Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics

The Rice Annotation Project Database (RAP-DB, http://rapdb.dna.affrc.go.jp/) has been providing a comprehensive set of gene annotations for the genome sequence of rice, Oryza sativa (japonica group) cv. Nipponbare.  To provide plant researchers with highly reliable and up-to-date rice gene annotations, we have been incorporating literature-based manually curated data, and 1,626 loci currently incorporate literature-based annotation data, including commonly used gene names or gene symbols.  Transcriptional activities are shown at the nucleotide level by mapping RNA-Seq reads derived from 27 samples.  We also mapped the Illumina reads of a Japanese leading japonica cultivar, Koshihikari, and a Chinese indica cultivar, Guangluai-4, to the genome and show alignments together with the SNPs and gene functional annotations through newly developed browser, Short-Read Assembly Browser.  We have developed two satellite databases, Plant Gene Family Database (PGFD) and Integrative Database of Cereal Gene Phylogeny (IDCGP), which display 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.