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. 2013 Feb;54(2):e6.
doi: 10.1093/pcp/pcs183. Epub 2013 Jan 7.

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

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Free PMC article

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

Hiroaki Sakai et al. Plant Cell Physiol. .
Free PMC article

Abstract

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. Since the first release in 2005, RAP-DB has been updated several times along with the genome assembly updates. Here, we present our newest RAP-DB based on the latest genome assembly, Os-Nipponbare-Reference-IRGSP-1.0 (IRGSP-1.0), which was released in 2011. We detected 37,869 loci by mapping transcript and protein sequences of 150 monocot species. 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 single nucleotide polymorphisms (SNPs) and gene functional annotations through a newly developed browser, Short-Read Assembly Browser (S-RAB). 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 access the data easily and facilitating a broad range of plant research topics.

Figures

Fig. 1
Fig. 1
Gene map view. In RNA-Seq tracks, gene expression levels are shown as a histogram generated from the depth of mapped reads. At the bottom, two tracks, ‘Koshihikari’ and ‘Guangluai-4’, are linked to the Short-Read Assembly Browser.
Fig. 2
Fig. 2
Gene details view. The ‘Details’ tab shows the detailed annotation information including the literature-based manual curation data. The ‘DB references’ tab provides hyperlinks to the external databases including the two satellite databases, Plant Gene Family Database and Integrative Database of Cereal Gene Phylogeny.
Fig. 3
Fig. 3
Short-Read Assembly Browser (S-RAB). The S-RAB window consists of (i) a Gene information view (upper left); (ii) an Alignment view (bottom); and (iii) a Short-read information view (upper right).
Fig. 4
Fig. 4
Integrative Database of Cereal Gene Phylogeny (IDCGP). (A) Main window of IDCGP showing the phylogenetic trees, hyperlinks to the downloadable data and buttons for adding sequences and editing multiple sequence alignments. (B) A window for editing multiple sequence alignments.

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