Rice Annotation Project Database (RAP-DB) and its Extension to Comparative Genomics

The Rice Annotation Project Database (RAP-DB, http://rapdb.dna.affrc.go.jp/) provides a comprehensive data set of gene annotations for the genome sequence of rice, Oryza sativa (japonica group) cv. Nipponbare.  For highly reliable, up-to-date rice gene annotations, we incorporated literature-based manual curation of automated annotation data.  In particular, for 1,626 loci, we employed commonly used gene names or gene symbols approved by CGSNL.  To utilize genome-wide resequencing data obtained from a Japanese leading japonica cultivar, Koshihikari, and a Chinese indica cultivar, Guangluai-4, all the Illumina reads were mapped to the Nipponbare reference genome. The alignments with the SNPs and gene functional annotations can be displayed by Short-Read Assembly Browser (S-RAB).  We also developed two satellite databases, Plant Gene Family Database (PGFD) and Integrative Database of Cereal Gene Phylogeny (IDCGP), which present gene family and homologous gene relationships among diverse plant species.  RAP-DB and the satellite databases offer simple and user-friendly web interfaces, enabling plant and genome researchers to easily access the data and facilitating a broad range of plant research topics.  We discuss how we deal with a large-scale next-generation sequencing data and display such information in an effective manner.  All of these data are available through our databases, which are maintained as a part of the database project of the Ministry of Agriculture, Forestry and Fisheries.