Accumulation, functional annotation, and comparative analysis of expressed sequence tags in eggplant ( Solanum melongena L.), the third pole of the genus Solanum species after tomato and potato
Eggplant ( Solanum melongena L.) is a widely grown vegetable crop that belongs to the genus Solanum, which is comprised of more than 1000 species of wide genetic and phenotypic variation. Unlike tomato and potato, Solanum crops that belong to subgenus Potatoe and have been targets for comprehensive...
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| Veröffentlicht in: | Gene 2010, Vol.450 (1), p.76-84 |
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| creator | Fukuoka, Hiroyuki Yamaguchi, Hirotaka Nunome, Tsukasa Negoro, Satomi Miyatake, Koji Ohyama, Akio |
| description | Eggplant (
Solanum melongena L.) is a widely grown vegetable crop that belongs to the genus
Solanum, which is comprised of more than 1000 species of wide genetic and phenotypic variation. Unlike tomato and potato,
Solanum crops that belong to subgenus
Potatoe and have been targets for comprehensive genomic studies, eggplant is endemic to the Old World and belongs to a different subgenus,
Leptostemonum, and therefore, would be a unique member for comparative molecular biology in
Solanum. In this study, more than 60,000 eggplant cDNA clones from various tissues and treatments were sequenced from both the 5′- and 3′-ends, and a unigene set consisting of 16,245 unique sequences was constructed. Functional annotations based on sequence similarity to known plant reference datasets revealed a distribution of functional categories almost similar to that of tomato, while 1316 unigenes were suggested to be eggplant-specific. Sequence-based comparative analysis using putative orthologous gene groups setup by reciprocal sequence comparison among six solanaceous species suggested that eggplant and its wild ally
Solanum torvum were clustered separately from subgenus
Potatoe species, and then, all
Solanum species were clustered separately from the genus
Capsicum. Microsatellite motif distribution was different among species and likely to be coincident with the phylogenetic relationships. Furthermore, the eggplant unigene dataset exhibited its utility in transcriptome analysis by the SAGE strategy where a considerable number of short tag sequences of interest were successfully assigned to unigenes and their functional annotations. The eggplant ESTs and 16k unigene set developed in this study would be a useful resource not only for molecular genetics and breeding in eggplant itself, but for expanding the scope of comparative biology in
Solanum species. |
| doi_str_mv | 10.1016/j.gene.2009.10.006 |
| format | Article |
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Solanum melongena L.) is a widely grown vegetable crop that belongs to the genus
Solanum, which is comprised of more than 1000 species of wide genetic and phenotypic variation. Unlike tomato and potato,
Solanum crops that belong to subgenus
Potatoe and have been targets for comprehensive genomic studies, eggplant is endemic to the Old World and belongs to a different subgenus,
Leptostemonum, and therefore, would be a unique member for comparative molecular biology in
Solanum. In this study, more than 60,000 eggplant cDNA clones from various tissues and treatments were sequenced from both the 5′- and 3′-ends, and a unigene set consisting of 16,245 unique sequences was constructed. Functional annotations based on sequence similarity to known plant reference datasets revealed a distribution of functional categories almost similar to that of tomato, while 1316 unigenes were suggested to be eggplant-specific. Sequence-based comparative analysis using putative orthologous gene groups setup by reciprocal sequence comparison among six solanaceous species suggested that eggplant and its wild ally
Solanum torvum were clustered separately from subgenus
Potatoe species, and then, all
Solanum species were clustered separately from the genus
Capsicum. Microsatellite motif distribution was different among species and likely to be coincident with the phylogenetic relationships. Furthermore, the eggplant unigene dataset exhibited its utility in transcriptome analysis by the SAGE strategy where a considerable number of short tag sequences of interest were successfully assigned to unigenes and their functional annotations. The eggplant ESTs and 16k unigene set developed in this study would be a useful resource not only for molecular genetics and breeding in eggplant itself, but for expanding the scope of comparative biology in
Solanum species.</description><identifier>ISSN: 0378-1119</identifier><identifier>EISSN: 1879-0038</identifier><identifier>DOI: 10.1016/j.gene.2009.10.006</identifier><identifier>PMID: 19857557</identifier><language>eng</language><publisher>Netherlands: Elsevier B.V</publisher><subject>EST ; Expressed Sequence Tags ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Lycopersicon esculentum - classification ; Lycopersicon esculentum - genetics ; Phylogeny ; Solanaceae ; Solanum melongena - classification ; Solanum melongena - genetics ; Solanum tuberosum - genetics ; Transcriptome ; Unigene</subject><ispartof>Gene, 2010, Vol.450 (1), p.76-84</ispartof><rights>2009 Elsevier B.V.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c421t-64445150947750d4ce064dca3a2e9aa383ce8abefe585218b54abaa3a4568d2a3</citedby><cites>FETCH-LOGICAL-c421t-64445150947750d4ce064dca3a2e9aa383ce8abefe585218b54abaa3a4568d2a3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.gene.2009.10.006$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3550,4024,27923,27924,27925,45995</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19857557$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Fukuoka, Hiroyuki</creatorcontrib><creatorcontrib>Yamaguchi, Hirotaka</creatorcontrib><creatorcontrib>Nunome, Tsukasa</creatorcontrib><creatorcontrib>Negoro, Satomi</creatorcontrib><creatorcontrib>Miyatake, Koji</creatorcontrib><creatorcontrib>Ohyama, Akio</creatorcontrib><title>Accumulation, functional annotation, and comparative analysis of expressed sequence tags in eggplant ( Solanum melongena L.), the third pole of the genus Solanum species after tomato and potato</title><title>Gene</title><addtitle>Gene</addtitle><description>Eggplant (
Solanum melongena L.) is a widely grown vegetable crop that belongs to the genus
Solanum, which is comprised of more than 1000 species of wide genetic and phenotypic variation. Unlike tomato and potato,
Solanum crops that belong to subgenus
Potatoe and have been targets for comprehensive genomic studies, eggplant is endemic to the Old World and belongs to a different subgenus,
Leptostemonum, and therefore, would be a unique member for comparative molecular biology in
Solanum. In this study, more than 60,000 eggplant cDNA clones from various tissues and treatments were sequenced from both the 5′- and 3′-ends, and a unigene set consisting of 16,245 unique sequences was constructed. Functional annotations based on sequence similarity to known plant reference datasets revealed a distribution of functional categories almost similar to that of tomato, while 1316 unigenes were suggested to be eggplant-specific. Sequence-based comparative analysis using putative orthologous gene groups setup by reciprocal sequence comparison among six solanaceous species suggested that eggplant and its wild ally
Solanum torvum were clustered separately from subgenus
Potatoe species, and then, all
Solanum species were clustered separately from the genus
Capsicum. Microsatellite motif distribution was different among species and likely to be coincident with the phylogenetic relationships. Furthermore, the eggplant unigene dataset exhibited its utility in transcriptome analysis by the SAGE strategy where a considerable number of short tag sequences of interest were successfully assigned to unigenes and their functional annotations. The eggplant ESTs and 16k unigene set developed in this study would be a useful resource not only for molecular genetics and breeding in eggplant itself, but for expanding the scope of comparative biology in
Solanum species.</description><subject>EST</subject><subject>Expressed Sequence Tags</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Plant</subject><subject>Lycopersicon esculentum - classification</subject><subject>Lycopersicon esculentum - genetics</subject><subject>Phylogeny</subject><subject>Solanaceae</subject><subject>Solanum melongena - classification</subject><subject>Solanum melongena - genetics</subject><subject>Solanum tuberosum - genetics</subject><subject>Transcriptome</subject><subject>Unigene</subject><issn>0378-1119</issn><issn>1879-0038</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9UU1v1DAQtRAVXQp_gAPyjSI1wU7sxJF6qSo-Kq3EAThbs85k61ViB9up2p_HP8NhV3DDF4-f3zy9mUfIG85Kznjz4VDu0WFZMdZloGSseUY2XLVdwVitnpMNq1tVcM67c_IyxgPLR8rqBTnnnZKtlO2G_LoxZpmWEZL17ooOizNrBSMF53w6weB6avw0Q8jAA-Y3jE_RRuoHio9zwBixpxF_LugM0gT7SK2juN_PI7hEL-k3n4tlohOO3mXbQLfl-yua7jP73oaezn7EVW5F8v8S_7bEGY3FSGFIGGjyEyT_x9G8-vOvyNkAY8TXp_uC_Pj08fvtl2L79fPd7c22MKLiqWiEEJJL1om2lawXBlkjegM1VNgB1Ko2qGCHA0olK652UsAu4yBko_oK6gvy7qg7B5_njElPNhocs0n0S9RtLXgnGqEyszoyTfAxBhz0HOwE4Ulzptfk9EGvyek1uRXLyeWmtyf5ZTdh_6_lFFUmXB8JmId8sBh0zGvJ6-5tQJN07-3_9H8DRzuuJA</recordid><startdate>2010</startdate><enddate>2010</enddate><creator>Fukuoka, Hiroyuki</creator><creator>Yamaguchi, Hirotaka</creator><creator>Nunome, Tsukasa</creator><creator>Negoro, Satomi</creator><creator>Miyatake, Koji</creator><creator>Ohyama, Akio</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>2010</creationdate><title>Accumulation, functional annotation, and comparative analysis of expressed sequence tags in eggplant ( Solanum melongena L.), the third pole of the genus Solanum species after tomato and potato</title><author>Fukuoka, Hiroyuki ; Yamaguchi, Hirotaka ; Nunome, Tsukasa ; Negoro, Satomi ; Miyatake, Koji ; Ohyama, Akio</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c421t-64445150947750d4ce064dca3a2e9aa383ce8abefe585218b54abaa3a4568d2a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>EST</topic><topic>Expressed Sequence Tags</topic><topic>Gene Expression Profiling</topic><topic>Gene Expression Regulation, Plant</topic><topic>Lycopersicon esculentum - classification</topic><topic>Lycopersicon esculentum - genetics</topic><topic>Phylogeny</topic><topic>Solanaceae</topic><topic>Solanum melongena - classification</topic><topic>Solanum melongena - genetics</topic><topic>Solanum tuberosum - genetics</topic><topic>Transcriptome</topic><topic>Unigene</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Fukuoka, Hiroyuki</creatorcontrib><creatorcontrib>Yamaguchi, Hirotaka</creatorcontrib><creatorcontrib>Nunome, Tsukasa</creatorcontrib><creatorcontrib>Negoro, Satomi</creatorcontrib><creatorcontrib>Miyatake, Koji</creatorcontrib><creatorcontrib>Ohyama, Akio</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>Gene</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Fukuoka, Hiroyuki</au><au>Yamaguchi, Hirotaka</au><au>Nunome, Tsukasa</au><au>Negoro, Satomi</au><au>Miyatake, Koji</au><au>Ohyama, Akio</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Accumulation, functional annotation, and comparative analysis of expressed sequence tags in eggplant ( Solanum melongena L.), the third pole of the genus Solanum species after tomato and potato</atitle><jtitle>Gene</jtitle><addtitle>Gene</addtitle><date>2010</date><risdate>2010</risdate><volume>450</volume><issue>1</issue><spage>76</spage><epage>84</epage><pages>76-84</pages><issn>0378-1119</issn><eissn>1879-0038</eissn><abstract>Eggplant (
Solanum melongena L.) is a widely grown vegetable crop that belongs to the genus
Solanum, which is comprised of more than 1000 species of wide genetic and phenotypic variation. Unlike tomato and potato,
Solanum crops that belong to subgenus
Potatoe and have been targets for comprehensive genomic studies, eggplant is endemic to the Old World and belongs to a different subgenus,
Leptostemonum, and therefore, would be a unique member for comparative molecular biology in
Solanum. In this study, more than 60,000 eggplant cDNA clones from various tissues and treatments were sequenced from both the 5′- and 3′-ends, and a unigene set consisting of 16,245 unique sequences was constructed. Functional annotations based on sequence similarity to known plant reference datasets revealed a distribution of functional categories almost similar to that of tomato, while 1316 unigenes were suggested to be eggplant-specific. Sequence-based comparative analysis using putative orthologous gene groups setup by reciprocal sequence comparison among six solanaceous species suggested that eggplant and its wild ally
Solanum torvum were clustered separately from subgenus
Potatoe species, and then, all
Solanum species were clustered separately from the genus
Capsicum. Microsatellite motif distribution was different among species and likely to be coincident with the phylogenetic relationships. Furthermore, the eggplant unigene dataset exhibited its utility in transcriptome analysis by the SAGE strategy where a considerable number of short tag sequences of interest were successfully assigned to unigenes and their functional annotations. The eggplant ESTs and 16k unigene set developed in this study would be a useful resource not only for molecular genetics and breeding in eggplant itself, but for expanding the scope of comparative biology in
Solanum species.</abstract><cop>Netherlands</cop><pub>Elsevier B.V</pub><pmid>19857557</pmid><doi>10.1016/j.gene.2009.10.006</doi><tpages>9</tpages></addata></record> |
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| source | MEDLINE; Elsevier ScienceDirect Journals Complete |
| subjects | EST Expressed Sequence Tags Gene Expression Profiling Gene Expression Regulation, Plant Lycopersicon esculentum - classification Lycopersicon esculentum - genetics Phylogeny Solanaceae Solanum melongena - classification Solanum melongena - genetics Solanum tuberosum - genetics Transcriptome Unigene |
| title | Accumulation, functional annotation, and comparative analysis of expressed sequence tags in eggplant ( Solanum melongena L.), the third pole of the genus Solanum species after tomato and potato |
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