title: The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology.
abstract: Over the past 10 years, genomes of cultivated rice cultivars and their wild counterparts have been sequenced although most efforts are focused on genome assembly and annotation of two major cultivated rice (Oryza sativa L.) subspecies, 93-11 (indica) and Nipponbare (japonica). To integrate information from genome assemblies and annotations for better analysis and application, we now introduce a comparative rice genome database, the Rice Genome Knowledgebase (RGKbase, http://rgkbase.big.ac.cn/RGKbase/). RGKbase is built to have three major components: (i) integrated data curation for rice genomics and molecular biology, which includes genome sequence assemblies, transcriptomic and epigenomic data, genetic variations, quantitative trait loci (QTLs) and the relevant literature; (ii) User-friendly viewers, such as Gbrowse, GeneBrowse and Circos, for genome annotations and evolutionary dynamics and (iii) Bioinformatic tools for compositional and synteny analyses, gene family classifications, gene ontology terms and pathways and gene co-expression networks. RGKbase current includes data from five rice cultivars and species: Nipponbare (japonica), 93-11 (indica), PA64s (indica), the African rice (Oryza glaberrima) and a wild rice species (Oryza brachyantha). We are also constantly introducing new datasets from variety of public efforts, such as two recent releases-sequence data from ∼1000 rice varieties, which are mapped into the reference genome, yielding ample high-quality single-nucleotide polymorphisms and insertions-deletions.
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, PR China.
authors.forename: Dapeng
authors.initials: D
authors.lastname: Wang
authors.forename: Yan
authors.initials: Y
authors.lastname: Xia
authors.forename: Xinna
authors.initials: X
authors.lastname: Li
authors.forename: Lixia
authors.initials: L
authors.lastname: Hou
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
mesh_terms: D030541:Databases, Genetic; D019143:Evolution, Molecular; D018745:Genome, Plant; D023281:Genomics; D020407:Internet; D058977:Molecular Sequence Annotation; D012275:Oryza / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics; D011110:Polymorphism, Genetic; D014176:Protein Biosynthesis; D012091:Repetitive Sequences, Nucleic Acid; D012984:Software; D014158:Transcription, Genetic; D014584:User-Computer Interface
chemical_list: D010940:Plant Proteins