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Current Release: OMAP Short Arm (FF genome type)
A minimum tiling path of BAC clones (Ammiraju et al. 2006) was selected across the short arm of chromosome 3 of Oryza brachyantha using a heavily manually edited physical map (Kim et al. 2008). The BACs were divided into six 3Mb pools and Roche GSFLX sequenced (Titanium and paired-end reads) to a depth of 24X. Sequence reads were assembled with Newbler (454) and Bambus (Pop et al. 2004), followed by manual inspection of the assembly (Rounsley et al. 2009). The assembly resulted in a total of 218 scaffolds with a scaffold N50 of 152,187bp.
Additional annotations generated by the Gramene project include:
- Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see more.
- Identification of various repeat features from MIPS and AGI repeat libraries
- Ab initio gene prediction with program fgenesh
- Pairwise Whole genome alignments (blastz-chain-net) with Oryza sativa Japonica
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