Oryza glumipatula Assembly and Gene Annotation

About Oryza glumipatula

Oryza glumipatula is a wild rice from South America, one of the rice species included in the OMAP project. It belongs to the AA genome group and has 12 chromosomes with a nuclear genome size of 464 Mb (flow cytometry). It is found in deep and sometimes flowing water. This work was part of the Oryza Genome Evolution project funded by NSF Award #1026200 and in collaboration with Antonio Oliveira (Brazil).

Assembly

The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) using accession GEN1233_2. Illumina reads of different library sizes were assembled with Allpaths-LG, scaffolds were constructed with SSPACE, and gaps were closed with GapFiller. The estimated coverage from the WGS was 135x. Total sequence length 372,860,283 bp; Number of contigs 17,912; Contig N50: 31,921 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.