Leersia perrieri Assembly and Gene Annotation

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. Users are encouraged use these data to advance their 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 the Leersia perrieri in a peer-reviewed journal. This description includes whole-genome comparative analyses, genome size evolution, gene family evolution, gene organization 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 inquiries and information on how to cite these data please contact Dr. Rod Wing.

About Leersia perrieri

Leersia perrieri comes from Madagascar. It was the nearest outgroup of the genus Oryza included in the OMAP project. It has 12 chromosomes with a nuclear genome size of 323Mb (flow cytometry). The sequencing and assembly of this genome was carried out as part of the Oryza Genome Evolution project funded by NSF Award #1026200.

Assembly

The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) using accession IRGC105164. Illumina reads of different library sizes were assembled with Allpaths-LG and gaps were closed with GapFiller. The estimated coverage from the WGS was 150x. Total sequence length is 266,687,832 bp; Number of contigs is 10,288; Contig N50: 48,151bp.

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 other Gramene species, see example.
  • Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
  • Identification of various repeat features by programs such as RepeatMasker with MIPS and AGI repeat libraries, and Dust, TRF.

Links

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyLperr_V1.4, INSDC Assembly GCA_000325765.3, Mar 2014
Database version90.14
Base Pairs266,687,832
Golden Path Length266,687,832
Genebuild byOGE
Genebuild methodImported from OGE MAKER annotation
Data sourceOryza Genome Evolution Project

Gene counts

Coding genes29,078
Non coding genes2,387
Small non coding genes2,386
Long non coding genes1
Gene transcripts41,422

Other

FGENESH gene prediction45,319

About this species