Oryza rufipogon Assembly and Gene Annotation
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
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.
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.
- Oryza Genome Evoltion Project Genome Browser
- Gramene species page for Oryza
- Oryza Genome Evolution Project in AGI (Arizona Genomics Institute)
- International Rice Genome Sequencing Consortium (IRGSP)
- Rice Knowledge Bank
General information about this species can be found in Wikipedia.
|Assembly||OR_W1943, INSDC Assembly GCA_000817225.1, Jan 2015|
|Golden Path Length||338,040,714|
|Data source||Oryza Genome Evolution Project|
|Non coding genes||740|
|Small non coding genes||723|
|Long non coding genes||17|