Resource Type
Genome Assembly
Whole Genome Assembly (IRGSP-1.0) and Annotation (RGAP 7) of Oryza sativa ssp japonica - cv. Nipponbare (MSU)
Program, Pipeline, Workflow or Method Name
MSU Assembly & annotation workflow
Program Version
MSU v 7.1
Date Performed
Saturday, October 10, 2015
Data Source
Source Name
: Os-Nipponbare-Reference-IRGSP-1.0 assembly
Source Version
: Release 7.1
Data Source

The Rice Genome Annotation Project


This is MSU Release 7.0 of the annotation of the genome of the Nipponbare/ japonica subspecies of Oryza sativa . This release is based on a new pseudomolecule assembly (Os-Nipponbare-Reference-IRGSP-1.0) made in collaboration with the Agrogenomics Research Center at the National Institute of Agrobiological Sciences, Tsukuba, Japan. This set of pseudomolecules unifies the previous MSU with the IRGSP/RAP effort.

Important note on Rice Gene Set: the Oryza sativa MSU release 7 rice annotation has been refiltered by the Phytozome annotation team. Phytozome always attempts to remove genes identified as likely Transposable elements (TE) and excludes them from the genes displayed in Phytozome. This is essential for proper constructdion of gene families. Previously, the rice set was filtered for TEs based on a flag in one of the MSU annotation auxillary files. After discovering that this file contained errors, we have redone the filtering using domain and defline-based information. This relaxed criteria rescued approximately 3,104 genes from being designated as TEs and thus excluded from the Phytozome gene set. The current Rice gene set in Phytozome v11 contains 42,189 non-TE genes.


372Mb arranged in 12 chromosomes


42,189 loci containing protein-coding transcripts, which include TE genes in this Phytozome release


52,424 protein-coding transcripts

Reference Publication(s)

Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L, Orvis J, Haas B, Wortman J, Buell CR, The TIGR Rice Genome Annotation Resource: improvements and new features.Nucleic acids research. 2007 Jan ; 35 Database issue D883-7

Source : Phytozome

About Oryza sativa Japonica

Oryza sativa Japonica (rice) is the staple food for 2.5 billion people. It is the grain with the second highest worldwide production after Zea mays. In addition to its agronomic importance, rice is an important model species for monocot plants and cereals such as maize, wheat, barley and sorghum. O. sativa has a compact diploid genome of approximately 500 Mb (n=12) compared with the multi-gigabase genomes of maize, wheat and barley.


Scientists from the MSU Rice Genome Annotation Project (MSU), the International Rice Genome Sequencing Project (IRGSP) and the Rice Annotation Project Database (RAP-DB) generated a unified assembly of the 12 rice pseudomolecules of Oryza sativa Japonica Group cv. Nipponbare.

The pseudomolecule for each chromosome was constructed by joining the nucleotide sequences of each PAC/BAC clone based on the order of the clones on the physical map. Overlapping sequences were removed and physical gaps were replaced with Ns. Updated pseudomolecules were constructed based on the original IRGSP sequence data in combination with a BAC-optical map and error correction using 44-fold coverage next generation sequencing read. The nucleotide sequences of seven new clones mapped on the euchromatin/telomere junctions were added in the new genome assembly. In addition, several clones in the centromere region of chromosome 5 were improved and one gap on chromosome 11 was closed.

Kawahara et al (2013) describe the integrated Os-Nipponbare-Reference-IRGSP-1.0 pseudomolecules, also known as MSU7. Gene loci, gene models and associated annotations were independently created by each group, but can be easily compared using the common reference.


Source : Gramene

Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S, Childs KL, Davidson RM, Lin H, Quesada-Ocampo L, Vaillancourt B, Sakai H, Lee SS, Kim J, Numa H, Itoh T, Buell CR, Matsumoto T. Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data.. Rice (New York, N.Y.). 2013 Feb 06; 6(1):4.