Oryza brachyantha Assembly and Gene Annotation

Project funding: National Science Foundation Plant Genome Research Program (#1026200) for the Oryza Genome Evolution (OGE) Project. These pre-publication data are being released under guidelines of the Fort Lauderdale Agreement, which reaffirms the balance between fair use (i.e. no pre-emptive publication) and early disclosure. You are encouraged use these data to advance your research on individual loci but are asked to respect the rights of the investigators who generated these data to publish the whole-genome level description of O. brachyantha in a peer-reviewed journal. This description includes whole-genome comparative analyses, genome size evolution, gene family evolution, gene organisation and movement, heterochromatin, centromere evolution. This genome falls under the scope of the I-OMAP (International Oryza Map Alignment Project) consortium. The I-OMAP consortium is an internationally coordinated effort to create high-quality reference assemblies representing the diversity of wild and crop-progenitor species in the genus Oryza (Jacquemin et al, 2012). For enquiries and information on how to cite these data please contact Dr. Mingsheng Chen or Dr. Rod Wing.

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.

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

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.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyOryza_brachyantha.v1.4b, INSDC Assembly GCA_000231095.2, Jan 2012
Database version98.14
Base Pairs260,838,168
Golden Path Length260,838,168
Genebuild byOGE
Genebuild methodImport
Data sourceOryza Genome Evolution Project

Gene counts

Coding genes32,038
Non coding genes425
Small non coding genes413
Long non coding genes12
Gene transcripts32,463

Other

FGENESH gene prediction26,828

About this species