About Oryza brachyantha
Oryza brachyantha (wild rice) is a distant relative of cultivated rice (O. satia Japonica and O. sativa Indica). It is placed on the basal lineage of Oryza and is the only member of the genus assigned to the F-genome type. An annual or weekly perennial tufted grass, it is distributed in west and central Africa, and grows in open wetland habitats. It has potentially useful traits for rice breeding, including resistance/tolerance to yellow stem borer, leaffolder, whorl maggot and bacterial blight. The O. brachyantha genome provides an important resource for functional and evolutionary studies in the genus Oryza. Its nuclear genome is diploid (2n = 24) and ~362 Mbp.
What can I find? Homologues, gene trees, and whole genome alignments across multiple species.
Download alignments (EMF)
|Oryza brachyantha : Arabidopsis thaliana||LASTZ_NET | stats|
|Oryza brachyantha : Oryza barthii||LASTZ_NET | stats|
|Oryza brachyantha : Oryza punctata||LASTZ_NET | stats|
|Oryza brachyantha : Oryza sativa Japonica||LASTZ_NET | stats|
This species currently has no variation database. However you can process your own variants using the Variant Effect Predictor:
Gramene/Ensembl Genomes Annotation
Additional annotations generated by the Gramene project include:
- Gene phylogenetic trees with other Gramene species, see example.
- Lastz Whole Genome Alignment to Oryza sativa Japonica (IRGSP v1), Arabidopsis thaliana and a few other AA genomes, see example.
- Ortholog based DAGchainer synteny detection against other AA genomes, see example.
- Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
- Identification of various repeat features from MIPS and AGI repeat libraries.