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.

Genome-wide association study of rice grain width variation

“…S1A 2 , S1B 2 ). Population assignments for individual accessions at K = 5 closely matched results of a previous STRUCTURE analysis that included these accessions (Huang et al 2012;Wang et al 2013); differences were mostly in the assignment of a few accessions to either the tropical japonica or closely related temperate japonica subgroup (see Table S1 2 for membership coefficient values).…”

“…Accession details are provided in the supplementary data, Table S1 2 . Cultivated rice accessions were selected from core germplasm resources of China and other countries to repre-sent all five major genetic subgroups within the crop based on previous analyses by Huang et al (2012) and Wang et al (2013). These include accessions of two rice variety groups not examined in previous association studies of grain width variation (aus and aromatic rice).…”

Integrated analysis of phenome, genome, and transcriptome of hybrid rice uncovered multiple heterosis-related loci for yield increase

“…We first sequenced the genome of the paternal variety 93-11 (31) and then profiled and compared the transcriptomes of LYP9 and its two parents at various life stages (32). Subsequently, we released the whole-genome sequence of the other parental line, PA64S (33), and developed a recombinant inbred line (RIL) population consisting of 219 RILs derived from LYP9 and a backcross population (RILBC1) derived from crossing each RIL with the female parent PA64S (34). In this study, we integrated phenome analyses, QTL mapping by genome resequencing, and transcriptome profiling to identify genes that drive yield heterosis in LYP9s.…”

Current status of genomic resources on wild relatives of rice

“…Presently, it holds information on 4 rice cultivars; Nipponbare (japonica), 93-11 (indica), PA64s (indica), the African rice (O. glaberrima) and a wild rice species (O. brachyantha). It has three major components: (i) integrated data curation for rice genomics and molecular biology; (ii) User-friendly viewers; (iii) Bioinformatic tools (Wang et al 2012). It is a user-friendly database as it provides three easy-to-use browsers.…”