Open Access Highly Accessed Research article

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

Shaogui Guo12, Yi Zheng23, Je-Gun Joung2, Shiqiang Liu4, Zhonghua Zhang4, Oswald R Crasta5, Bruno W Sobral5, Yong Xu1, Sanwen Huang4* and Zhangjun Fei26*

Author Affiliations

1 National Engineering Research Center for Vegetables, Beijing 100097, China

2 Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA

3 Department of Ornamental Horticulture, China Agricultural University, Beijing 100094, China

4 Key Laboratory of Horticultural Crops Genetic Improvement of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics Technology, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China

5 Virginia Bioinformatics Institute, Virginia Tech University, Blacksburg, VA 24061, USA

6 USDA Robert W. Holley Center for Agriculture and Health, Tower Road, Ithaca, NY 14853, USA

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BMC Genomics 2010, 11:384  doi:10.1186/1471-2164-11-384

Published: 17 June 2010

Abstract

Background

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.