The Rice Annotation Project Database: update for a new genome assembly (Os-Nipponbare-Reference-IRGSP-1.0)

Since 2005, The Rice Annotation Project Database (RAP-DB, http://rapdb.dna.affrc.go.jp/) has provided manually curated functional annotation and other genomics information on the genome assembly of Oryza sativa (japonica, cv. Nipponbare). Here we present an updated version of the RAP-DB that contains novel functions and annotation for a new genome assembly (Os-Nipponbare-Reference-IRGSP-1.0) released on October 31st, 2011. Because the genome sequence was validated thoroughly by illumina and 454 sequence reads, precise annotation on this genome is anticipated to expedite in-depth analyses of rice cultivars. Mapping of rice and other cereal FLcDNAs to the genome identified 37,878 loci with evidence of expression. In addition, 8,121 loci without any transcripts were also predicted by ab initio gene prediction methods. In collaboration with Oryzabase, we assigned gene symbols of 901 loci proposed by CGSNL. NGS data (Genome-seq of other cultivars and RNA-seq) are displayed through the GBrowse and Short-Read Assembly Browser, which was newly developed for the RAP-DB. Phylogenetic trees are displayed in a satellite database "Interactive Database of Cereal Gene Phylogeny" that provides users with an interactive editing function of multiple-sequence alignments and phylogenetic trees.