Whole genome sequence comparisons and "full-length" cDNA sequences:: A combined approach to evaluate and improve Arabidopsis genome annotation
Whole genome sequence comparisons and "full-length" cDNA sequences:: A combined approach to evaluate and improve Arabidopsis genome annotation
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DOI：
10.1101/gr.1515604
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发表时间：
2004-03-01
期刊：
影响因子：
7
通讯作者：
Salanoubat, M
中科院分区：
文献类型：
--
作者：
Castelli, V;Aury, JM;Salanoubat, M
为了进一步评估拟南芥基因组现有的注释，我们构建了拟南芥和水稻之间的进化保守区域（ecores）集合。ecore分析提供的证据表明，拟南芥的基因目录尚不完整，其中一些注释需要重新检查。为了进一步改进拟南芥基因组注释，我们使用了从多种组织制备的一种新型的“全长”富集cDNA集合。另外有1931个基因被新的“全长”cDNA序列覆盖，使具有相应“全长”cDNA序列的注释基因数量增加到约14000个。这些“全长”cDNA序列和注释基因之间的详细比较表明，这一资源在确定基因的正确结构方面非常有帮助，特别是对于那些尚未有“全长”cDNA支持的基因。此外，通过这种cDNA资源共检测到326个先前未包含在拟南芥基因组注释中的基因组区域，为新基因的发现提供了线索。因为正如预期的那样，这两个数据集只是部分重叠，它们的结合为改进拟南芥基因组注释提供了非常有用的信息。
To evaluate the existing annotation of the Arabidopsis genome further, we generated a collection of evolutionary conserved regions (ecores) between Arabidopsis and rice. The ecore analysis provides evidence that the gene catalog of Arabidopsis is not yet complete, and that a number of these annotations require re-examination. To improve the Arabidopsis genome annotation further, we used a novel "full-length" enriched cDNA collection prepared from several tissues. An additional 1931 genes were covered by new "full-length" cDNA sequences, raising the number of annotated genes with a corresponding "full-length" cDNA sequence to about 14,000. Detailed comparisons between these "full-length" cDNA sequences and annotated genes show that this resource is very helpful in determining the correct structure of genes, in particular, those not yet supported by "full-length" cDNAs. In addition, a total of 326 genomic regions not included previously in the Arabidopsis genome annotation were detected by this cDNA resource, providing clues for new gene discovery. Because, as expected, the two data sets only partially overlap, their combination produces very useful information for improving the Arabidopsis genome annotation.