Information about Rice Genome
Rice (Oryza sativa) is not only an important model organism for monocot plants and cereals but also the most widely consumed staple food for a large part of the world's human population (2.5 billion people). The genome of O. sativaJaponicawas sequenced in 2002 by IRGSP.In 2013, Kawahara et al. describedan integrated Os-Nipponbare-Reference-IRGSP-1.0 pseudomolecule(http://rice.plantbiology.msu.edu/annotation_pseudo_current.shtml
,also known as MSU7), which represents a final and unified set of pseudomolecule. The current genome assembly can be downloaded from the rap-db(http://rapdb.dna.affrc.go.jp/
O. sativaJaponicahas a compact diploid genome of approximately 500 Mbp (n=12) compared with the multi-gigabase genomes of maize, wheat and barley.There are the 12 chromosomes, one pseudomolecule representing the unanchored BAC clones, one pseudomolecule representing unmapped Syngenta sequences plus the two organellar genomes. It has the following facts:
● Genome size: ~370M (373,245,519bp)
● Number of chromosomes: 12 (2n=24)
● Number of unplaced scaffolds: 3793
● Number of protein-coding genes: 35679(RAP-DB)
● Number of non-coding genes: 55401
● Number of transcripts: 97751
● TE-Related Genes: 17272
Genome Re-sequencing Projects and Variation Identification
Recently, thousands of rice accessions (see in 'Species Summary'-'Material Number') includingindica, japonica and wild rice have been re-sequenced, such as:
● 2014 - The 3,000 rice genomes project
● 2010 – Huang et al.sequenced 517 rice landraces
The genome of O. sativaJaponicawas taken as the reference genome in our variation database. Sequence variations were identified from those public available and in-housed sequenced ricere-sequenced reads using a unified computational pipeline (seeGuidelines).
 Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S et al.Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice (N Y) 2013. 6:4.
 Sakai H, Lee SS, Tanaka T, Numa H, Kim J, Kawahara Y, Wakimoto H, Yang CC, Iwamoto M, Abe T et al.Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. Plant Cell Physiol. 2013.54:e6.