Improved rat genome gene prediction by integration of ESTs with RNA-Seq information
Improved rat genome gene prediction by integration of ESTs with RNA-Seq information
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通过将 EST 与 RNA-Seq 信息整合改进大鼠基因组基因预测
DOI：
10.1093/bioinformatics/btu608
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发表时间：
2015-01-01
期刊：
影响因子：
5.8
通讯作者：
Lu, Yan
中科院分区：
文献类型：
--
作者：
Li, Liping;Chen, Enguo;Lu, Yan
动机：RNA - Seq（也称为全转录组测序）是一种新兴技术，它利用新一代测序的能力来检测和量化整个转录本。其重要应用之一是改进现有的基因组注释。与表达序列标签（EST）相比，RNA - Seq为发现新基因和转录本提供了快速、全面且具有成本效益的工具，这对基因发现和基因序列测定很有帮助。大鼠被广泛用作实验室疾病模型，但与人类和小鼠相比，其基因组注释不够完善。在这项研究中，我们将来自大鼠三种组织——骨髓、大脑和肾脏的深度RNA - Seq数据与EST数据相结合，以改进大鼠基因组的注释。
结果：我们的分析确定了32197个转录本，包括13461个已知转录本、13934个新的异构体和4802个新基因，这几乎使当前公共大鼠基因组数据库（rn5）中的转录本数量增加了一倍。将我们预测的蛋白质编码基因集与公共数据集中的基因集进行比较表明，RNA - Seq显著改进了基因组注释，并在大鼠中识别出了新基因和异构体。重要的是，绝大多数新基因和异构体都有RNA - Seq实验的直接证据支持。这些预测的基因已整合到大鼠基因组数据库（RGD）中，可作为研究界进行功能研究的重要资源。
Motivation: RNA-Seq (also called whole-transcriptome sequencing) is an emerging technology that uses the capabilities of next-generation sequencing to detect and quantify entire transcripts. One of its important applications is the improvement of existing genome annotations. RNA-Seq provides rapid, comprehensive and cost-effective tools for the discovery of novel genes and transcripts compared with expressed sequence tag (EST), which is instrumental in gene discovery and gene sequence determination. The rat is widely used as a laboratory disease model, but has a less well-annotated genome as compared with humans and mice. In this study, we incorporated deep RNA-Seq data from three rat tissues-bone marrow, brain and kidney-with EST data to improve the annotation of the rat genome.Results: Our analysis identified 32 197 transcripts, including 13 461 known transcripts, 13 934 novel isoforms and 4802 new genes, which almost doubled the numbers of transcripts in the current public rat genome database (rn5). Comparisons of our predicted protein-coding gene sets with those in public datasets suggest that RNA-Seq significantly improves genome annotation and identifies novel genes and isoforms in the rat. Importantly, the large majority of novel genes and isoforms are supported by direct evidence of RNA-Seq experiments. These predicted genes were integrated into the Rat Genome Database (RGD) and can serve as an important resource for functional studies in the research community.