Oryza glaberrima

Oryza glaberrima

Data Source AGI | Taxonomy ID 4538

Acknowledgements

Project funding: National Science Foundation Plant Genome Research Program (#082224) awarded to R. Wing, S. Rounsley and Y. Yu.

About Oryza glaberrima

Oryza glaberrima (African rice) is a cultivated grain distinct from its better known cousin Oryza sativa (Asian rice). African rice was independently domesticated ~3000 years ago in the Niger River Delta from its still extant progenitor, Oryza barthii. While lacking many of the agronomic and quality traits found in Asian rice, O. glaberrima is significant for its resistance to many pests and diseases and for its tolerance of drought and infertile soils. Interspecific crosses between African and Asian rice have produced cultivars with improved yield and quality traits, that have been adopted by many African countries to meet the growing need for rice as a staple food. From a scientific perspective the genome of O. glaberrima provides insight into the genetic basis of domestication and other traits by finding commonalities and differences with O. sativa. Similar to Asian rice, African rice is a diploid A-type genome, having 12 chromosomes and an estimated size of ~358 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)

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 Arabidopsis thaliana, Oryza sativa Japonica (IRGSP v1), and a few AA oryza 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.
  • Variation effect prediction with sequence ontology, for example.

Links