RRC ID 25688
Author Sakai H, Lee SS, Tanaka T, Numa H, Kim J, Kawahara Y, Wakimoto H, Yang CC, Iwamoto M, Abe T, Yamada Y, Muto A, Inokuchi H, Ikemura T, Matsumoto T, Sasaki T, Itoh T.
Title Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics.
Journal Plant Cell Physiol.
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.
Volume 54(2)
Pages e6
Published 2013-2
DOI 10.1093/pcp/pcs183
PII pcs183
PMID 23299411
PMC PMC3583025
MeSH Base Sequence Databases, Genetic* Gene Expression Profiling Genes, Plant Genetic Loci Genomics / methods Microsatellite Repeats Molecular Sequence Annotation* Molecular Sequence Data Oryza / classification Oryza / genetics* Phylogeny Polymorphism, Single Nucleotide Search Engine Sequence Homology
IF 4.059
Times Cited 130
WOS Category PLANT SCIENCES CELL BIOLOGY
Resource
Rice
INFORMATION Oryzabase