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About Oryza sativa Indica Group
Of the two most commonly cultivated sub-species of rice, varieties of the Indica Group are the most widely grown in the hot climates of Southern Asia. The other sub-species, Japonica, is generally restricted to temperate climes such as Japan. The genome of O. sativa Indica Group is very similar to that presented on the main O. sativa genome browser.
Genome Sequencing and Gene Prediction (release BGI-2005)
The genome of O. sativa Indica Group cultivar 93-11 was sequenced by the Beijing Genome Institute (BGI) following a whole-genome shotgun strategy and published in 2002 [1]. Gene annotations were predicted by BGI using Glean as released on 10-28-2008. This browser presents data from the 2010 release of the BGI RISe Rice Information System [2].
Gramene/Ensembl Genomes Annotation
Additional annotations generated by the Gramene/Ensembl Genomes projects include:
- The standard set of Gramene analyses detailed here.
- Phylogenetic gene trees and whole-genome alignments with several plant and metazoan species, using Ensembl's Compara pipeline.
- Mapping of Oryza indica variation data from NCBI dbSNP onto the genome assembly.
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Probes from the
for two rice cultivars were aligned to the genome.
Links
- Main Gramene/EnsemblGenomes browser for Oryza sativa
- Gramene species page for Oryza
- BGI Rise Rice Genome Database
References
- Yu J, Hu S, Wang J, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science. 2002;296(5565):79-92. PubMed ID: 11935017
- Zhao W, Wang J, He X, et al. BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics. Nucl. Acids Res. 2004;32(suppl_1):D377-382. PubMed ID: 14681438
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