Improvement to OARv3.1 Using Long Read Technology

High quality reference genomes are the foundation of genomic analyses. Even "high quality" draft sequences have thousands of remaining gaps that impact the assessment of genes and other functional elements. We are applying our successful methods using Pacific Biosciences (PacBio) sequence and our PBJelly software (English, et al. 2012) to improve the high quality draft genome sequences for agriculturally important animals. We have produced whole genome shotgun sequence using the PacBio technology from the Texel ram.  The sequence reads are long (up to 10 kb average) and therefore useful for spanning gaps in the draft genome. For the sequences mapped to chromosomes, the PBJelly method closed 70% of the gaps, reducing the number of contigs from 117,293 to 35,267.  The assembly is more contiguous, with the contig N50 increased from 41.7 kb to 165.2 kb and almost ¼ of the contigs larger than 100kb (8,527; increased from 2,355).  The PacBio data appears to improve the GC representation, increasing the G+C content slightly (0.1% of the contig bases). The fraction of the ambiguous bases (Ns) in the scaffolds decreased from 3.12% to 0.87% of the genome.

We will report on progress assessing the quality of the genome assembly, including the ability of PBJelly and PacBio data to address known issues in OARv3.1.  We will also discuss ongoing research with other methods to approach finished quality genomes without using traditional expensive and manually intensive finishing efforts.