Characterization of transcriptome dynamics during watermelon fruit development: sequencing, assembly, annotation and gene expression profiles.
Characterization of transcriptome dynamics during watermelon fruit development: sequencing, assembly, annotation and gene expression profiles.
复制标题
西瓜果实发育过程中转录组动态的表征：测序、组装、注释和基因表达谱
DOI：
10.1186/1471-2164-12-454
复制
发表时间：
2011-09-21
期刊：
影响因子：
4.4
通讯作者：
Xu Y
中科院分区：
文献类型：
--
作者：
Guo S;Liu J;Zheng Y;Huang M;Zhang H;Gong G;He H;Ren Y;Zhong S;Fei Z;Xu Y
背景栽培西瓜[Citrullus lanatus（Thunb.）马特森& Nakaivar.lanatus]是世界范围内重要的农业作物。西瓜的果实经历了不同的发育阶段，其大小，颜色，甜度，质地和香气都发生了巨大的变化。为了更好地了解这些变化的遗传和分子基础，并显着扩大西瓜转录本目录，我们选择了西瓜果实发育的四个关键阶段，并使用Roche/454下一代测序技术生成了西瓜果实果肉组织的大表达序列标签（EST）数据集和全面的转录组图谱。FLX运行四个西瓜果实发育阶段中的每一个结果表明，利用该方法获得了577，023条平均长度为302.8bp的高质量EST序列，与GenBank中收集的11，786条西瓜EST序列进行重新拼接，共获得75条，068个单基因，总长度约31.8 Mb。总体而言，54.9%的unigenes与GenBank非冗余（nr）蛋白质数据库中的已知序列显示出显著的相似性，其中约三分之二与黄瓜的蛋白质匹配，黄瓜是基因组测序中最接近的物种。unigenes进一步分配与基因本体论（GO）的条款和映射到生化途径。从EST收集中确定了5，000多个SSR。此外，我们对这些EST进行了数字基因表达分析，并确定了3，023个在西瓜果实发育和成熟过程中差异表达的基因，这为西瓜果实生物学提供了新的见解，并为未来的功能分析提供了候选基因的全面资源。然后，我们生成了几个有趣的代谢产物的配置文件，这些代谢产物对水果质量很重要，包括色素沉着和甜度。代谢产物和数字基因表达谱的综合分析有助于阐明西瓜果实发育过程中这些重要的质量相关性状的分子机制。ConclusionWe已经产生了大量的西瓜EST，这代表了当前西瓜转录本目录的显着扩展和西瓜和其他密切相关物种的基因组学未来研究的宝贵资源。这个EST集合的数字表达分析使我们能够识别西瓜果实发育和成熟过程中差异表达的大量基因，这为未来的功能分析提供了丰富的候选基因来源，并代表了我们对西瓜果实生物学知识基础的宝贵增加。
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 novoassembly 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.
登录
查看更多内容
影响因子：
1.5
作者：
Bethke, Paul C.;Sabba, Robert;Bussan, Alvin J.
通讯作者：
Bussan, Alvin J.
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
14.9
作者：
Finn RD;Mistry J;Tate J;Coggill P;Heger A;Pollington JE;Gavin OL;Gunasekaran P;Ceric G;Forslund K;Holm L;Sonnhammer EL;Eddy SR;Bateman A
通讯作者：
Bateman A
DOI：
10.1073/pnas.0509279102
发表时间：
2005-12-20
影响因子：
11.1
作者：
Erickson, DL;Smith, BD;Tuross, N
通讯作者：
Tuross, N
不同性型黄瓜花转录组测序及比较分析
影响因子：
4.4
作者：
Guo, Shaogui;Zheng, Yi;Fei, Zhangjun
通讯作者：
Fei, Zhangjun