Improving the Reference - Better Genomes for the Sheep and the Cow

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 Hereford cow and the Texel ram.  The sequence reads are long (up to 10 kb average) and therefore useful for spanning gaps in a draft genome. The PBJelly method closes many gaps (35 % to 70 %) and improves contiguity. PBJelly takes genome scaffold sequences as input, produces an improved genome scaffold as output and can be combined with other genome improvement efforts to benefit from each method. These better genomes will impact the genetic studies of production animals and breeds around the world.

We will report on progress assessing the available genome assemblies to minimize known problems in the starting assemblies before improving the genomes with the PacBio data and PBJelly and evaluations of improvements of the current assemblies made with these methods. Once vetted, the new, post-PBJelly version of the genomes will be released to GenBank and from there to the appropriate animal genome databases.