Evidence-based gene predictions in plant genomes
Evidence-based gene predictions in plant genomes
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DOI：
10.1101/gr.088997.108
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发表时间：
2009-10-01
期刊：
影响因子：
7
通讯作者：
Stein, Lincoln
中科院分区：
文献类型：
--
作者：
Liang, Chengzhi;Mao, Long;Stein, Lincoln
自动循证基因构建是一种快速且具有成本效益的方法，可以为新测序的基因组提供可靠的基因注释。然而，基于证据的基因构建者的局限性之一是，他们需要转录证据-已知的蛋白质，全长cDNA或表达序列标签（EST）-在感兴趣的物种。这种限制对于植物基因组尤其令人担忧，因为基因组测序的速度大大超过EST和cDNA测序项目的速度。为了克服这一限制，我们开发了一个基于证据的基因构建系统（Gramene管道），可以使用相关物种的转录证据。Gramene管道使用Ensembl计算基础设施和一种新颖的数据处理方案。使用先前注释的植物基因组，双子叶植物拟南芥和单子叶植物水稻，我们表明，跨物种的ESTs从单子叶植物或双子叶植物类基因预测的证据是一个有价值的来源。我们还发现，仅使用EST和跨物种证据，Gramene管道可以生成与基于已知蛋白质和全长cDNA的人类基因质量相当的植物基因集。我们比较了Gramene管道在水稻中的几个广泛使用的从头算基因预测程序;这种比较表明，管道在基因和外显子水平上都表现良好，仅具有跨物种基因产物。我们讨论了在新测序的玉米基因组的22 Mb区域上测试管道的结果，并讨论了管道在其他基因组中的潜在应用。
Automated evidence-based gene building is a rapid and cost-effective way to provide reliable gene annotations on newly sequenced genomes. One of the limitations of evidence-based gene builders, however, is their requirement for transcriptional evidence-known proteins, full-length cDNAs, or expressed sequence tags (ESTs)-in the species of interest. This limitation is of particular concern for plant genomes, where the rate of genome sequencing is greatly outpacing the rate of EST-and cDNA-sequencing projects. To overcome this limitation, we have developed an evidence-based gene build system (the Gramene pipeline) that can use transcriptional evidence across related species. The Gramene pipeline uses the Ensembl computing infrastructure with a novel data processing scheme. Using the previously annotated plant genomes, the dicot Arabidopsis thaliana and the monocot Oryza sativa, we show that the cross-species ESTs from within monocot or dicot class are a valuable source of evidence for gene predictions. We also find that, using only EST and cross-species evidence, the Gramene pipeline can generate a plant gene set that is comparable in quality to the human genes based on known proteins and full-length cDNAs. We compare the Gramene pipeline to several widely used ab initio gene prediction programs in rice; this comparison shows the pipeline performs favorably at both the gene and exon levels with cross-species gene products only. We discuss the results of testing the pipeline on a 22-Mb region of the newly sequenced maize genome and discuss potential application of the pipeline to other genomes.