BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics

Abstract

Rice is a major food staple for the world's population and serves as a model species in cereal genome research. The Beijing Genomics Institute (BGI) has long been devoting itself to sequencing, information analysis and biological research of the rice and other crop genomes. In order to facilitate the application of the rice genomic information and to provide a foundation for functional and evolutionary studies of other important cereal crops, we implemented our Rice Information System (BGI-RIS), the most up-to-date integrated information resource as well as a workbench for comparative genomic analysis. In addition to comprehensive data from Oryza sativa L. ssp. indica sequenced by BGI, BGI-RIS also hosts carefully curated genome information from Oryza sativa L. ssp. japonica and EST sequences available from other cereal crops. In this resource, sequence contigs of indica (93-11) have been further assembled into Mbp-sized scaffolds and anchored onto the rice chromosomes referenced to physical/genetic markers, cDNAs and BAC-end sequences. We have annotated the rice genomes for gene content, repetitive elements, gene duplications (tandem and segmental) and single nucleotide polymorphisms between rice subspecies. Designed as a basic platform, BGI-RIS presents the sequenced genomes and related information in systematic and graphical ways for the convenience of in-depth comparative studies (http://rise.genomics.org.cn/).

Plant noncoding RNA gene discovery by “single-genome comparative genomics”

“…We used the tiling microarray data from Li et al (2006) generated by a minimal tiling strategy using 36-mer oligonucleotides representing the nonrepetitive sequences of the rice indica genome (August 2003 assembly, BGI) (Zhao et al 2004). We extracted the 660-nt region around each repeat family member according to its location in the japonica genome and used the Megablast program with default setting to align the extended sequence to the indica genome.…”

Genomic and Genetic Database Resources for the Grasses

“…The three main rice genome annotation resources are the Michigan State University Rice Genome Annotation Project (formerly hosted at The Institute for Genomic Research), the Rice Annotation Project (RAP), and the Rice Information System (Rise; Zhao et al, 2004;Ouyang et al, 2007;Tanaka et al, 2008). The maize genome sequence can be viewed at the MaizeSequence database (http://www.…”

“…Each of the rice databases uses its own genome assembly of japonica (Rise, RAP, and MSU) or indica (Rise) rice (Zhao et al, 2004;Ouyang et al, 2007;Tanaka et al, 2008). All three projects each have their own gene model sets and provide genome browsers to graphically view their annotations (Supplemental Table S1).…”

Current status of rice informatics resources and breeding applications

“…Central to these genomics efforts are the genome sequence databases, namely, the RAP-DB (Rice Annotation Project 2008) and the MSU Rice Genome Annotation Project Database representing the map-based genome sequence of the japonica cultivar Nipponbare generated by the International Rice Genome Sequencing Project (2005). In addition, genome sequence data derived by whole genome sequencing of indica rice cultivar 93-11 (Yu et al 2002) and japonica rice cultivar Nipponbare (Goff et al 2002) are also available via the BGI-RISe Database (Zhao et al 2004). These databases have been conceptualized with the aim of providing a comprehensive analysis of the rice genome and include both structural annotations to identify the genomic elements and functional annotations to attach biological meaning to the sequence data.…”