Using Bacterial Artificial Chromosomes to Refine Genome Assemblies and to Build Virtual Genomes

Abstract

Recent years have seen an explosion in the sequencing of genomes, including those of ruminants. A number of assemblies of the sequence of the bovine genome are now available (Elsik, et al., 2009; Zimin, et al., 2009). Although the sheep genome sequence is not such a high priority, the International Sheep Genomics Consortium (ISGC_website) has a long term strategy to develop a number of tools for the application of genomics in sheep research and breeding (Archibald, et al., 2010). We have demonstrated recently how comparative genomics and Bacterial Artificial Chromosome (BAC)-libraries can be used to construct detailed virtual genomes as a framework for genome assemblies of related species (Dalrymple, et al., 2007). As new and improved genome assemblies of the genomes contributing to an initial virtual genome assembly are produced, the virtual genomes will need to be regularly updated to incorporate the latest available information. In the original analysis, three genomes (bovine, dog and human) with various levels of coverage and stages of assembly were used (Dalrymple, et al., 2007). With the availability of increasing numbers of assemblies, the benefit of using more than three genomes, or the most appropriate evolutionary distances of the genomes, is not immediately clear. Here we describe the construction of a modified version of the bovine Btau3.1 assembly using cattle and sheep BACs and the use of this assembly in the construction of an updated virtual sheep genome, combining information from the original sheep virtual genome (vsg 1.2) and the horse (Wade, et al., 2009) and dog (Lindblad-Toh, et al., 2005) genomes. The impact of inclusion of additional genome sequences is analysed. The approach described here for sheep is an example of an approach which can be applied more broadly to genomes of any source, for example for the fish species, tilapia (Soler, et al., 2010) and catfish (Liu, et al., 2009). Indeed, the same principles also apply to the detection of differences between different individuals of the same species.