RNA-Seq improves annotation of protein-coding genes in the cucumber genome.
RNA-Seq improves annotation of protein-coding genes in the cucumber genome.
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DOI：
10.1186/1471-2164-12-540
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发表时间：
2011-11-02
期刊：
影响因子：
4.4
通讯作者：
Lin K
中科院分区：
文献类型：
--
作者：
Li Z;Zhang Z;Yan P;Huang S;Fei Z;Lin K
随着越来越多的基因组被测序，基因组注释在弥合序列和生物学之间的鸿沟方面变得越来越重要。基因预测是基因组注释的核心，通常整合各种资源来计算一致的基因结构。然而，许多新测序的基因组用于基因预测的资源有限。为了创建高质量的黄瓜基因组基因模型(Cucumis sativus var.，在EVidenceModeler基因预测管道的基础上，我们将10个黄瓜组织的大规模并行互补DNA测序(RNA-Seq)读数整合到EVidenceModeler中。我们将新的流水线应用于重组的黄瓜基因组，并将我们预测的蛋白质编码基因集与已发表的基因集进行了比较。重组的黄瓜基因组，用来自10个组织的RNA-Seq读数注释，有23,248个已识别的蛋白质编码基因。与2009年发表的预测相比，大约8700个基因揭示了结构修改，5285个基因只出现在重组的黄瓜基因组中。所有相关的结果，包括基因组序列和注释，都可以在http://cmb.bnu.edu.cn/Cucumis_sativus_v20/.上获得我们的结论是，RNA-Seq极大地提高了重组黄瓜基因组中蛋白质编码基因预测的准确性。这两组基因之间的比较也表明，使用RNA-Seq读数来注释新测序或较少研究的基因组是可行的。
As more and more genomes are sequenced, genome annotation becomes increasingly important in bridging the gap between sequence and biology. Gene prediction, which is at the center of genome annotation, usually integrates various resources to compute consensus gene structures. However, many newly sequenced genomes have limited resources for gene predictions. In an effort to create high-quality gene models of the cucumber genome (Cucumis sativus var. sativus), based on the EVidenceModeler gene prediction pipeline, we incorporated the massively parallel complementary DNA sequencing (RNA-Seq) reads of 10 cucumber tissues into EVidenceModeler. We applied the new pipeline to the reassembled cucumber genome and included a comparison between our predicted protein-coding gene sets and a published set. The reassembled cucumber genome, annotated with RNA-Seq reads from 10 tissues, has 23, 248 identified protein-coding genes. Compared with the published prediction in 2009, approximately 8, 700 genes reveal structural modifications and 5, 285 genes only appear in the reassembled cucumber genome. All the related results, including genome sequence and annotations, are available at http://cmb.bnu.edu.cn/Cucumis_sativus_v20/. We conclude that RNA-Seq greatly improves the accuracy of prediction of protein-coding genes in the reassembled cucumber genome. The comparison between the two gene sets also suggests that it is feasible to use RNA-Seq reads to annotate newly sequenced or less-studied genomes.
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影响因子：
1.7
作者：
Jurka, J;Kapitonov, VV;Walichiewicz, J
通讯作者：
Walichiewicz, J
影响因子：
5.4
作者：
Haas BJ;Wortman JR;Ronning CM;Hannick LI;Smith RK Jr;Maiti R;Chan AP;Yu C;Farzad M;Wu D;White O;Town CD
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Town CD
影响因子：
12.3
作者：
Denoeud F;Aury JM;Da Silva C;Noel B;Rogier O;Delledonne M;Morgante M;Valle G;Wincker P;Scarpelli C;Jaillon O;Artiguenave F
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Artiguenave F
影响因子：
64.8
作者：
Jaillon, Olivier;Aury, Jean-Marc;Wincker, Patrick
通讯作者：
Wincker, Patrick
将cDNA序列映射到基因组序列上的空间有效和准确的方法。
影响因子：
14.9
作者：
Gotoh, Osamu
通讯作者：
Gotoh, Osamu