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. 2013 Jan;41(Database issue):D1199-205.
doi: 10.1093/nar/gks1225. Epub 2012 Nov 28.

The Rice Genome Knowledgebase (RGKbase): An Annotation Database for Rice Comparative Genomics and Evolutionary Biology

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Free PMC article

The Rice Genome Knowledgebase (RGKbase): An Annotation Database for Rice Comparative Genomics and Evolutionary Biology

Dapeng Wang et al. Nucleic Acids Res. .
Free PMC article

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.

Figures

Figure 1.
Figure 1.
Snapshots of selected browser functions. (A) Gbrowse; an example displays RefSeq mapping, gene structure and repetitive elements annotations in a selected window. (B) Gbrowse-syn; a window displays syntenic regions and selected tracks between two genomes, Nipponbare and 93-11. (C) GeneBrowse; it lists details of gene and genome annotations (93-11 genome). (D) Circos; it displays a link map of homologous genic regions of rice chromosomes (93-11).

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References

    1. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, et al. A draft sequence of the rice genome (Oryza sativa L ssp. indica) Science. 2002;296:79–92. - PubMed
    1. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica) Science. 2002;296:92–100. - PubMed
    1. Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C, et al. The Genomes of Oryza sativa: a history of duplications. PLoS Biol. 2005;3:e38. - PMC - PubMed
    1. International Rice Genome Sequencing Project. The map-based sequence of the rice genome. Nature. 2005;436:793–800. - PubMed
    1. Zhao K, Tung CW, Eizenga GC, Wright MH, Ali ML, Price AH, Norton GJ, Islam MR, Reynolds A, Mezey J, et al. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat. Commun. 2011;2:467. - PMC - PubMed

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