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. 2004 Jan 1;32(Database issue):D377-82.
doi: 10.1093/nar/gkh085.

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

Wenming Zhao  1 , Jing Wang, Ximiao He, Xiaobing Huang, Yongzhi Jiao, Mingtao Dai, Shulin Wei, Jian Fu, Ye Chen, Xiaoyu Ren, Yong Zhang, Peixiang Ni, Jianguo Zhang, Songgang Li, Jian Wang, Gane Ka-Shu Wong, Hongyu Zhao, Jun Yu, Huanming Yang, Jun Wang
Affiliations

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

Wenming Zhao et al. Nucleic Acids Res. .

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/).

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Figures

Figure 1
Figure 1
Examples of the of BGI-RIS viewer for O.sativa L. ssp. indica (93-11). Screenshots of (A) the ContigView, (B) the GeneView, which offers zoomed-in information for the predicted genes chosen in the ContigView and (C) the cDNAView, with two highlighted SNPs identified between the genome sequences of indica (93-11) and japonica (Nipponbare).
Figure 1
Figure 1
Examples of the of BGI-RIS viewer for O.sativa L. ssp. indica (93-11). Screenshots of (A) the ContigView, (B) the GeneView, which offers zoomed-in information for the predicted genes chosen in the ContigView and (C) the cDNAView, with two highlighted SNPs identified between the genome sequences of indica (93-11) and japonica (Nipponbare).
Figure 1
Figure 1
Examples of the of BGI-RIS viewer for O.sativa L. ssp. indica (93-11). Screenshots of (A) the ContigView, (B) the GeneView, which offers zoomed-in information for the predicted genes chosen in the ContigView and (C) the cDNAView, with two highlighted SNPs identified between the genome sequences of indica (93-11) and japonica (Nipponbare).
Figure 2
Figure 2
An example of the CompView features. Rice genetic markers are identified on rice chromosome 10 of indica (93-11) and japonica (Nipponbare).
See this image and copyright information in PMC

References

    1. Yu J., Hu,S.N., Wang,J., Gane,K.W., Li,S.G., Liu,B., Deng,Y.J., Li,D., Zhou,Y., Zhang X. Q. et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science, 296, 79–92. - PubMed
    1. Goff S.A., Ricke,D., Lan, T-H., Presting,G., Wang,R., Dunn,M., Glazebrook,J., Sessions,A., Oeller,P., Varma,H. et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science, 296, 92–100. - PubMed
    1. Chen M., SanMiguel,P., De Oliveira,A.C., Woo,S.-S., Zhang,H., Wing,R.A. and Bennetzen,J.L. (1997) Microcolinearity in sh2-homologous regions of the maize, rice and sorghum genomes. Proc. Natl Acad. Sci. USA, 94, 3431–3435. - PMC - PubMed
    1. Bevan M. and Murphy,G. (1999) The small, the large and the wild—the value of comparison in plant genomics. Plant Genomics, 15, 211–215. - PubMed
    1. McCouch S. (1998) Toward a plant genomics initiative: thought on the value of cross-species and cross-genera comparisons in the grasses. Proc. Natl Acad. Sci. USA, 95, 1983–1985. - PMC - PubMed

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