RUMINANT T2T WORKSHOP 2023

<b>Project Methods</b><br> The workshop will be held February 23 & 24, 2023 at the USDA Meat and Animal Research Center (USMARC) in Clay Center, Nebraska, and we anticipate approximately 40-50 total attendees. The location selection is based on the historical role of USMARC in livestock genome assembly, the fact that the institution has generated the recommended data for species of agricultural importance (cattle, sheep, goat, and pig), and the fact the concept was developed by Dr. Smith who is based at that location. In our view, detaching the workshop from any coincident conferences will enhance the interactions and informal nature of the discussions to produce more active outcomes. Furthermore, holding this conference at USMARC will reduce the venue and technology associated expenses. Finally, the venue will provide the opportunity for others to meet and interact with agricultural animal scientists and see the research station and available technologies.2. Overview of Conference TopicsSpecific topics to be addressed at the workshop include:a. Latest advancements in technology and procedures and their impact on T2T assemblyb. Best practices for implementation of Verkko or alternative assemblers specific for T2T of mammalian, diploid species.c. Most efficient means to move from contigs to finished genomes, i.e. "untangling" graphs and assigning rDNA arrays and HOR appropriately.d. Making use of DNA base modification data generated by sequencinge. Impactful orthogonal assays (e.g. 3D chromatin modeling; chromatin states; transcript abundances)f. Most fruitful avenues of T2T assembly analysis and comparisons between speciesg. Discussions of sample procurement/availability for non-livestock ruminant species, including prioritization based on impact and practicability.h. Development of working groups to address each species, conduct orthogonal data production, perform analyses.