Comparative transcriptome analysis of eggplant (Solanum melongena L.) and turkey berry (Solanum torvum Sw.): phylogenomics and disease resistance analysis
Identifieur interne : 000B54 ( Main/Exploration ); précédent : 000B53; suivant : 000B55Comparative transcriptome analysis of eggplant (Solanum melongena L.) and turkey berry (Solanum torvum Sw.): phylogenomics and disease resistance analysis
Auteurs : Xu Yang [République populaire de Chine] ; Yu-Fu Cheng [République populaire de Chine] ; Cao Deng [République populaire de Chine] ; Yan Ma [République populaire de Chine] ; Zhi-Wen Wang [République populaire de Chine] ; Xue-Hao Chen [République populaire de Chine] ; Lin-Bao Xue [République populaire de Chine]Source :
- BMC Genomics [ 1471-2164 ] ; 2014.
Abstract
Eggplant (
We built comprehensive, high-quality
This study provides a comprehensive transcriptome resource for two
The online version of this article (doi: 10.1186/1471-2164-15-412) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/1471-2164-15-412
PubMed: 24885385
PubMed Central: 4070557
Affiliations:
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225009 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture and Plant Protection of Yangzhou University, Yangzhou</wicri:regionArea><wicri:noRegion>Yangzhou</wicri:noRegion></affiliation></author><author><name sortKey="Deng, Cao" sort="Deng, Cao" uniqKey="Deng C" first="Cao" last="Deng">Cao Deng</name><affiliation wicri:level="1"><nlm:aff id="Aff10">PubBio-Tech Services Corporation, Wuhan, 430070 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>PubBio-Tech Services Corporation, Wuhan</wicri:regionArea><wicri:noRegion>Wuhan</wicri:noRegion></affiliation></author><author><name sortKey="Ma, Yan" sort="Ma, Yan" uniqKey="Ma Y" first="Yan" last="Ma">Yan Ma</name><affiliation wicri:level="1"><nlm:aff id="Aff9">College of Horticulture and Plant Protection of Yangzhou University, Yangzhou, 225009 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture and Plant Protection of Yangzhou University, Yangzhou</wicri:regionArea><wicri:noRegion>Yangzhou</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Zhi Wen" sort="Wang, Zhi Wen" uniqKey="Wang Z" first="Zhi-Wen" last="Wang">Zhi-Wen Wang</name><affiliation wicri:level="1"><nlm:aff id="Aff10">PubBio-Tech Services Corporation, Wuhan, 430070 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>PubBio-Tech Services Corporation, Wuhan</wicri:regionArea><wicri:noRegion>Wuhan</wicri:noRegion></affiliation></author><author><name sortKey="Chen, Xue Hao" sort="Chen, Xue Hao" uniqKey="Chen X" first="Xue-Hao" last="Chen">Xue-Hao Chen</name><affiliation wicri:level="1"><nlm:aff id="Aff9">College of Horticulture and Plant Protection of Yangzhou University, Yangzhou, 225009 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture and Plant Protection of Yangzhou University, Yangzhou</wicri:regionArea><wicri:noRegion>Yangzhou</wicri:noRegion></affiliation></author><author><name sortKey="Xue, Lin Bao" sort="Xue, Lin Bao" uniqKey="Xue L" first="Lin-Bao" last="Xue">Lin-Bao Xue</name><affiliation wicri:level="1"><nlm:aff id="Aff9">College of Horticulture and Plant Protection of Yangzhou University, Yangzhou, 225009 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture and Plant Protection of Yangzhou University, Yangzhou</wicri:regionArea><wicri:noRegion>Yangzhou</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24885385</idno><idno type="pmc">4070557</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4070557</idno><idno type="RBID">PMC:4070557</idno><idno type="doi">10.1186/1471-2164-15-412</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000570</idno><idno type="wicri:Area/Pmc/Curation">000569</idno><idno type="wicri:Area/Pmc/Checkpoint">000873</idno><idno type="wicri:Area/Ncbi/Merge">001705</idno><idno type="wicri:Area/Ncbi/Curation">001705</idno><idno type="wicri:Area/Ncbi/Checkpoint">001705</idno><idno type="wicri:Area/Main/Merge">000B57</idno><idno type="wicri:Area/Main/Curation">000B54</idno><idno type="wicri:Area/Main/Exploration">000B54</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Comparative transcriptome analysis of eggplant (<italic>Solanum melongena</italic> L.) and turkey berry (<italic>Solanum torvum</italic> Sw.): phylogenomics and disease resistance analysis</title><author><name sortKey="Yang, Xu" sort="Yang, Xu" uniqKey="Yang X" first="Xu" last="Yang">Xu Yang</name><affiliation wicri:level="1"><nlm:aff id="Aff9">College of Horticulture and Plant Protection of Yangzhou University, Yangzhou, 225009 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture and Plant Protection of Yangzhou University, Yangzhou</wicri:regionArea><wicri:noRegion>Yangzhou</wicri:noRegion></affiliation></author><author><name sortKey="Cheng, Yu Fu" sort="Cheng, Yu Fu" uniqKey="Cheng Y" first="Yu-Fu" last="Cheng">Yu-Fu Cheng</name><affiliation wicri:level="1"><nlm:aff id="Aff9">College of Horticulture and Plant Protection of Yangzhou University, Yangzhou, 225009 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture and Plant Protection of Yangzhou University, Yangzhou</wicri:regionArea><wicri:noRegion>Yangzhou</wicri:noRegion></affiliation></author><author><name sortKey="Deng, Cao" sort="Deng, Cao" uniqKey="Deng C" first="Cao" last="Deng">Cao Deng</name><affiliation wicri:level="1"><nlm:aff id="Aff10">PubBio-Tech Services Corporation, Wuhan, 430070 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>PubBio-Tech Services Corporation, Wuhan</wicri:regionArea><wicri:noRegion>Wuhan</wicri:noRegion></affiliation></author><author><name sortKey="Ma, Yan" sort="Ma, Yan" uniqKey="Ma Y" first="Yan" last="Ma">Yan Ma</name><affiliation wicri:level="1"><nlm:aff id="Aff9">College of Horticulture and Plant Protection of Yangzhou University, Yangzhou, 225009 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture and Plant Protection of Yangzhou University, Yangzhou</wicri:regionArea><wicri:noRegion>Yangzhou</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Zhi Wen" sort="Wang, Zhi Wen" uniqKey="Wang Z" first="Zhi-Wen" last="Wang">Zhi-Wen Wang</name><affiliation wicri:level="1"><nlm:aff id="Aff10">PubBio-Tech Services Corporation, Wuhan, 430070 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>PubBio-Tech Services Corporation, Wuhan</wicri:regionArea><wicri:noRegion>Wuhan</wicri:noRegion></affiliation></author><author><name sortKey="Chen, Xue Hao" sort="Chen, Xue Hao" uniqKey="Chen X" first="Xue-Hao" last="Chen">Xue-Hao Chen</name><affiliation wicri:level="1"><nlm:aff id="Aff9">College of Horticulture and Plant Protection of Yangzhou University, Yangzhou, 225009 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture and Plant Protection of Yangzhou University, Yangzhou</wicri:regionArea><wicri:noRegion>Yangzhou</wicri:noRegion></affiliation></author><author><name sortKey="Xue, Lin Bao" sort="Xue, Lin Bao" uniqKey="Xue L" first="Lin-Bao" last="Xue">Lin-Bao Xue</name><affiliation wicri:level="1"><nlm:aff id="Aff9">College of Horticulture and Plant Protection of Yangzhou University, Yangzhou, 225009 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture and Plant Protection of Yangzhou University, Yangzhou</wicri:regionArea><wicri:noRegion>Yangzhou</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Eggplant (<italic>Solanum melongena</italic> L<italic>.</italic>) and turkey berry (<italic>S. torvum</italic> Sw.), a wild ally of eggplant with promising multi-disease resistance traits, are of great economic, medicinal and genetic importance, but genomic resources for these species are lacking. In the present study, we sequenced the transcriptomes of eggplant and turkey berry to accelerate research on these two non-model species.</p></sec><sec><title>Results</title><p>We built comprehensive, high-quality <italic>de novo</italic> transcriptome assemblies of the two <italic>Leptostemonum</italic> clade <italic>Solanum</italic> species from short-read RNA-Sequencing data. We obtained 34,174 unigenes for eggplant and 38,185 unigenes for turkey berry. Functional annotations based on sequence similarity to known plant datasets revealed a distribution of functional categories for both species very similar to that of tomato. Comparison of eggplant, turkey berry and another 11 plant proteomes resulted in 276 high-confidence single-copy orthologous groups, reasonable phylogenetic tree inferences and reliable divergence time estimations. From these data, it appears that eggplant and its wild <italic>Leptostemonum</italic> clade relative turkey berry split from each other in the late Miocene, ~6.66 million years ago, and that <italic>Leptostemonum</italic> split from the <italic>Potatoe</italic> clade in the middle Miocene, ~15.75 million years ago. Furthermore, 621 and 815 plant resistance genes were identified in eggplant and turkey berry respectively, indicating the variation of disease resistance genes between them.</p></sec><sec><title>Conclusions</title><p>This study provides a comprehensive transcriptome resource for two <italic>Leptostemonum</italic> clade <italic>Solanum</italic> species and insight into their evolutionary history and biological characteristics. These resources establish a foundation for further investigations of eggplant biology and for agricultural improvement of this important vegetable. More generally, we show that RNA-Seq is a fast, reliable and cost-effective method for assessing genome evolution in non-model species.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi: 10.1186/1471-2164-15-412) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Xu, X" uniqKey="Xu X">X Xu</name></author><author><name sortKey="Pan, S" uniqKey="Pan S">S Pan</name></author><author><name sortKey="Cheng, S" uniqKey="Cheng S">S Cheng</name></author><author><name sortKey="Zhang, B" uniqKey="Zhang B">B Zhang</name></author><author><name sortKey="Mu, D" uniqKey="Mu D">D Mu</name></author><author><name sortKey="Ni, P" uniqKey="Ni P">P Ni</name></author><author><name sortKey="Zhang, G" uniqKey="Zhang G">G Zhang</name></author><author><name sortKey="Yang, S" uniqKey="Yang S">S Yang</name></author><author><name 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Sa</name></author><author><name sortKey="Drouin, G" uniqKey="Drouin G">G Drouin</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Yang, Xu" sort="Yang, Xu" uniqKey="Yang X" first="Xu" last="Yang">Xu Yang</name></noRegion><name sortKey="Chen, Xue Hao" sort="Chen, Xue Hao" uniqKey="Chen X" first="Xue-Hao" last="Chen">Xue-Hao Chen</name><name sortKey="Cheng, Yu Fu" sort="Cheng, Yu Fu" uniqKey="Cheng Y" first="Yu-Fu" last="Cheng">Yu-Fu Cheng</name><name sortKey="Deng, Cao" sort="Deng, Cao" uniqKey="Deng C" first="Cao" last="Deng">Cao Deng</name><name sortKey="Ma, Yan" sort="Ma, Yan" uniqKey="Ma Y" first="Yan" last="Ma">Yan Ma</name><name sortKey="Wang, Zhi Wen" sort="Wang, Zhi Wen" uniqKey="Wang Z" first="Zhi-Wen" last="Wang">Zhi-Wen Wang</name><name sortKey="Xue, Lin Bao" sort="Xue, Lin Bao" uniqKey="Xue L" 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