Genome reannotation aims for complete and accurate characterization of gene models and thus is of critical significance for in-depth exploration of gene function. Although the availability of massive RNA-seq data provides great opportunities for gene model refinement, few efforts have been made to adopt these precious data in rice genome reannotation. Here we reannotate the rice (Oryza sativa L. ssp. japonica) genome based on integration of large-scale RNA-seq data and release a new annotation system IC4R-2.0. In general, IC4R-2.0 significantly improves the completeness of gene structure, identifies a number of novel genes, and integrates a variety of functional annotations. Furthermore, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are systematically characterized in the rice genome. Performance evaluation shows that compared to previous annotation systems, IC4R-2.0 achieves higher integrity and quality, primarily attributable to massive RNA-seq data applied in genome annotation. Consequently, we incorporate the improved annotations into the Information Commons for Rice (IC4R), a database integrating multiple omics data of rice, and accordingly update IC4R by providing more user-friendly web interfaces and implementing a series of practical online tools. Together, the updated IC4R, which is equipped with the improved annotations, bears great promise for comparative and functional genomic studies in rice and other monocotyledonous species. The IC4R-2.0 annotation system and related resources are freely accessible at http://ic4r.org/.
基因组重注释是不断修正基因模型的过程，对模式生物与非模式生物功能基因的深度解析具有重要意义。转录组测序技术由于能有效地识别基因组中的可变剪接位点，敏感地鉴定出低丰度表达基因与组织特异性基因，在基因组重注释研究中有巨大的应用潜力。鉴于目前水稻中已积累了海量转录组测序数据，我们开发了一套以公共RNA-Seq数据大规模整合分析为基础的基因组注释流程，对水稻基因组开展重注释研究，进而获得了一套新的水稻基因组注释系统：IC4R-2.0。结果表明，IC4R-2.0通过外显子/内含子区域矫正，新UTR区域识别，基因融合及新基因挖掘等方式，对原注释系统中蛋白质编码基因的结构进行了更新。同时，我们对水稻基因组中的长链非编码RNA（lncRNA）与环形RNA（circRNA）进行了鉴定。通过整合多个基因组功能注释平台的资源，我们为水稻基因提供了更为丰富的功能注释信息。不同版本水稻基因组注释系统的定量评估与比较分析表明，大规模整合转录组测序数据的确可以使水稻基因模型的完整度与注释质量获得提升。为方便用户获取水稻基因组重注释信息，我们在水稻生物信息门户IC4R (v 1.0)的基础上进行了重新设计及二次开发，不但有效地整合了水稻基因组重注释信息，还提供了更为友好的数据展示界面，提高了数据检索效率，并提供了一系列丰富而实用的在线分析工具。本研究为在水稻和其他单子叶植物中开展大规模基因功能解析等相关工作提供了数据基础。IC4R-2.0注释系统及相关资源可通过http://ic4r.org/ 来获取。





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