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Oryza longistaminata (O_longistaminata_v1.0)

Oryza longistaminata Assembly and Gene Annotation

About Oryza longistaminata

Oryza longistaminata (AA genome type) is a wild rice, Perennial, tall (2 m or more), erect, and rhizomatous grass; ligule of lower leaves >15 mm, acute or 2-cleft; panicles open to intermediately open; spikelets 4.5-11.4 mm long and 2-3 mm wide, awned (2-5 cm long); anther 1.5-8.2 mm long.

Assembly

A whole genome shotgun assembly (i.e. Illumina sequence, SOAP de novo assembly) of O. longistaminata was generated by Professor Wen Wang (Kunming Institute of Zoology, Chinese Academy of Sciences) in collaboration with BGI-Shenzhen. The genome assembly was composed of 135,973 scaffolds spanning 344.6 Mb with a N50 scaffold size of 62.4 kb. Using this assembly, the Arizona Genomics Institute (AGI) selected scaffolds and contigs that were syntenic to the short arm of chromosome 3 of O. sativa ssp.japonica, and the order and orientation of each scaffold/contig was confirmed using Genome Puzzle Mater software (GPM, unpublished) to produce a Chr3S pseudomolecule. The final O. longistaminata chromosome 3 short arm resulted in a single scaffold of 14,404,039 bp composed of 4,724 contigs.

Annotation

Protein-coding genes, annotation of repeats and transposable elements were conducted at Arizona Genomics Institute (AGI) led by Dr. Rod Wing. MAKER-P was used as evidence-based genome annotation pipeline. RepeatMasker was used to annotate repeats and transposable elements using species-specific de novo repeat libraries. Non coding RNA genes were predicted by AGI with Infernal, tRNA genes with tRNAScan.

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..

Picture credit: Paul Sanchez, Arizona Genomics Institute.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyO_longistaminata_v1.0, INSDC Assembly GCA_000789195.1, Dec 2014
Database version112.2
Golden Path Length326,442,508
Genebuild byAGI
Genebuild methodImport
Data sourceBeijing Genomics Institute

Gene counts

Coding genes31,686
Non coding genes1,121
Small non coding genes1,101
Long non coding genes20
Gene transcripts32,807