Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types
Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types
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不同性型黄瓜花转录组测序及比较分析
DOI：
10.1186/1471-2164-11-384
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发表时间：
2010-06-17
期刊：
影响因子：
4.4
通讯作者：
Fei, Zhangjun
中科院分区：
文献类型：
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作者：
Guo, Shaogui;Zheng, Yi;Fei, Zhangjun
背景：黄瓜（Cucumis sativus L.）是葫芦科的一种经济和营养上重要的作物，长期以来一直作为性别决定研究的主要模型系统。近日，其全基因组测序已经完成。然而，该物种的转录组信息仍然匮乏，目前GenBank中共有约8000个表达序列标签（EST）和mRNA序列。为了深入了解植物性别决定的分子机制，为公众提供有利于葫芦研究和育种的功能基因组学资源，我们对两个近等基因系的黄瓜花芽进行了转录组测序：WI1983G（一种只开雌花的雌雄同体植物）和WI1983H（一种只开雌花的雌雄同体植物） 结果：利用Roche-454大规模并行焦磷酸测序技术，共生成353,941条高质量EST序列，平均长度为175bp，其中雌雄花188,255条，两性花165,686条。这些EST序列与GenBank中可用的5,600个高质量黄瓜EST和mRNA序列一起被聚类并组装成81,401个unigenes，其中28,452个是重叠群，52,949个是单基因。 Unigenes 和 EST 进一步定位到黄瓜基因组，并在 443 个黄瓜基因中鉴定出 500 多个可变剪接事件。通过将unigenes的序列与不同的蛋白质和功能域数据库进行比较，并使用基因本体论（GO）术语对unigenes进行进一步的功能注释。还根据unigenes的注释创建了包含343条预测途径的生化途径数据库。数字表达分析鉴定了 WI1983G 和 WI1983H 花之间相似的 200 个差异表达基因，为植物性别决定过程的分子机制提供了新的见解。此外，从EST中鉴定出WI1983G和WI1983H之间的一组SSR基序和高置信度SNP，为今后的遗传连锁和QTL分析提供了物质基础。结论：两种不同性别类型的黄瓜花芽产生了一大批EST序列。鉴定了这两种不同性别类型花之间的差异表达基因以及推定的 SSR 和 SNP 标记。这些EST序列为进一步了解植物性别决定过程的分子机制提供了有价值的信息，并为未来的功能基因组学分析、标记开发和黄瓜育种形成了丰富的资源。
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 similar to 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 similar to 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.