Oryza rufipogon (OR_W1943)

Oryza rufipogon Assembly and Gene Annotation

These pre-publication data are being released under guidelines of the Fort Lauderdale Agreement, which reaffirms the balance between fair use (i.e. no pre-emptive publication) and early disclosure. Users are encouraged use these data to advance their research on individual loci but are asked to respect the rights of the investigators who generated these data to publish the whole-genome level description of the O. rufipogon in a peer-reviewed journal. This description includes whole-genome comparative analyses, genome size evolution, gene family evolution, gene organization and movement, heterochromatin, centromere evolution. This genome falls under the scope of the I-OMAP (International Oryza Map Alignment Project) consortium. The I-OMAP consortium is an internationally coordinated effort to create high-quality reference assemblies representing the diversity of wild and crop-progenitor species in the genus Oryza (Jacquemin et al, 2012). For inquiries and information on how to cite these data please contact Dr. Bin Han and Dr. Rod Wing.

About Oryza rufipogon

Oryza rufipogon (AA genome type) is a wild rice, perennial, tufted, and scrambling grass with nodal tillering; plant height variable (1-5 m) depending on the depth of water; panicles open; spikelets usually 4.5-10.6 mm long and 1.6-3.5 mm wide with awns usually 4-10 cm long; anthers >3 mm reaching 7.4 mm long.

Chromosome number: 2n=2x=24

Genome: AA

Distribution: Australia, Bangladesh, China, India, Indonesia, Laos, Malaysia, Myanmar, Nepal, Papua New Guinea, Philippines, Sri Lanka, Thailand, and Vietnam.

Habitat: Found in swamps and marshes, in open ditches, swampy grassland, ponds, along river banks, at the edges of lakes, and in or at the margins of rice fields, commonly found in deep water areas (0.2-4m). Grows in clay/loam soil and black soil, in full sun.


The sequencing and assembly was done by Dr. Bin Han's group in Shanghai Institutes for Biological Sciences, CAS.


Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline. Non coding RNA genes were predicted with Infernal and tRNA genes with tRNAscan. RepeatMasker was used to annotate repeats and transposable elements with Oryza-specific de novo repeat libraries. These analyses were conducted at Arizona Genomics Institute (AGI) led by Dr. Rod Wing.

Gramene/Ensembl Genomes Annotation

Additional annotations generated by the Gramene and Ensembl Plants project include:

  • Gene phylogenetic trees with other other Gramene species, see example.
  • Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
  • Identification of various repeat features by programs such as RepeatMasker with MIPS and AGI repeat libraries, and Dust, TRF.

More information

General information about this species can be found in Wikipedia.



AssemblyOR_W1943, INSDC Assembly GCA_000817225.1, Jan 2015
Database version104.11
Golden Path Length338,040,714
Genebuild byOGE
Genebuild methodImport
Data sourceOryza Genome Evolution Project

Gene counts

Coding genes37,071
Non coding genes740
Small non coding genes723
Long non coding genes17
Gene transcripts48,332

About this species