RT2T: A Global Collaborative Project to Study Chromosomal Evolution in the Suborder Ruminantia
Authors: Kalbfleisch Ted , McKay Stephanie , Murdoch Brenda , Adelson David L. , Almansa Diego , Becker Gabrielle , Beckett Linda M. , Benítez-Galeano María José , Biase Fernando , Casey Theresa , Chuong Edward , Clark Emily , Clarke Shannon , Cockett Noelle , Couldrey Christine , Davis Brian W. , Elsik Christine G. , Faraut Thomas , Gao Yahui , Genet Carine , Grady Patrick , Green Jonathan , Green Richard , Guan Dailu , Hagen Darren , Hartley Gabrielle A. , Heaton Mike , Hoyt Savannah J. , Huang Wen , Jarvis Erich , Kalleberg Jenna , Khatib Hasan , Koepfi Klaus-Peter , Koltes James , Koren Sergey , Kuehn Christa , Leeb Tosso , Leonard Alexander , Liu George E. , Low Wai Yee , McConnell Hunter , McRae Kathryn , Miga Karen , Mousel Michelle , Neibergs Holly , O'Neill Rachel , Olagunju Temitayo , Pennell Matt , Petry Bruna , Pewsner Mirjam , Phillippy Adam M. , Pickett Brandon D. , Pineda Paulene , Potapova Tamara , Rachagani Satyanarayana , Rhie Arang , Rijnkels Monique , Robic Annie , Osorio Nelida Rodriguez , Safonova Yana , Schettini Gustavo , Schnabel Robert D. , Natesh Nagabhishek Sirpu , Stegemiller Morgan , Storer Jessica , Stothard Paul , Stull Caleb , Tosser-Klopp Gwenola , Traglia Germán M. , Tuggle Chris , Tassell Curtis P. Van , Watson Corey , Weikard Rosemarie , Wimmers Klaus , Xie Shangqian , Yang Liu , Smith Tim , Rosen Ben 
Published: February 2024

Abstract
The publication of the first complete, haploid telomere-to-telomere (T2T) human genome revealed new insights into the structure and function of the heretofore “invisible” parts of the genome including centromeres, tandem repeat arrays, and segmental duplications. Refinement of T2T processes now enables comparative analyses of complete genomes across entire clades to gain a broader understanding of the evolution of chromosome structure and function. The human T2T project involved a unique ad hoc effort involving many researchers and laboratories, serving as a model for collaborative open science. Subsequent generation and analysis of diploid, near T2T assemblies for multiple species represents a substantial increase in scale and would be daunting for any single laboratory. Efforts focused on the primate lineage continue to employ the successful open collaboration strategy and are revealing details of chromosomal evolution, species-specific gene content, and genomic adaptations, which may be general or lineage-specific features. The suborder Ruminantia has a rich history within the field of chromosome biology and includes a broad range of species at varying evolutionary distances with separation of tens of millions of years to subspecies that are still able to interbreed. We propose an open collaborative effort dubbed the “Ruminant T2T Consortium” (RT2T) to generate complete diploid assemblies for species in the Artiodactyla order, focusing on suborder Ruminantia. Here we present the initial near T2T assemblies of cattle, gaur, domestic goat, bighorn sheep, and domestic sheep, and describe the motivation, goals, and proposed comparative analyses to examine chromosomal evolution in the context of natural selection and domestication of species for use as livestock.