BMC Genomics | |
Characterization of transcriptome dynamics during watermelon fruit development: sequencing, assembly, annotation and gene expression profiles | |
Research Article | |
Yi Zheng1  Silin Zhong1  Mingyun Huang1  Zhangjun Fei2  Hongju He3  Haiying Zhang3  Guoyi Gong3  Yong Xu3  Jingan Liu3  Yi Ren3  Shaogui Guo4  | |
[1] Boyce Thompson Institute for Plant Research, Cornell University, 14853, Ithaca, NY, USA;Boyce Thompson Institute for Plant Research, Cornell University, 14853, Ithaca, NY, USA;USDA Robert W. Holley Center for Agriculture and Health, Tower Road, 14853, Ithaca, NY, USA;National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, 100097, Beijing, China;National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, 100097, Beijing, China;Boyce Thompson Institute for Plant Research, Cornell University, 14853, Ithaca, NY, USA; | |
关键词: Gene Ontology; Lycopene; Fruit Development; Soluble Solid Content; Digital Gene Expression; | |
DOI : 10.1186/1471-2164-12-454 | |
received in 2011-07-05, accepted in 2011-09-21, 发布年份 2011 | |
来源: Springer | |
【 摘 要 】
BackgroundCultivated watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus] is an important agriculture crop world-wide. The fruit of watermelon undergoes distinct stages of development with dramatic changes in its size, color, sweetness, texture and aroma. In order to better understand the genetic and molecular basis of these changes and significantly expand the watermelon transcript catalog, we have selected four critical stages of watermelon fruit development and used Roche/454 next-generation sequencing technology to generate a large expressed sequence tag (EST) dataset and a comprehensive transcriptome profile for watermelon fruit flesh tissues.ResultsWe performed half Roche/454 GS-FLX run for each of the four watermelon fruit developmental stages (immature white, white-pink flesh, red flesh and over-ripe) and obtained 577,023 high quality ESTs with an average length of 302.8 bp. De novo assembly of these ESTs together with 11,786 watermelon ESTs collected from GenBank produced 75,068 unigenes with a total length of approximately 31.8 Mb. Overall 54.9% of the unigenes showed significant similarities to known sequences in GenBank non-redundant (nr) protein database and around two-thirds of them matched proteins of cucumber, the most closely-related species with a sequenced genome. The unigenes were further assigned with gene ontology (GO) terms and mapped to biochemical pathways. More than 5,000 SSRs were identified from the EST collection. Furthermore we carried out digital gene expression analysis of these ESTs and identified 3,023 genes that were differentially expressed during watermelon fruit development and ripening, which provided novel insights into watermelon fruit biology and a comprehensive resource of candidate genes for future functional analysis. We then generated profiles of several interesting metabolites that are important to fruit quality including pigmentation and sweetness. Integrative analysis of metabolite and digital gene expression profiles helped elucidating molecular mechanisms governing these important quality-related traits during watermelon fruit development.ConclusionWe have generated a large collection of watermelon ESTs, which represents a significant expansion of the current transcript catalog of watermelon and a valuable resource for future studies on the genomics of watermelon and other closely-related species. Digital expression analysis of this EST collection allowed us to identify a large set of genes that were differentially expressed during watermelon fruit development and ripening, which provide a rich source of candidates for future functional analysis and represent a valuable increase in our knowledge base of watermelon fruit biology.
【 授权许可】
Unknown
© Guo et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
【 预 览 】
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