Oryza nivara (Oryza_nivara_v1.0)

Oryza nivara Assembly and Gene Annotation

About Oryza nivara

Oryza nivara is a wild rice from India; one of rice species being used in the OMAP project. It belongs to the AA genome group. Breeders are interested in this organism because it exhibits resistance to grassy stunt virus. It is found in swampy areas, at edges of ponds and tanks, beside streams, in ditches, in or around rice fields. It usually grows in shallow water up to 0.3 m. seasonally dry; in open habitats. It has 12 chromosomes and a nuclear genome size of 448 Mb (flow cytometry). This work was part of the Oryza Genome Evolution project funded by NSF Award #1026200 and in collaboration with Yue-Ie Hsing.


The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) using accession IRGC100897. 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 102x. Total sequence length 337,950,324 bp; Number of contigs 16,484; Contig N50: 37,688 bp.


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.


  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.

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.



AssemblyOryza_nivara_v1.0, INSDC Assembly GCA_000576065.1, Feb 2014
Database version111.10
Golden Path Length337,950,324
Genebuild byOGE
Genebuild methodImport
Data sourceOryza Genome Evolution Project

Gene counts

Coding genes36,313
Non coding genes713
Small non coding genes694
Long non coding genes19
Gene transcripts49,073


FGENESH gene prediction45,102