Oryza sativa Indica Group Assembly and Gene Annotation

About Oryza sativa Indica

Oryza sativa Indica is one of the two most commonly cultivated sub-species of rice (along with O. sativa Japonica) and is the most widely grown in the hot climates of Southern Asia. The genome of Indica is very similar to that of Japonica, which is generally restricted to temperate climes such as Japan.

Assembly

The genome of Oryza sativa Indica Group cultivar 93-11 was sequenced by the Beijing Genome Institute (BGI) following a whole-genome shotgun strategy.

Annotation

Gene annotations were predicted by BGI using Glean as released in 2008. This browser presents data from the 2010 release of the BGI RISe Rice Information System.

Regulation

Probes from the Rice Genome Array for two rice cultivars were aligned to the genome.

Variation

Two sources of variation data from NCBI dbSNP has been mapped onto the genome assembly:

1. SNPs called from the comparison of Oryza sativa Indica and Oryza sativa Japonica.
2. SNPs resulting from OMAP project alignments between O. glaberrima, O. punctata, O. nivara, and O. rufipogon agains O. sativa Japoinca mapped to O. sativa indica.

References

1. A draft sequence of the rice genome (Oryza sativa L. ssp. indica).
   Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X et al. 2002. Science. 296:79-92.
2. BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics.
   Zhao W, Wang J, He X, Huang X, Jiao Y, Dai M, Wei S, Fu J, Chen Y, Ren X et al. 2004. Nucleic Acids Res.. 32:D377-82.

Links

• Main Gramene/Ensembl Genomes browser for Oryza sativa
• Gramene species page for Oryza
• BGI Rise Rice Genome Database

More information

General information about this species can be found in Wikipedia.