Examining Conflict Regions Of The Bovine Genome Assembly Through Optical Mapping Analysis

Two bovine genome reference assemblies have been produced using the same sequence data, Btau_4.6.1 and UMD3.1. The assemblies are quite distinct and both assemblies suffer from inadequacies of sequence depth across the genome. There are many regions of the genome and specific genes that are improperly assembled and numerous gaps are present.  A large scale collaborative effort is currently underway to fix these problems by a complete re-assembly using both additional next-gen WGS sequence coverage, an updated linkage map and Optical Mapping to better define current inconsistencies. Optical mapping offers the unique opportunity of creating high resolution sequence-compatible physical maps to build clone-free, independent scaffolds to guide many stages of the genome assembly and validation. As an early start to this effort, preliminary, single-molecule restriction map data (Dominette; Rmaps) were commercially acquired that are being combined with enhanced data from University of Wisconsin for a whole genome assembly (map) and analysis that will comprehensively delineate discordances in the sequence builds. As a demonstration project of the benefits that can be derived from the Optical Map data, four conflicting chromosomal regions in Bta 01, 10, 11 and 23 have been analyzed. Optical contigs were aligned to these regions to define missing and misassembled structural problems in the reference assembly. The approach utilized in this preliminary analysis will be useful to improve target regions where fine mapping of functional traits is desired.