In this study, we reported the characterization of the first transcriptome of the mud crab (Scylla paramamosain). Pooled cDNAs of four tissue types from twelve wild individuals were sequenced using the Roche 454 FLX platform. Analysis performed included de novo assembly of transcriptome sequences, functional annotation, and molecular marker discovery. A total of 1,314,101 high quality reads with an average length of 411 bp were generated by 454 sequencing on a mixed cDNA library. De novo assembly of these 1,314,101 reads produced 76,778 contigs (consisting of 818,154 reads) with 5.4-fold average sequencing coverage. The remaining 495,947 reads were singletons. A total of 78,268 unigenes were identified based on sequence similarity with known proteins (E≤0.00001) in UniProt and non-redundant protein databases. Meanwhile, 44,433 sequences were identified (E≤0.00001) using a BLASTN search against the NCBI nucleotide database. Gene Ontology (GO) analysis indicated that biosynthetic process, cell part, and ion binding were the most abundant terms in biological process, cellular component, and molecular function categories, respectively. Kyoto Encyclopedia of Genes and Genome (KEGG) pathway analysis revealed that 4,878 unigenes distributed in 281 different pathways. In addition, 19,011 microsatellites and 37,063 potential single nucleotide polymorphisms were detected from the transcriptome of S. paramamosain. Finally, thirty polymorphic microsatellite markers were developed and used to assess genetic diversity of a wild population of S. paramamosain. So far, existing sequence resources for S. paramamosain are extremely limited. The present study provides a characterization of transcriptome from multiple tissues and individuals, as well as an assessment of genetic diversity of a wild population. These sequence resources will facilitate the investigation of population genetic diversity, the development of genetic maps, and the conduct of molecular marker-assisted breeding in S. paramamosain and related crab species. |
| doi_str_mv | 10.1371/journal.pone.0102668 |
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Pooled cDNAs of four tissue types from twelve wild individuals were sequenced using the Roche 454 FLX platform. Analysis performed included de novo assembly of transcriptome sequences, functional annotation, and molecular marker discovery. A total of 1,314,101 high quality reads with an average length of 411 bp were generated by 454 sequencing on a mixed cDNA library. De novo assembly of these 1,314,101 reads produced 76,778 contigs (consisting of 818,154 reads) with 5.4-fold average sequencing coverage. The remaining 495,947 reads were singletons. A total of 78,268 unigenes were identified based on sequence similarity with known proteins (E≤0.00001) in UniProt and non-redundant protein databases. Meanwhile, 44,433 sequences were identified (E≤0.00001) using a BLASTN search against the NCBI nucleotide database. Gene Ontology (GO) analysis indicated that biosynthetic process, cell part, and ion binding were the most abundant terms in biological process, cellular component, and molecular function categories, respectively. Kyoto Encyclopedia of Genes and Genome (KEGG) pathway analysis revealed that 4,878 unigenes distributed in 281 different pathways. In addition, 19,011 microsatellites and 37,063 potential single nucleotide polymorphisms were detected from the transcriptome of S. paramamosain. Finally, thirty polymorphic microsatellite markers were developed and used to assess genetic diversity of a wild population of S. paramamosain. So far, existing sequence resources for S. paramamosain are extremely limited. The present study provides a characterization of transcriptome from multiple tissues and individuals, as well as an assessment of genetic diversity of a wild population. These sequence resources will facilitate the investigation of population genetic diversity, the development of genetic maps, and the conduct of molecular marker-assisted breeding in S. paramamosain and related crab species.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0102668</identifier><identifier>PMID: 25054331</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Animals ; Annotations ; Aquaculture ; Arthropod Proteins - genetics ; Assembly ; Bioinformatics ; Biological activity ; Biology and Life Sciences ; Brachyura - genetics ; Breeding ; Chromosomes ; Crabs ; Crustaceans ; Deoxyribonucleic acid ; DNA ; Encyclopedias ; Exploitation ; Fish ; Fishery sciences ; Gene expression ; Gene Expression Profiling ; Gene Library ; Gene mapping ; Gene Ontology ; Genetic diversity ; Genetic markers ; Genomes ; Genomics ; High-Throughput Nucleotide Sequencing - methods ; Laboratories ; Microsatellite Repeats - genetics ; Microsatellites ; Molecular Sequence Annotation ; Mud ; Polymorphism, Single Nucleotide ; Population ; Population genetics ; Proteins ; Scylla ; Scylla paramamosain ; Signal Transduction - genetics ; Single nucleotide polymorphisms ; Single-nucleotide polymorphism ; Tissues</subject><ispartof>PloS one, 2014-07, Vol.9 (7), p.e102668-e102668</ispartof><rights>COPYRIGHT 2014 Public Library of Science</rights><rights>2014 Ma et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2014 Ma et al 2014 Ma et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c593t-e5558058577b6108df8d9e3c54fd6419320a3b474e9d81fcd522c9a513ecd03f3</citedby><cites>FETCH-LOGICAL-c593t-e5558058577b6108df8d9e3c54fd6419320a3b474e9d81fcd522c9a513ecd03f3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4108364/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4108364/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25054331$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Gibas, Cynthia</contributor><creatorcontrib>Ma, Hongyu</creatorcontrib><creatorcontrib>Ma, Chunyan</creatorcontrib><creatorcontrib>Li, Shujuan</creatorcontrib><creatorcontrib>Jiang, Wei</creatorcontrib><creatorcontrib>Li, Xincang</creatorcontrib><creatorcontrib>Liu, Yuexing</creatorcontrib><creatorcontrib>Ma, Lingbo</creatorcontrib><title>Transcriptome analysis of the mud crab (Scylla paramamosain) by 454 deep sequencing: assembly, annotation, and marker discovery</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>In this study, we reported the characterization of the first transcriptome of the mud crab (Scylla paramamosain). Pooled cDNAs of four tissue types from twelve wild individuals were sequenced using the Roche 454 FLX platform. Analysis performed included de novo assembly of transcriptome sequences, functional annotation, and molecular marker discovery. A total of 1,314,101 high quality reads with an average length of 411 bp were generated by 454 sequencing on a mixed cDNA library. De novo assembly of these 1,314,101 reads produced 76,778 contigs (consisting of 818,154 reads) with 5.4-fold average sequencing coverage. The remaining 495,947 reads were singletons. A total of 78,268 unigenes were identified based on sequence similarity with known proteins (E≤0.00001) in UniProt and non-redundant protein databases. Meanwhile, 44,433 sequences were identified (E≤0.00001) using a BLASTN search against the NCBI nucleotide database. Gene Ontology (GO) analysis indicated that biosynthetic process, cell part, and ion binding were the most abundant terms in biological process, cellular component, and molecular function categories, respectively. Kyoto Encyclopedia of Genes and Genome (KEGG) pathway analysis revealed that 4,878 unigenes distributed in 281 different pathways. In addition, 19,011 microsatellites and 37,063 potential single nucleotide polymorphisms were detected from the transcriptome of S. paramamosain. Finally, thirty polymorphic microsatellite markers were developed and used to assess genetic diversity of a wild population of S. paramamosain. So far, existing sequence resources for S. paramamosain are extremely limited. The present study provides a characterization of transcriptome from multiple tissues and individuals, as well as an assessment of genetic diversity of a wild population. These sequence resources will facilitate the investigation of population genetic diversity, the development of genetic maps, and the conduct of molecular marker-assisted breeding in S. paramamosain and related crab species.</description><subject>Analysis</subject><subject>Animals</subject><subject>Annotations</subject><subject>Aquaculture</subject><subject>Arthropod Proteins - genetics</subject><subject>Assembly</subject><subject>Bioinformatics</subject><subject>Biological activity</subject><subject>Biology and Life Sciences</subject><subject>Brachyura - genetics</subject><subject>Breeding</subject><subject>Chromosomes</subject><subject>Crabs</subject><subject>Crustaceans</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Encyclopedias</subject><subject>Exploitation</subject><subject>Fish</subject><subject>Fishery sciences</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Library</subject><subject>Gene mapping</subject><subject>Gene Ontology</subject><subject>Genetic diversity</subject><subject>Genetic markers</subject><subject>Genomes</subject><subject>Genomics</subject><subject>High-Throughput Nucleotide Sequencing - methods</subject><subject>Laboratories</subject><subject>Microsatellite Repeats - genetics</subject><subject>Microsatellites</subject><subject>Molecular Sequence Annotation</subject><subject>Mud</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Population</subject><subject>Population genetics</subject><subject>Proteins</subject><subject>Scylla</subject><subject>Scylla paramamosain</subject><subject>Signal Transduction - genetics</subject><subject>Single nucleotide polymorphisms</subject><subject>Single-nucleotide polymorphism</subject><subject>Tissues</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNptUk1v1DAUjBCIlsI_QGCJS5HYxY4_4nBAqio-KlXiQDlbjv2y9ZLYwc5Wyom_jtNNqy6qfLBlz5v3ZjxF8ZrgNaEV-bgNu-h1tx6ChzUmuBRCPimOSU3LlSgxffrgfFS8SGmLMadSiOfFUckxZ5SS4-LvVdQ-meiGMfSAdGackksotGi8BtTvLDJRN-j0p5m6TqNBR93rPiTt_HvUTIhxhizAgBL82YE3zm8-IZ0S9E03fciEPox6dMHPZ4t6HX9DRNYlE24gTi-LZ63uErxa9pPi19cvV-ffV5c_vl2cn12uDK_puALOucRc8qpqBMHSttLWQA1nrRVs1ok1bVjFoLaStMbysjS15oSCsZi29KR4u-cdupDU4l1ShLNK1qWsZEZc7BE26K0aosujTipop24vQtwoHUdnOlCllLYhmT27yLiQWhhCSINNxSWpoMpcn5duu6YHa8CPUXcHpIcv3l2rTbhRLGujgmWC04UghmxrGlWfHYP8Ax7C7nZuKSgTfIa--w_6uLoFtdFZgPNtyH3NTKrOGJGkrCThGbV-BJWXhd6ZHLTW5fuDArYvMDGkFKG910iwmmN6N4yaY6qWmOayNw_9uS-6yyX9B0IV5D8</recordid><startdate>20140723</startdate><enddate>20140723</enddate><creator>Ma, Hongyu</creator><creator>Ma, Chunyan</creator><creator>Li, Shujuan</creator><creator>Jiang, Wei</creator><creator>Li, Xincang</creator><creator>Liu, Yuexing</creator><creator>Ma, Lingbo</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</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>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20140723</creationdate><title>Transcriptome analysis of the mud crab (Scylla paramamosain) by 454 deep sequencing: assembly, annotation, and marker discovery</title><author>Ma, Hongyu ; Ma, Chunyan ; Li, Shujuan ; Jiang, Wei ; Li, Xincang ; Liu, Yuexing ; Ma, Lingbo</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c593t-e5558058577b6108df8d9e3c54fd6419320a3b474e9d81fcd522c9a513ecd03f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Analysis</topic><topic>Animals</topic><topic>Annotations</topic><topic>Aquaculture</topic><topic>Arthropod Proteins - genetics</topic><topic>Assembly</topic><topic>Bioinformatics</topic><topic>Biological activity</topic><topic>Biology and Life Sciences</topic><topic>Brachyura - genetics</topic><topic>Breeding</topic><topic>Chromosomes</topic><topic>Crabs</topic><topic>Crustaceans</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>Encyclopedias</topic><topic>Exploitation</topic><topic>Fish</topic><topic>Fishery sciences</topic><topic>Gene expression</topic><topic>Gene Expression Profiling</topic><topic>Gene Library</topic><topic>Gene mapping</topic><topic>Gene Ontology</topic><topic>Genetic diversity</topic><topic>Genetic markers</topic><topic>Genomes</topic><topic>Genomics</topic><topic>High-Throughput Nucleotide Sequencing - methods</topic><topic>Laboratories</topic><topic>Microsatellite Repeats - genetics</topic><topic>Microsatellites</topic><topic>Molecular Sequence Annotation</topic><topic>Mud</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Population</topic><topic>Population genetics</topic><topic>Proteins</topic><topic>Scylla</topic><topic>Scylla paramamosain</topic><topic>Signal Transduction - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ma, Hongyu</au><au>Ma, Chunyan</au><au>Li, Shujuan</au><au>Jiang, Wei</au><au>Li, Xincang</au><au>Liu, Yuexing</au><au>Ma, Lingbo</au><au>Gibas, Cynthia</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Transcriptome analysis of the mud crab (Scylla paramamosain) by 454 deep sequencing: assembly, annotation, and marker discovery</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2014-07-23</date><risdate>2014</risdate><volume>9</volume><issue>7</issue><spage>e102668</spage><epage>e102668</epage><pages>e102668-e102668</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>In this study, we reported the characterization of the first transcriptome of the mud crab (Scylla paramamosain). Pooled cDNAs of four tissue types from twelve wild individuals were sequenced using the Roche 454 FLX platform. Analysis performed included de novo assembly of transcriptome sequences, functional annotation, and molecular marker discovery. A total of 1,314,101 high quality reads with an average length of 411 bp were generated by 454 sequencing on a mixed cDNA library. De novo assembly of these 1,314,101 reads produced 76,778 contigs (consisting of 818,154 reads) with 5.4-fold average sequencing coverage. The remaining 495,947 reads were singletons. A total of 78,268 unigenes were identified based on sequence similarity with known proteins (E≤0.00001) in UniProt and non-redundant protein databases. Meanwhile, 44,433 sequences were identified (E≤0.00001) using a BLASTN search against the NCBI nucleotide database. Gene Ontology (GO) analysis indicated that biosynthetic process, cell part, and ion binding were the most abundant terms in biological process, cellular component, and molecular function categories, respectively. Kyoto Encyclopedia of Genes and Genome (KEGG) pathway analysis revealed that 4,878 unigenes distributed in 281 different pathways. In addition, 19,011 microsatellites and 37,063 potential single nucleotide polymorphisms were detected from the transcriptome of S. paramamosain. Finally, thirty polymorphic microsatellite markers were developed and used to assess genetic diversity of a wild population of S. paramamosain. So far, existing sequence resources for S. paramamosain are extremely limited. The present study provides a characterization of transcriptome from multiple tissues and individuals, as well as an assessment of genetic diversity of a wild population. These sequence resources will facilitate the investigation of population genetic diversity, the development of genetic maps, and the conduct of molecular marker-assisted breeding in S. paramamosain and related crab species.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>25054331</pmid><doi>10.1371/journal.pone.0102668</doi><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Analysis Animals Annotations Aquaculture Arthropod Proteins - genetics Assembly Bioinformatics Biological activity Biology and Life Sciences Brachyura - genetics Breeding Chromosomes Crabs Crustaceans Deoxyribonucleic acid DNA Encyclopedias Exploitation Fish Fishery sciences Gene expression Gene Expression Profiling Gene Library Gene mapping Gene Ontology Genetic diversity Genetic markers Genomes Genomics High-Throughput Nucleotide Sequencing - methods Laboratories Microsatellite Repeats - genetics Microsatellites Molecular Sequence Annotation Mud Polymorphism, Single Nucleotide Population Population genetics Proteins Scylla Scylla paramamosain Signal Transduction - genetics Single nucleotide polymorphisms Single-nucleotide polymorphism Tissues |
| title | Transcriptome analysis of the mud crab (Scylla paramamosain) by 454 deep sequencing: assembly, annotation, and marker discovery |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-29T12%3A07%3A47IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Transcriptome%20analysis%20of%20the%20mud%20crab%20(Scylla%20paramamosain)%20by%20454%20deep%20sequencing:%20assembly,%20annotation,%20and%20marker%20discovery&rft.jtitle=PloS%20one&rft.au=Ma,%20Hongyu&rft.date=2014-07-23&rft.volume=9&rft.issue=7&rft.spage=e102668&rft.epage=e102668&rft.pages=e102668-e102668&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0102668&rft_dat=%3Cgale_plos_%3EA418127815%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1547892878&rft_id=info:pmid/25054331&rft_galeid=A418127815&rft_doaj_id=oai_doaj_org_article_288db1a510544568a6c111b0c75817e7&rfr_iscdi=true |