Resources, and Progress Toward a Fully Annotated EquCab3

Approximately 30 million Sanger reads were generated from the Thoroughbred mare Twilight to produce the reference Equine genome assembly (EquCab2, Wade et al 2009).  In the time since, work has been done to aggregate available resources for an EquCab3 assembly. We report progress on this effort, as well as additional work with the currently available 42x Illumina and the above mentioned 6.8x Sanger data which have produced a new list of unordered contigs, chrUn2.  Work has also been done toward developing an optical map of Twilight’s genomic DNA.  We will also be able to report progress on the work to generate long reads via Illumina’s Moleculo technology. 

A great deal of Illumina paired end genomic sequence data has been generated recently for Twilght.  By itself, this high quality data would be useful in helping to identify basecalling errors, and poorly characterized homopolymers or tandem repeats in the EquCab2 assembly. However, due to the short read lengths and insert size, it is not of much value in an effort to repair errors or gaps present in its structural organization. A great deal of progress has been made in the last several years with respect to the informatics tools necessary for a robust genome assembly process.  In addition to faster, more memory efficient assemblers, new such as MaSuRCA (Zimin et al. 2013) tools have emerged that allow for the productive use of complementary data sets.  Specifically, the ability to use high throughput, high quality Illumina reads to improve the accuracy of reads produced using sequencing technologies more suitable to whole genome assembly such as Sanger or other long read technologies.  We are now working to leverage the existing Sanger sequence data from the original EquCab2 assembly, as well as the high throughput Illumina data, and newly generated long read data to produce an improved horse genome assembly.

At this meeting, we will report the progress that we have made toward a new EquCab3 assembly, describe the data resources that we have been able to collect toward evaluating this progress, and welcome input as we discuss strategies to annotate this new resource.