Oryza brachyantha

Oryza brachyantha

Data Source OGE | Taxonomy ID 4533

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. bracgyantha 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. For inquiries and information on how to cite these data please contact Dr. Mingsheng Chen or Dr. Rod Wing.

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.

More information and statistics

Gene annotation

What can I find? Protein-coding and non-coding genes, splice variants, cDNA and protein sequences, non-coding RNAs.

More about this genebuild

Download genes, cDNAs, ncRNA, proteins - FASTA - GFF3

Update your old Ensembl IDs

Comparative genomics

What can I find? Homologues, gene trees, and whole genome alignments across multiple species.

More about comparative analysis

Download alignments (EMF)

Variation

This species currently has no variation database. However you can process your own variants using the Variant Effect Predictor:

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.

Links