Search Oryza sativa

About Oryza sativa

Oryza sativa (rice) is the staple food for 2.5 billion people, and, after maize, the grain with the second highest worldwide production. In addition to it's agronomic importance, O. sativa is also an important biological model species for monocot plants, and major cereal crops such as maize, wheat, barley and sorghum. O. sativa has a compact genome of approx. 500 Mbase (n=12) compared with the multi-gigabase genomes of maize, wheat and barley. [more].

Genome Sequencing and Gene Prediction (MSU6)

Two sub-species of O. sativa have been sequenced; the Japonica Group, and the Indica Group. This browser presents the Japonica sequence, which has become the most widely used reference genome for rice. A separate browser presents the Indica sequence.

Whilst the completion of the rice genome (O. sativa Japonica Group cultivar Nipponbare) sequencing was announced by the International Rice Genome Sequencing Consortium (IRGSP) in 2002, the assembly was not published until 2005 [1]. An assembly of the draft IRGSP sequence was, however, made available by the TIGR Rice Genome Annotation Project somewhat earlier [2]. The sequencing strategy followed a BAC-by-BAC approach, with clones anchored to chromosomes via genetic and physical maps. This browser uses the sixth iteration of the TIGR, latterly MSU assembly, released in January 2009.[more]

MSU's gene prediction pipeline uses a number of ab initio methods, EST/mRNA alignments, and the PASA alignment assembler. [more].

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 sativa variation data from NCBI dbSNP onto the genome assembly. Includes OryzaSNP large scale SNP variation study (McNally, K et al. PNAS 2009) - ~160K SNPs x 20 diversity rice accessions, mapped from IRGSP4 to MSU6. Now also includes a further SNP variation study (Zhao et al PLoS One 2010) - 1311 SNPs x 395 accessions.
• Probes from the Rice Genome Array for two rice cultivars were aligned to the genome.

This release of the assembly (MSU6) for Oryza sativa is composed of 3522 clones with a total length of 488.0 Mb assembled into 16 chromosomes with a total length of 374.3 Mb.

Links

• Gramene/EnsemblGenomes browser for Oryza sativa Indica Group
• Gramene species page for Oryza
• MSU Rice Genome Annotation Project
• International Rice Genome Sequencing Consortium (IRGSP)

References

1. International Rice Genome Sequencing Project.The map-based sequence of the rice genome. Nature. 2005;436(7052):793-800. PubMed ID: 16100779
2. Yuan Q, Ouyang S, Liu J, et al. The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists. Nucleic Acids Res. 2003;31(1):229-233. PubMed ID: 12519988
3. Ouyang S, Zhu W, Hamilton J, et al. The TIGR Rice Genome Annotation Resource: improvements and new features. Nucl. Acids Res. 2007;35(suppl_1):D883-887. PubMed ID: 17145706
4. Zhao K, Wright M, Kimball J, et al. Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome. PubMed ID: 20520727