Molecular Plant
2017-10 | journal-article
Oryza sativa subsp. indica and japonica are two subspecies of Asian cultivated rice, among which indica rice is much more widely grown and genetically diverse. Over the past years, the Rice Annotation Project Database (RAP-DB) (Ohyanagi et al., 2006) and Michigan State University Rice Genome Annotation Project (MSU-RGAP) (Ouyang et al., 2007) are two popular databases that have been developed to manage rice genomic and transcriptomic data based on the unified reference genome of japonica cultivar Nipponbare (International Rice Genome Sequencing Project, 2005). Beijing Genomics Institute Rice Information System (BGI-RIS) (Zhao et al., 2004) is an available resource for indica rice cultivar 93-11; however, its application was limited due to the lack of high-quality indica reference genomes. To fill the gap, we constructed an integrative and comprehensive platform, Rice Information GateWay (RIGW, http://rice.hzau.edu.cn/), to provide genomics, transcriptomics, protein–protein interactions (PPIs), metabolic network, metabolites, and computational tools by using our newly obtained map-based reference genomes of indica rice Zhenshan 97 (ZS97) and Minghui 63 (MH63) (Zhang et al., 2016). RIGW serves the rice community by making a wealth of genomics and other omics data available through an intuitive web-based interface.
Cite this article
Song J-M, Lei Y, Shu C-C, Ding Y, Xing F, Liu H, Wang J, Xie W, Zhang J* and Chen L-L* (*corresponding authors). Rice Information GateWay: A Comprehensive Bioinformatics Platform for Indica Rice Genomes. Molecular Plant, 2018, 11(3):505-507. DOI: 10.1016/j.molp.2017.10.003