RT2T: A Global Collaborative Project to Study Chromosomal Evolution in the Suborder Ruminantia-Reference-Cited by-同舟云学术

RT2T: A Global Collaborative Project to Study Chromosomal Evolution in the Suborder Ruminantia

Published:2024-02-05 Issue: Volume: Page:
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Kalbfleisch Ted¹^ORCID,McKay Stephanie²^ORCID,Murdoch Brenda³^ORCID,Adelson David L.⁴^ORCID,Almansa Diego⁵^ORCID,Becker Gabrielle³^ORCID,Beckett Linda M.⁶^ORCID,Benítez-Galeano María José⁵^ORCID,Biase Fernando⁷^ORCID,Casey Theresa⁶^ORCID,Chuong Edward⁸^ORCID,Clark Emily⁹^ORCID,Clarke Shannon¹⁰^ORCID,Cockett Noelle¹¹^ORCID,Couldrey Christine¹²^ORCID,Davis Brian W.¹³^ORCID,Elsik Christine G.²^ORCID,Faraut Thomas¹⁴^ORCID,Gao Yahui¹⁵^ORCID,Genet Carine¹⁴^ORCID,Grady Patrick¹⁶^ORCID,Green Jonathan²^ORCID,Green Richard¹⁶^ORCID,Guan Dailu¹⁷^ORCID,Hagen Darren¹⁸^ORCID,Hartley Gabrielle A.¹⁶^ORCID,Heaton Mike¹⁹^ORCID,Hoyt Savannah J.¹⁶^ORCID,Huang Wen²⁰^ORCID,Jarvis Erich²¹^ORCID,Kalleberg Jenna²^ORCID,Khatib Hasan²²^ORCID,Koepfi Klaus-Peter²³^ORCID,Koltes James²⁴^ORCID,Koren Sergey²⁵^ORCID,Kuehn Christa²⁶^ORCID,Leeb Tosso²⁷^ORCID,Leonard Alexander²⁸^ORCID,Liu George E.¹⁵^ORCID,Low Wai Yee²⁹^ORCID,McConnell Hunter²^ORCID,McRae Kathryn¹⁰^ORCID,Miga Karen³⁰^ORCID,Mousel Michelle³¹^ORCID,Neibergs Holly³²^ORCID,O'Neill Rachel¹⁶^ORCID,Olagunju Temitayo³^ORCID,Pennell Matt³³^ORCID,Petry Bruna²⁴^ORCID,Pewsner Mirjam³⁴^ORCID,Phillippy Adam M.²⁵^ORCID,Pickett Brandon D.²⁵^ORCID,Pineda Paulene²⁹^ORCID,Potapova Tamara³⁵^ORCID,Rachagani Satyanarayana³⁶^ORCID,Rhie Arang²⁵^ORCID,Rijnkels Monique³⁷^ORCID,Robic Annie¹⁴^ORCID,Osorio Nelida Rodriguez⁵^ORCID,Safonova Yana³⁸^ORCID,Schettini Gustavo⁷^ORCID,Schnabel Robert D.²^ORCID,Natesh Nagabhishek Sirpu³⁹^ORCID,Stegemiller Morgan³^ORCID,Storer Jessica⁴⁰^ORCID,Stothard Paul⁴¹^ORCID,Stull Caleb²^ORCID,Tosser-Klopp Gwenola¹⁴^ORCID,Traglia Germán M.⁵^ORCID,Tuggle Chris²⁴^ORCID,Tassell Curtis P. Van¹⁵^ORCID,Watson Corey⁴²^ORCID,Weikard Rosemarie⁴³^ORCID,Wimmers Klaus⁴³^ORCID,Xie Shangqian³^ORCID,Yang Liu¹⁵^ORCID,Smith Tim¹⁹^ORCID,Rosen Ben¹⁵^ORCID

Affiliation:

1. Department of Veterinary Science, University of Kentucky, Lexington, KY 40546

2. Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA

3. Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, 83844, USA

4. School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, 5000, SA, Australia

5. Genomics and Bioinformatics Unit, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Salto, Universidad de la República, Uruguay

6. Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA

7. School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA

8. BioFrontiers Institute, Department of Molecular Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80303 USA

9. The Roslin Institute, University of Edinburgh, EH25 9RG, Edinburgh, UK.

10. Invermay Agricultural Centre, AgResearch Ltd, Mosgiel, New Zealand

11. Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT 84322-4815 USA

12. Livestock improvement corporation, Hamilton 3286, New Zealand

13. Department of Veterinary Pathobiology, School of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA

14. GenPhySE, Université de Toulouse, INRAE, ENVT, 31326 Castanet Tolosan, France

15. Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, 20705, USA

16. Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269

17. Department of Animal Science, University of California Davis, Davis, California, USA

18. Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK 74078, USA

19. USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA

20. Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA

21. Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA 10065

22. Department of Animal and Dairy Sciences, The University of Wisconsin-Madison, Wisconsin, USA

23. Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630, USA

24. Department of Animal Science, Iowa State University, Ames, IA 50011, USA

25. Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health (Bethesda, MD, USA)

26. Friedrich-Loeffler-Institute (German Federal Research Institute for Animal Health), 18357 Greifswald-Insel Riems, Germany

27. Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland

28. Animal Genomics, ETH Zurich, 8092 Zurich, Switzerland

29. The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia

30. UC Santa Cruz Genomics Institute, University of California, CA 95064

31. USDA, ARS, Animal Disease Research Unit, Pullman, WA 99164, USA and School for Global Animal Health, Washington State University, Pullman, WA 99164, USA

32. Department of Animal Science, Washington State University, Pullman, WA

33. Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089

34. Institute of Fish and Wildlife Health, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland

35. Stowers Institute for Medical Research (Kansas City, MO, USA)

36. Veterinary Medicine and Surgery, NextGen Precision Health Institute, University of Missouri, Columbia

37. Department of Veterinary Integrative Biosciences , School of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA

38. Computer Science and Engineering Department, Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA 16801, USA

39. Department of Veterinary Medicine and Surgery, University of Missouri, Columbia, MO 65211, USA.

40. Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT

41. Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.

42. Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, USA

43. Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.

Abstract

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.

Publisher

Research Square Platform LLC

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