Construction Of Rice Bioinformatic Platform

Rice is a major food for the world’s population and serves as a model plant in cereal genome research. Asian cultivated rice is composed of two major ecotypes (indica and japonica ecotypes) with significant difference. Japonica rice has a good reference genome, Oryza sativa ssp. japonica cv. Nipponbare, which was sequenced by the International Rice Genome Sequencing Project in2004. However, there is no good reference genome for indica rice up to now. Therefore, studies for indica rice were more difficult by using the japonica genome as a reference genome because of the significant difference between indica and japonica.Shanyou63, a hybrid between the two indica rice cultivars Zhenshan97and Minghui63, is the most-widely used hybrid in rice production in China. The Rice Information Gate Way (RIGW) was constructed in2013upon the completion of the Oryza sativa ssp. indica cv. Zhenshan97and Minghui63genomes sequenced by Huazhong Agricultural University with the aim of providing accurate and timely annotation of indica rice genome sequences. We have annotated the indica rice genomes ZS97and MH63for gene content, repetitive elements, non-coding RNA, SNPs, etc.RIGW presents the sequenced genomes and related information in a systematic and graphical way for the convenience of in-depth comparative studies. Users can access to the detailed gene information and browse the genome with RIGW. Some useful tools such as GBrowse, BLAST, CRISPR designer, and enrichment analysis, were added to the platform, which improved the functionality of the website. RIGW provides important genome and annotation information for the research of indica rice.