White Tailed Deer Genome Assembly Improvement: Moving Toward Named Chromosomes

A updated assembly of a white-tailed deer (Odocoileus virginianus borealis) genome (2.6 Gbase) was generated from PacBio reads, Illumina reads, and BioNano optical maps. A protocol modified from the PacBio SMRTbell Template Prep Kit was used to generate 10-50 kb DNA libraries from muscle tissue and sequencing was performed on the PacBio RSII platform. DNA was also extracted from 30 mg of the same muscle sample, digested with Nt.BspQI and Nb.BssSI and optically mapped with 4 runs of BioNano Irys system. An NEBNext Ultra II DNA Library Prep Kit was used to generate a 250 bp, size-selected library from the same tissue and sequenced to ~ 150X coverage using 2 X 150 bp reads. Illumina reads were used to correct raw reads and assembled contigs at various points in the assembly process. Multiple combinations of assemblers (FALCON, CANU), correction (Quiver, PILON), and hybrid reassembly with optical data were attempted, and ultimately produced long assemblies ( N50 > 17 Mbase). A description of results from the various assembly workflows attempted will be presented.