Projects
RT2T: A Global Collaborative Project to Study Chromosomal Evolution in the Suborder Ruminantia
RT2T embraces an open science model, ensuring that the data and results produced are freely accessible to the global research community. This project advances collaboration derives input and guidance from diverse perspectives and encourages the engaged participation necessary to accelerate scientific discoveries and drive innovation in agricultural research. Scientists worldwide can access this data to conduct further studies, thereby fostering innovations that could reshape farming practices and animal breeding.
In addition to agricultural benefits, the comprehensive genome data produced by the RT2T can play a critical role in conservation efforts. High-quality genomic information is essential for managing the genetic diversity of endangered ruminant species and developing strategies to improve their populations' survival chances.
Establishing a Pan-Epigenome for Cattle and Sheep
Epigenetic modifications include chemical changes to DNA and RNA base pairs that can influence gene function and subsequently affect economically important traits in livestock species. The collection of sequences representative of the DNA in a population or pangenome, is important to capture the breadth of genomic variation between breeds and populations of livestock species. However, to fully comprehend diversity in livestock species, one must also exhaustively characterize a variety of epigenetic modifications so that we can truly understand variation at a molecular level. The proposed project is designed to establish a cattle and sheep pan-epigenome.
Development of the ovine pangenome
Available sequence data in sheep suggest that diversity of ovine genomes among existing global populations will exceed that of the human species. This project aims to deliver high-quality genomes, using the recently describe trio binning approach, for eight breeds/species of sheep selected for their divergent economically important traits which will serve as the basis of the ovine pangenome.This research effort will leverage complementary efforts including genome assembly, transcriptome, and functional annotation efforts, and provide training for students in the field of animal genomics. Further, it will enhance efforts to identify structural and sequence variants that influence phenotypic variation in economically important traits of sheep. The ovine pangenome project will increase our understanding of how different genomes and gene products from diverse breeds of sheep affect a variety of important biological phenotypes, supporting more accurate prediction of traits and improving breeding strategies. The pangenome will contribute to comparative studies across species, while complementing and leveraging the pangenome being constructed for cattle.
Research & Initiatives
Overview of Ruminant T2T Consortium
Timothy P.L. Smith, Brenda M. Murdoch, Benjamin D. Rosen, and Stephanie D. McKay
The first draft human genome assembly was released over twenty years ago, but a gapless
telomere to telomere (T2T) “complete” assembly was elusive until last year. The highly
repetitive nature of the pericentromeric, subtelomeric and duplicated gene families such as the
rRNA arrays made them impossible to assemble until advances in long read sequencing
technologies, coupled with new bioinformatic tools, resolved these structures. We recently
proposed application of these new resources, tools and knowledge in support of a “Ruminant
T2T Consortium” with the goal of generating complete genomes for the ruminant evolutionary
lineage.
The ruminant Suborder is represented by six Families and 66 living genera, found in
geographically dispersed areas, adapted to a wide variety of environments, and subjected to both
natural and artificial selection. Our hypothesis is that generating T2T assemblies of ruminant
species with a resolution from closely related (e.g. capable of interbreeding, even if only
generating sterile offspring) to higher evolutionary distance (up to the estimated 25 million
years ago last common ancestor) will inform our understanding of the underpinnings of
ruminant evolution, shed light on the genomic consequences of domestication, and enhance
our knowledge of the functional roles of heterochromatin and other repeat regions of the
genome.
A ruminant T2T workshop, held in February at the USDA Meat and Animal Research Center in
Nebraska, featured presentations from the founders of the human T2T effort and leaders of the
vertebrate genomes and earth biogenome projects to provide details of their experience and lend
assistance in designing/optimizing the project. The consortium developed working groups to
conduct orthogonal data production and analyses. The working groups include Chromosome
Evolution, 3D Genome Architecture, Comparative Methylome, Assemblers and Curation,
Annotation, Variant Discovery and population sequencing, Immunome analyses, Cytogenetic.
This update is intended to share the outcomes of the ruminant T2T workshop and provide an
opportunity for interested members of the International Genomes community to participate.
