Oryza brachyantha Assembly and Gene Annotation

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 Mb.

Assembly

The genome of Oryza brachyantha was sequenced and assembled in the laboratory of Dr. Mingsheng Chen at the Institute of Genetics and Developmental Biology (IGDB), Chinese Academy of Sciences, Beijing, China. A whole genome shotgun sequencing approach was used to generate ~ 104X coverage using the Illumina GA II platform. The genome was initially assembled using SOAPdenovo at BGI-Shenzhen, followed by integration with BAC-end sequences generated at the Arizona Genomics Institute (AGI). The final assembled sequence was 261 Mb with a scaffold N50 size of 1.6 Mb.

Ordering of the scaffolds into twelve pseudomolecules was accomplished by anchoring to the BAC-based physical map generated at AGI, and confirmed by a cytogenetic approaches. The current assembly is v1.4 and is deposited in DDBJ/EMBL/GenBank under the accession AGAT00000000.

Annotation

Protein-coding genes were annotated using an evidence-based approach as implemented in the Gramene gene-build pipeline by collaboration with Dr. Chengzhi Liang at IGDB. Transposable elements were annotated by collaboration with Dr. Scott A. Jackson at University of Georgia. Non coding RNA genes were predicted with Infernal and tRNA genes with tRNAscan at Arizona Genomics Institute (AGI) led by Dr. Rod Wing.

References

1. Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution.
   Chen J, Huang Q, Gao D, Wang J, Lang Y, Liu T, Li B, Bai Z, Luis Goicoechea J, Liang C et al. 2013. Nat Commun. 4:1595.
2. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.
   Stein JC, Yu Y, Copetti D, Zwickl DJ, Zhang L, Zhang C, Chougule K, Gao D, Iwata A, Goicoechea JL, Wei S, Wang J, Liao Y, Wang M, Jacquemin J, Becker C, Kudrna D, Zhang J, Londono CEM, Song X, Lee S, Sanchez P, Zuccolo A, Ammiraju JSS, Talag J, Danowitz A, Rivera LF, Gschwend AR, Noutsos C, Wu CC, Kao SM, Zeng JW, Wei FJ, Zhao Q, Feng Q, El Baidouri M, Carpentier MC, Lasserre E, Cooke R, Rosa Farias DD, da Maia LC, Dos Santos RS, Nyberg KG, McNally KL, Mauleon R, Alexandrov N, Schmutz J, Flowers D, Fan C, Weigel D, Jena KK, Wicker T, Chen M, Han B, Henry R, Hsing YC, Kurata N, de Oliveira AC, Panaud O, Jackson SA, Machado CA, Sanderson MJ, Long M, Ware D, Wing RA..
3. The International Oryza Map Alignment Project: development of a genus-wide comparative genomics platform to help solve the 9 billion-people question.
   Jacquemin J, Bhatia D, Singh K, Wing RA..

Gramene/Ensembl Genomes Annotation

Additional annotations generated by the Gramene and Ensembl Plants project include:

• Gene phylogenetic trees with other Gramene species.
• LastZ Whole Genome Alignment to Arabidopsis thaliana, Oryza sativa Japonica (IRGSP v1) and other Oryza AA genomes.
• Orthologue based DAGchainer synteny detection against other AA genomes.
• Mapping to the genome of multiple sequence-based feature sets using Gramene BLAT pipeline.
• Identification of various repeat features by programs such as RepeatMasker with MIPS and AGI repeat libraries, and Dust, TRF.

More information

General information about this species can be found in Wikipedia.