Oryza punctata (Oryza_punctata_v1.2)

Oryza punctata 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. punctata 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. Rod Wing.

About Oryza punctata

Oryza punctata is a wild rice species native to Africa. Breeders are interested because of demonstrated resistance to bacterial blight and brown plant hoppers. O. punctata, a diploid, belongs to the O. officinalis complex within the Oryzeae genome groups, and belongs to the BB genome type. It can be found in open or semi-open habitats such as forest margins, grassland and thickets, scrub lands, open bush or shifting cultivation fields, and rice fields. It has 12 chromosomes and a nuclear genome size of 423Mb (flow cytometry). 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 IRGC105690. The sequence data were generated by 454 and Illumina and assembled with Newbler and All Paths LG. The estimated coverage from the WGS was 130x. Total sequence length 393,816,603 bp; Number of contigs 16,598; Contig N50 43,035 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.

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.

Statistics

Summary

AssemblyOryza_punctata_v1.2, INSDC Assembly GCA_000573905.1, Feb 2014
Database version104.12
Golden Path Length393,816,603
Genebuild byOGE
Genebuild methodImport
Data sourceOryza Genome Evolution Project

Gene counts

Coding genes31,762
Non coding genes788
Small non coding genes782
Long non coding genes6
Gene transcripts41,848

Other

FGENESH gene prediction45,833

About this species