AmphiEST: Enabling comparative analysis of ESTs from five developmental stages of amphioxus
AmphiEST: Enabling comparative analysis of ESTs from five developmental stages of amphioxus
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AmphiEST：能够对文昌鱼五个发育阶段的 EST 进行比较分析
DOI：
10.1016/j.margen.2010.09.003
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发表时间：
2010-09-01
期刊：
影响因子：
1.9
通讯作者：
Ma, Fei
中科院分区：
文献类型：
--
作者：
Jin, Ping;Ji, Xinglai;Ma, Fei
文昌鱼一直是了解脊索动物进化和脊椎动物起源的重要模型。比较转录组分析有助于描述文昌鱼在不同发育阶段的基因表达模式。然而，到目前为止，这样的分析还很少进行。在这里，我们系统地比较了文昌鱼在五个发育阶段的est。文昌鱼卵期、原肠期、神经期、幼虫期和成虫期的est序列分别为3364、3230、10,299、4052和3866个contigs，以及193、183、933、178和151个singlets。鉴定出25796个orf，其中6529个预测orf（卵922个；原肠997个；神经2159个；幼虫1014个；成虫1437个）在UniProt数据库中找到匹配。对于所有五个阶段，更多的GO术语被分配给特定阶段的配置，而不是保留程序。分别有2个、5个、11个、4个和2个miRNA与5个阶段的ESTs匹配，从3' UTR序列中预测出12,232个、10,147个、43170个、8,049个和12,811个miRNA靶点。开发了一个web界面，用于可视化contigs， mirna和注释（http://www.rich.yunda.org/test/amphioxusest/）。所构建的文昌鱼数据库可作为文昌鱼发育进化研究的重要资源。(C) 2010 Elsevier B.V.版权所有
Amphioxus has been an important model for understanding the evolution of chordates and origin of vertebrates. Comparative transcriptome analysis can facilitate delineation of gene expression patterns of amphioxus at different developmental stages. So far, however, few such analyses have been performed. Here we have systematically compared amphioxus ESTs from five developmental stages. For the egg, gastrula, neurula, larva and adult stages, amphioxus ESTs were assembled, respectively, into 3364, 3230, 10,299, 4052 and 3866 contigs, and 193, 183, 933, 178 and 151 singlets. 25,796 ORFs were identified, of which 6,529 predicted ORFs (egg, 922; gastrula, 997; neurula, 2,159; larva, 1,014; adult, 1,437) have found matches from the UniProt database. For all five stages, more GO terms were assigned to stage-specific contigs than to repertoire ones. Respectively, 2, 5, 11, 4 and 2 miRNAs were matched with ESTs from the five stages, and 12,232, 10,147, 43,170, 8,049 and 12,811 miRNA target sites were predicted from the 3' UTR sequences. A web interface was developed for visualization of the contigs, miRNAs and annotations (http://www.rich.yunda.org/test/amphioxusest/). The constructed AmphiEST database may serve as an essential resource for future studies of the development and evolution of amphioxus. (C) 2010 Elsevier B.V. All rights reserved.