Approaches taken, progress made, and enhanced utility of long read-based goat, swine, cattle and sheep reference genomes

Deficiencies in the current livestock reference genomes continue to hamper genomic analysis in these species, despite the extensive efforts to create, re-create, update and curate them. On the other hand, a change of reference genomes incurs substantial cost due to the need to reanalyze data and account for the new information and reference position. In livestock genomics research, which has limited resources compared to the human or biomedical model species communities, it is critical that updates to be termed a “new reference” be of sufficiently increased quality, stability, and utility that the many annotation analyses are worth re-doing. Recent advances in long-read sequencing combined with new technologies for scaffolding the resulting contigs, have made it possible to make a step change in the quality of genome assemblies for a very small fraction of the price required to create the originals. Efforts to improve the goat, swine, cattle and sheep genomes through long read-based de novo assemblies scaffolded with a variety of approaches are in various stages of production. We believe that these new resources represent sufficient improvement to be worth the effort to transport and enhance annotation on these new assemblies. A brief update on the status of these genomes upgrade efforts will be presented, details of which will be available in other presentations. We then follow with examples of ongoing projects making use of the preliminary outputs, to illustrate that the switch to these new references will be worthwhile.