Leersia perrieri Assembly and Gene Annotation

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 323 Mb (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

• Oryza Genome Evoltion Project Genome Browser
• Gramene species page for Oryza
• Oryza Genome Evolution Project in AGI (Arizona Genomics Institute)
• International Rice Genome Sequencing Consortium (IRGSP)
• Rice Knowledge Bank

More information

General information about this species can be found in Wikipedia.