The Ruminant Telomere-to-Telomere (RT2T) Consortium

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

doi:10.1038/s41588-024-01835-2

The Ruminant Telomere-to-Telomere (RT2T) Consortium

Nat Genet. 2024 Aug;56(8):1566-1573. doi: 10.1038/s41588-024-01835-2. Epub 2024 Aug 5.

Authors

Theodore S Kalbfleisch^#¹, Stephanie D McKay^#², Brenda M Murdoch^#³, David L Adelson⁴, Diego Almansa-Villa⁵, Gabrielle Becker³, Linda M Beckett⁶, María José Benítez-Galeano⁵, Fernando Biase⁷, Theresa Casey⁶, Edward Chuong⁸, Emily Clark⁹, Shannon Clarke¹⁰, Noelle Cockett¹¹, Christine Couldrey¹², Brian W Davis¹³, Christine G Elsik², Thomas Faraut¹⁴, Yahui Gao¹⁵, Carine Genet¹⁴, Patrick Grady¹⁶, Jonathan Green², Richard Green¹⁶, Dailu Guan¹⁷, Darren Hagen¹⁸, Gabrielle A Hartley¹⁶, Mike Heaton¹⁹, Savannah J Hoyt¹⁶, Wen Huang²⁰, Erich Jarvis^{21

22}, Jenna Kalleberg², Hasan Khatib²³, Klaus-Peter Koepfi^{24

25}, James Koltes²⁶, Sergey Koren²⁷, Christa Kuehn²⁸, Tosso Leeb²⁹, Alexander Leonard³⁰, George E Liu¹⁵, Wai Yee Low³¹, Hunter McConnell², Kathryn McRae¹⁰, Karen Miga^{32

33}, Michelle Mousel^{34

35}, Holly Neibergs³⁶, Temitayo Olagunju³, Matt Pennell³⁷, Bruna Petry²⁶, Mirjam Pewsner³⁸, Adam M Phillippy²⁷, Brandon D Pickett²⁷, Paulene Pineda³¹, Tamara Potapova³⁹, Satyanarayana Rachagani⁴⁰, Arang Rhie²⁷, Monique Rijnkels⁴¹, Annie Robic¹⁴, Nelida Rodriguez Osorio⁵, Yana Safonova⁴², Gustavo Schettini⁷, Robert D Schnabel², Nagabhishek Sirpu Natesh⁴³, Morgan Stegemiller³, Jessica Storer⁴⁴, Paul Stothard⁴⁵, Caleb Stull², Gwenola Tosser-Klopp¹⁴, Germán M Traglia⁵, Christopher K Tuggle²⁶, Curtis P Van Tassell¹⁵, Corey Watson⁴⁶, Rosemarie Weikard⁴⁷, Klaus Wimmers⁴⁷, Shangqian Xie³, Liu Yang¹⁵, Timothy P L Smith⁴⁸, Rachel J O'Neill^{49

50}, Benjamin D Rosen⁵¹

Affiliations

¹ Department of Veterinary Science, University of Kentucky, Lexington, KY, USA.
² Division of Animal Sciences, University of Missouri, Columbia, MO, USA.
³ Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, USA.
⁴ School of Biological Sciences, the University of Adelaide, North Terrace, Adelaide, South Australia, Australia.
⁵ Genomics and Bioinformatics Unit, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Salto, Uruguay.
⁶ Department of Animal Sciences, Purdue University, West Lafayette, IN, USA.
⁷ School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
⁸ BioFrontiers Institute, Department of Molecular Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA.
⁹ The Roslin Institute, University of Edinburgh, Edinburgh, UK.
¹⁰ Invermay Agricultural Centre, AgResearch Ltd, Mosgiel, New Zealand.
¹¹ Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA.
¹² Livestock Improvement Corporation, Hamilton, New Zealand.
¹³ Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA.
¹⁴ GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France.
¹⁵ Animal Genomics and Improvement Laboratory, USDA ARS, Beltsville, MD, USA.
¹⁶ Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.
¹⁷ Department of Animal Science, University of California, Davis, Davis, CA, USA.
¹⁸ Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, USA.
¹⁹ U.S. Meat Animal Research Center, USDA ARS, Clay Center, NE, USA.
²⁰ Department of Animal Science, Michigan State University, East Lansing, MI, USA.
²¹ Vertebrate Genome Laboratory, the Rockefeller University, New York, NY, USA.
²² Howard Hughes Medical Institute, Chevy Chase, MD, USA.
²³ Department of Animal and Dairy Sciences, the University of Wisconsin-Madison, Madison, WI, USA.
²⁴ Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA.
²⁵ Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, USA.
²⁶ Department of Animal Science, Iowa State University, Ames, IA, USA.
²⁷ Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
²⁸ Friedrich-Loeffler-Institute (German Federal Research Institute for Animal Health), Greifswald-Insel Riems, Germany.
²⁹ Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
³⁰ Animal Genomics, ETH Zürich, Zurich, Switzerland.
³¹ The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, South Australia, Australia.
³² UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
³³ Biomolecular Engineering Department, University of California, Santa Cruz, Santa Cruz, CA, USA.
³⁴ Animal Disease Research Unit, USDA ARS, Pullman, WA, USA.
³⁵ School for Global Animal Health, Washington State University, Pullman, WA, USA.
³⁶ Department of Animal Science, Washington State University, Pullman, WA, USA.
³⁷ Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
³⁸ Institute of Fish and Wildlife Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
³⁹ Stowers Institute for Medical Research, Kansas City, MO, USA.
⁴⁰ Veterinary Medicine and Surgery, NextGen Precision Health Institute, University of Missouri, Columbia, MO, USA.
⁴¹ Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA.
⁴² Computer Science and Engineering Department, Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA, USA.
⁴³ Department of Veterinary Medicine and Surgery, University of Missouri, Columbia, MO, USA.
⁴⁴ Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
⁴⁵ Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
⁴⁶ Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, USA.
⁴⁷ Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.
⁴⁸ U.S. Meat Animal Research Center, USDA ARS, Clay Center, NE, USA. tim.smith2@usda.gov.
⁴⁹ Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA. rachel.oneill@uconn.edu.
⁵⁰ Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA. rachel.oneill@uconn.edu.
⁵¹ Animal Genomics and Improvement Laboratory, USDA ARS, Beltsville, MD, USA. ben.rosen@usda.gov.

^# Contributed equally.

PMID: 39103649
DOI: 10.1038/s41588-024-01835-2

Abstract

Telomere-to-telomere (T2T) assemblies reveal new insights into the structure and function of the previously 'invisible' parts of the genome and allow comparative analyses of complete genomes across entire clades. We present here an open collaborative effort, termed the 'Ruminant T2T Consortium' (RT2T), that aims to generate complete diploid assemblies for numerous species of the Artiodactyla suborder Ruminantia to examine chromosomal evolution in the context of natural selection and domestication of species used as livestock.

Publication types

Review

MeSH terms

Animals
Diploidy
Evolution, Molecular
Genome / genetics
Phylogeny
Ruminants* / genetics
Selection, Genetic
Telomere* / genetics

Grants and funding

Grant Number 2023-67015-39000/United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)