Description

Oryza punctata is an annual grass in the rice genus Oryza, also known as red rice, related to cultivated rice O. sativa. O. punctata forms clumps or tussocks from 50–120 cm tall. It is a native to tropical Africa and Madagascar but is also found in Thailand and other parts of Indochina. O. punctata is a weed species in commercial rice growing operations although it appears to be rare in its native range. O. punctata has an IUCN status of least concern. It is not generally eaten or used as fodder by farmers but there is some evidence that it has been used as such during periods of famine. Due to the importance of the crop varieties of rice (Oryza sativa and O. glaberrima) globally, the evolution of the Oryza genus as a whole has been studied extensively. A lot of information about O. punctata has been elucidated as a secondary benefit to this commercial research. O. punctata evolved some 5 million years ago in the second of two rapid radiation events that occurred in the Oryza L. genus.

Whole Genomes

Whole Genome Sequences & Annotations for Oryza punctata

• Oryza punctata OpunRS2

S genes

Oryza punctata OpunRS2 S genes

Query	Chromosome	Size(bp)	Coordinates	tBLASTn Hit	tBLASTn %ID	Domain
DUF247I-SΨ	CM002492.2	32501981	6383914-6384396	Olongistaminata	73	DUF247
DUF247II-SΨ	CM002492.2	32501981	6380474-6380620	Olongistaminata	68	DUF247
HPS10-S	CM002492.2	32501981	6381576-6381657, 6381876-6382000	OcoarctataS1	60	-
DUF247I-ZΨ	CM002491.2	34321815	31603253-31603642	AsativaDUF247I-Z	73	DUF247
DUF247II-Z	CM002491.2	34321815	31608630-31609940	Ocoarctata	86	DUF247
HPS10-Z	CM002491.2	34321815	31605786-31605939, 31605990-31606135	Omeridionalis	43	-

Downloads

The Oryza punctata S gene sequences are available in FASTA format.

CDS and Protein (FASTA file)

S-gene_Oryza_punctata

Publications

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. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nat Genet. 2018 Feb;50(2):285-296. doi: 10.1038/s41588-018-0040-0.