Recipient Organization
AGRICULTURAL RESEARCH SERVICE
(N/A)
BROOKINGS,SD 57006
Performing Department
(N/A)
Non Technical Summary
The first genome assembly for a mammalian genome was described in the year 2000 upon release of the human genome draft. This draft was far from complete, and in the ensuing 20 years incremental improvements have been made to the public assembly. In spring 2022, a group of researchers reported the first truly complete, "telomere to telomere" (T2T) assembly that featured an unbroken sequence with no gaps or uncertain sequences. Associated analyses revealed the scope of information that had been previously missed using less complete versions of the human genome, including addition of thousands of previously undescribed genes. Subsequent unpublished reports have demonstrated the value of comparative analysis between closely related species. The ruminant group of organisms, that includes cattle, sheep, and goat as well as a variety of deer and antelope species, is of interest for agricultural as well as evolutionary reasons. We believe that comparisons between complete genomes of ruminant species will inform our understanding of their evolution, shed light on genomic consequences of domestication, and enhance understanding of functional roles of all of the DNA in the genome. The workshop is intended to provide a platform for the human T2T research community to transfer knowledge and expertise in a focused forum beyond that possible in less focused scientific conferences.
Animal Health Component
(N/A)
Research Effort Categories
Basic
100%
Applied
(N/A)
Developmental
(N/A)
Goals / Objectives
Genome assemblies have increased in both quality and contiguity over the past 20 years, but the ultimate goal of a complete, gapless assembly including all euchromatin and heterochromatin for every chromosome of a mammalian species has been elusive. Technological advances in DNA sequencing and assembly algorithms have finally produced a complete "telomere to telomere" (T2T) genome assembly for humans from a special diploid human cell line in which both copies of each chromosome are identical. A series of papers in March 2022 presented the technology for completion of the genome and detailed analyses that the complete assembly made possible. The ad hoc group of researchers that achieved this milestone blazed a trail of technical and analytical advancements which can now be applied to other species. A recent human T2T conference (August 2022) celebrated the accomplishment and presented newer data extending the technology to true diploid samples and detailing the knowledge gained by comparing T2T assemblies of primate species. The purpose of the present proposal is to support a workshop for researchers interested in ruminant species for agriculture, conservation, and evolution, to learn from the human T2T effort. The proposed, highly focused workshop will bring together these researchers along with some of the pioneers from the human effort to enable transferal of the knowledge and skills while the enthusiasm from the human project remains high. The goals of the workshop are to launch a "Ruminant T2T" project, establishbest practices for creating complete genome assemblies, conceiveanalysis goals, determine sample types/characteristicsand data generation required to support each proposed analysis, and form teams to prosecute the analyses,
Project Methods
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.