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

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.

Assembly

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

Annotation

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.

References

1. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.
   Stein JC, Yu Y, Copetti D, Zwickl DJ, Zhang L, Zhang C, Chougule K, Gao D, Iwata A, Goicoechea JL, Wei S, Wang J, Liao Y, Wang M, Jacquemin J, Becker C, Kudrna D, Zhang J, Londono CEM, Song X, Lee S, Sanchez P, Zuccolo A, Ammiraju JSS, Talag J, Danowitz A, Rivera LF, Gschwend AR, Noutsos C, Wu CC, Kao SM, Zeng JW, Wei FJ, Zhao Q, Feng Q, El Baidouri M, Carpentier MC, Lasserre E, Cooke R, Rosa Farias DD, da Maia LC, Dos Santos RS, Nyberg KG, McNally KL, Mauleon R, Alexandrov N, Schmutz J, Flowers D, Fan C, Weigel D, Jena KK, Wicker T, Chen M, Han B, Henry R, Hsing YC, Kurata N, de Oliveira AC, Panaud O, Jackson SA, Machado CA, Sanderson MJ, Long M, Ware D, Wing RA..
2. The International Oryza Map Alignment Project: development of a genus-wide comparative genomics platform to help solve the 9 billion-people question.
   Jacquemin J, Bhatia D, Singh K, Wing RA..

Picture credit: Paul Sanchez, Arizona Genomics Institute.

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.

Links

• International Rice Genome Sequencing Consortium (IRGSP)

More information

General information about this species can be found in Wikipedia.