title: Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics.
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.
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan.
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Sakai
authors.forename: Sung Shin
authors.initials: SS
authors.lastname: Lee
authors.forename: Tsuyoshi
authors.initials: T
authors.lastname: Tanaka
authors.forename: Hisataka
authors.initials: H
authors.lastname: Numa
authors.forename: Jungsok
authors.initials: J
authors.lastname: Kim
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Kawahara
authors.forename: Hironobu
authors.initials: H
authors.lastname: Wakimoto
authors.forename: Ching-chia
authors.initials: CC
authors.lastname: Yang
authors.forename: Masao
authors.initials: M
authors.lastname: Iwamoto
authors.forename: Takashi
authors.initials: T
authors.lastname: Abe
authors.forename: Yuko
authors.initials: Y
authors.lastname: Yamada
authors.forename: Akira
authors.initials: A
authors.lastname: Muto
authors.forename: Hachiro
authors.initials: H
authors.lastname: Inokuchi
authors.forename: Toshimichi
authors.initials: T
authors.lastname: Ikemura
authors.forename: Takashi
authors.initials: T
authors.lastname: Matsumoto
authors.forename: Takuji
authors.initials: T
authors.lastname: Sasaki
authors.forename: Takeshi
authors.initials: T
authors.lastname: Itoh
mesh_terms: D001483:Base Sequence; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D017343:Genes, Plant; D056426:Genetic Loci; D023281:Genomics / Q000379:methods; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D012275:Oryza / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D057386:Search Engine; D017385:Sequence Homology