Oryza barthii Assembly and Gene Annotation

About Oryza barthii

Oryza barthii is the AA genome progenitor of the West African cultivated rice, O. glaberrima. It belongs to the AA genome group and has 12 chromosomes and a nuclear genome size of 411 Mb (flow cytometry). It is found in mopane or savanna woodland, savanna or fadama. Grows in deep water, seasonally flooded land, stagnant water, and slowly flowing water or pools; prefers clay or black cotton soils. Found in open habitats. This work was part of the OGE project funded by NSF Award #1026200.

Assembly

The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) using accession IRGC105608. The sequence data were generated by 454 and Illumina and assembled with Newbler and All Paths LG. The estimated coverage from the WGS was 110x. Total sequence length 308,273,932 bp; Number of contigs 25,404; Contig N50 18,930 bp.

Annotation

Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline. Non coding RNA genes were predicted with Infernal and tRNA genes with tRNAscan. RepeatMasker was used to annotate repeats and transposable elements with Oryza-specific de novo repeat libraries. These analyses were conducted at Arizona Genomics Institute (AGI) led by Dr. Rod Wing.

References

1. 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..
2. 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.

Links

• International Rice Genome Sequencing Consortium (IRGSP)

More information

General information about this species can be found in Wikipedia.