Search Oryza glaberrima

Description

About Oryza glaberrima

Oryza glaberrima is the scientific name for African rice, a cultivated grain distinct from its better known cousin Asian rice (O. sativa). African rice was independently domesticated ~3000 years ago in the Niger River Delta from its still extant progenitor, O. 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 better tolerance of drought and infertile soils. Interspecific crosses between African and Asian rice have produced cultivars with improved yield and quality traits, and 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 will provide insight into the genetic basis of domestication and other traits by finding commonalities and differences with O. sativa. Similar to Asian rice, African rice carries the AA-type genome, having 12 chromosomes and an estimated size of 358 Mb.

Genome Sequencing and Gene Prediction

The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) using strain IRGC:96717. The current assembly is "Oryza_glaberrima_AGI1.1". It incorporates the previously assembled chromosome 3 short arm (Chr3s) sequence and consists of 12 chromosome pseudomolecules and 1939 unplaced scaffolds. Chr3s was sequenced and assembled using a heavily manually edited physical map. BAC clones were shotgun Sanger sequenced to 8x coverage and phase II finished. Assembly of the tile sequence was performed manually. The rest of the genome was sequenced with a hybrid BAC pooling/ whole genome shotgun approach with 30X coverage of Roche GSFLX/454 Titanium sequencing technology. Sequences were assembled and combined with a subset of previously sequenced BAC clones to produce a whole genome assembly. The underlying scaffolds have been deposited in GenBank with the accession number ADWL01000000. Protein-coding genes were annotated by the Munich Information Center for Protein Sequences (MIPS) led by Klaus Meyer using an evidence-based approach. Annotation of repeats and transposable elements was conducted at AGI. Project funding: National Science Foundation Plant Genome Research Program (#082224) awarded to R. Wing, S. Rounsley and Y. Yu.

Gramene/Ensembl Genomes Annotation

Additional annotations generated by the Gramene/Ensembl Genomes projects include:

The standard set of Gramene analyses detailed here.
Phylogenetic gene trees and whole-genome alignments with several plant and metazoan species, using Ensembl's Compara pipeline.

References

Guyot, R., et al., Patterns of Sequence Divergence and Evolution of the S Orthologous Regions between Asian and African Cultivated Rice Species. PLoS One. 6(3): p. e17726. PubMed ID: 21423767
Li, Z.M., X.M. Zheng, and S. Ge, Genetic diversity and domestication history of African rice (Oryza glaberrima) as inferred from multiple gene sequences. Theor Appl Genet. PubMed ID: 21400109
Tian, Z., et al., Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis. BMC Genomics. 12: p. 142. PubMed ID: 21385395
Sakai, H., et al., Distinct evolutionary patterns of Oryza glaberrima deciphered by genome sequencing and comparative analysis. Plant J. PubMed ID: 21323774
Hurwitz, B.L., et al., Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza. Plant J. 63(6): p. 990-1003. PubMed ID: 20626650
Sanyal, A., et al., Orthologous comparisons of the Hd1 region across genera reveal Hd1 gene lability within diploid Oryza species and disruptions to microsynteny in Sorghum. Mol Biol Evol. 27(11): p. 2487-506. PubMed ID: 20522726
Roulin, A., et al., Paleogenomic analysis of the short arm of chromosome 3 reveals the history of the African and Asian progenitors of cultivated rices. Genome Biol Evol. 2: p. 132-9. PubMed ID: 20333229

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