Castelli Vanina, Aury Jean-Marc, Jaillon Olivier, Wincker Patrick, Clepet Christian, Menard Manuella, Cruaud Corinne, Quétier Francis, Scarpelli Claude, Schächter Vincent, Temple Gary, Caboche Michel, Weissenbach Jean, Salanoubat Marcel
Genoscope-Centre National de Séquençage and Centre National de la Recherche Scientifique Unité Mixte de Recherche-3080, 91000 Evry, France.
Genome Res. 2004 Mar;14(3):406-13. doi: 10.1101/gr.1515604.
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.
为了进一步评估拟南芥基因组的现有注释，我们构建了拟南芥和水稻之间的进化保守区域（ecores）集合。ecore分析提供了证据，表明拟南芥的基因目录尚未完整，并且其中一些注释需要重新审查。为了进一步改进拟南芥基因组注释，我们使用了从多个组织制备的新型“全长”富集cDNA集合。另外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序列与注释基因之间的详细比较表明，该资源对于确定基因的正确结构非常有帮助，特别是那些尚未得到“全长”cDNA支持的基因。此外，通过该cDNA资源检测到总共326个以前未包含在拟南芥基因组注释中的基因组区域，为新基因发现提供了线索。由于正如预期的那样，这两个数据集仅部分重叠，它们的组合为改进拟南芥基因组注释产生了非常有用的信息。
