Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types

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dc.contributor.authorGuo, Shaoguien
dc.contributor.authorZheng, Yien
dc.contributor.authorJoung, Je-Gunen
dc.contributor.authorLiu, Shiqiangen
dc.contributor.authorZhang, Zhonghuaen
dc.contributor.authorCrasta, Oswald R.en
dc.contributor.authorSobral, Brunoen
dc.contributor.authorXu, Yongen
dc.contributor.authorHuang, Sanwenen
dc.contributor.authorFei, Zhangjunen
dc.date.accessioned2012-08-24T11:20:43Zen
dc.date.available2012-08-24T11:20:43Zen
dc.date.issued2010-06-17en
dc.date.updated2012-08-24T11:20:43Zen
dc.description.abstractBackground Cucumber, Cucumis sativus L., is an economically and nutritionally important crop of the Cucurbitaceae family and has long served as a primary model system for sex determination studies. Recently, the sequencing of its whole genome has been completed. However, transcriptome information of this species is still scarce, with a total of around 8,000 Expressed Sequence Tag (EST) and mRNA sequences currently available in GenBank. In order to gain more insights into molecular mechanisms of plant sex determination and provide the community a functional genomics resource that will facilitate cucurbit research and breeding, we performed transcriptome sequencing of cucumber flower buds of two near-isogenic lines, WI1983G, a gynoecious plant which bears only pistillate flowers, and WI1983H, a hermaphroditic plant which bears only bisexual flowers. Result Using Roche-454 massive parallel pyrosequencing technology, we generated a total of 353,941 high quality EST sequences with an average length of 175bp, among which 188,255 were from gynoecious flowers and 165,686 from hermaphroditic flowers. These EST sequences, together with ~5,600 high quality cucumber EST and mRNA sequences available in GenBank, were clustered and assembled into 81,401 unigenes, of which 28,452 were contigs and 52,949 were singletons. The unigenes and ESTs were further mapped to the cucumber genome and more than 500 alternative splicing events were identified in 443 cucumber genes. The unigenes were further functionally annotated by comparing their sequences to different protein and functional domain databases and assigned with Gene Ontology (GO) terms. A biochemical pathway database containing 343 predicted pathways was also created based on the annotations of the unigenes. Digital expression analysis identified ~200 differentially expressed genes between flowers of WI1983G and WI1983H and provided novel insights into molecular mechanisms of plant sex determination process. Furthermore, a set of SSR motifs and high confidence SNPs between WI1983G and WI1983H were identified from the ESTs, which provided the material basis for future genetic linkage and QTL analysis. Conclusion A large set of EST sequences were generated from cucumber flower buds of two different sex types. Differentially expressed genes between these two different sex-type flowers, as well as putative SSR and SNP markers, were identified. These EST sequences provide valuable information to further understand molecular mechanisms of plant sex determination process and forms a rich resource for future functional genomics analysis, marker development and cucumber breeding.en
dc.description.versionPublished versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationBMC Genomics. 2010 Jun 17;11(1):384en
dc.identifier.doihttps://doi.org/10.1186/1471-2164-11-384en
dc.identifier.urihttp://hdl.handle.net/10919/18835en
dc.language.isoenen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.holderShaogui Guo et al.; licensee BioMed Central Ltd.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.titleTranscriptome sequencing and comparative analysis of cucumber flowers with different sex typesen
dc.title.serialBMC Genomicsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
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