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.
What can I find? Homologues, gene trees, and whole genome alignments across multiple species.
Download alignments (EMF)
|Oryza glaberrima : Arabidopsis thaliana||BLASTZ_NET | stats|
|Oryza glaberrima : Leersia perrieri||LASTZ_NET | stats|
|Oryza glaberrima : Oryza barthii||LASTZ_NET | stats|
|Oryza glaberrima : Oryza brachyantha||LASTZ_NET | stats|
|Oryza glaberrima : Oryza glumaepatula||LASTZ_NET | stats|
|Oryza glaberrima : Oryza longistaminata||LASTZ_NET | stats|
|Oryza glaberrima : Oryza meridionalis||LASTZ_NET | stats|
|Oryza glaberrima : Oryza nivara||LASTZ_NET | stats|
|Oryza glaberrima : Oryza punctata||LASTZ_NET | stats|
|Oryza glaberrima : Oryza rufipogon||LASTZ_NET | stats|
|Oryza glaberrima : Oryza sativa Indica||LASTZ_NET | stats|
|Oryza glaberrima : 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 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.