Evolution of the ancestral mammalian karyotype and syntenic regions
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Published:2022-09-26
Issue:40
Volume:119
Page:
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ISSN:0027-8424
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Container-title:Proceedings of the National Academy of Sciences
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language:en
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Short-container-title:Proc. Natl. Acad. Sci. U.S.A.
Author:
Damas Joana1ORCID, Corbo Marco1, Kim Jaebum2, Turner-Maier Jason3, Farré Marta4, Larkin Denis M.5, Ryder Oliver A.67ORCID, Steiner Cynthia8, Houck Marlys L.9, Hall Shaune10, Shiue Lily10, Thomas Stephen10, Swale Thomas10, Daly Mark10, Korlach Jonas11, Uliano-Silva Marcela121314, Mazzoni Camila J.1314, Birren Bruce W.3, Genereux Diane P.3ORCID, Johnson Jeremy3, Lindblad-Toh Kerstin315ORCID, Karlsson Elinor K.31617ORCID, Nweeia Martin T.181920ORCID, Johnson Rebecca N.2122ORCID, Lewin Harris A.12324ORCID, Andrews Gregory, Armstrong Joel C., Bianchi Matteo, Birren Bruce W., Bredemeyer Kevin R., Breit Ana M., Christmas Matthew J., Clawson Hiram, Damas Joana, Palma Federica Di, Diekhans Mark, Dong Michael X., Eizirik Eduardo, Fan Kaili, Fanter Cornelia, Foley Nicole M., Forsberg-Nilsson Karin, Garcia Carlos J., Gatesy John, Gazal Steven, Genereux Diane P., Goodman Linda, Grimshaw Jenna, Halsey Michaela K., Harris Andrew J., Hickey Glenn, Hiller Michael, Hindle Allyson G., Hubley Robert M., Hughes Graham M., Johnson Jeremy, Juan David, Kaplow Irene M., Karlsson Elinor K., Keough Kathleen C., Kirilenko Bogdan, Koepfli Klaus-Peter, Korstian Jennifer M., Kowalczyk Amanda, Kozyrev Sergey V., Lawler Alyssa J., Lawless Colleen, Lehmann Thomas, Levesque Danielle L., Lewin Harris A., Li Xue, Lind Abigail, Lindblad-Toh Kerstin, Mackay-Smith Ava, Marinescu Voichita D., Marques-Bonet Tomas, Mason Victor C., Meadows Jennifer R. S., Meyer Wynn K., Moore Jill E., Moreira Lucas R., Moreno-Santillan Diana D., Morrill Kathleen M., Muntané Gerard, Murphy William J., Navarro Arcadi, Nweeia Martin, Ortmann Sylvia, Osmanski Austin, Paten Benedict, Paulat Nicole S., Pfenning Andreas R., Phan BaDoi N., Pollard Katherine S., Pratt Henry E., Ray David A., Reilly Steven K., Rosen Jeb R., Ruf Irina, Ryan Louise, Ryder Oliver A., Sabeti Pardis C., Schäffer Daniel E., Serres Aitor, Shapiro Beth, Smit Arian F. A., Springer Mark, Srinivasan Chaitanya, Steiner Cynthia, Storer Jessica M., Sullivan Kevin A. M., Sullivan Patrick F., Sundström Elisabeth, Supple Megan A., Swofford Ross, Talbot Joy-El, Teeling Emma, Turner-Maier Jason, Valenzuela Alejandro, Wagner Franziska, Wallerman Ola, Wang Chao, Wang Juehan, Weng Zhiping, Wilder Aryn P., Wirthlin Morgan E., Xue James R., Zhang Xiaomeng,
Affiliation:
1. The Genome Center, University of California, Davis, CA 95616 2. Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, South Korea 3. Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142 4. School of Biosciences, University of Kent, Canterbury CT2 7NJ, United Kingdom 5. The Royal Veterinary College, University of London, London NW1 0TU, United Kingdom 6. Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027 7. Department of Evolution, Behavior, and Ecology, Division of Biology, University of California San Diego, La Jolla, CA 92093 8. Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, Escondido, CA 92027 9. Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA 92027 10. Dovetail Genomics, LLC, Scotts Valley, CA 95066 11. Pacific Biosciences, Menlo Park, CA 94025 12. Wellcome Sanger Institute, Cambridgeshire CB10 1SA, United Kingdom 13. Berlin Center for Genomics in Biodiversity Research, D-14195 Berlin, Germany 14. Evolutionary Genetics Department, Leibniz Institut für Zoo- und Wildtierforschung, 10315 Berlin, Germany 15. Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 751 23, Sweden 16. Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655 17. Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655 18. Department of Restorative Dentistry and Biomaterials Sciences, Harvard School of Dental Medicine, Boston, MA 02115 19. Department of Comprehensive Care, Case Western Reserve University School of Dental Medicine, Cleveland, OH 44106 20. Marine Mammal Program, Department of Vertebrate Zoology, Smithsonian Institution, Washington, DC 20002 21. Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia 22. School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, NSW 2006, Australia 23. Department of Evolution and Ecology, University of California, Davis, CA 95616 24. John Muir Institute for the Environment, University of California, Davis, CA 95616
Abstract
Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding the molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded and 26 chromosome-scale genome assemblies representing 23/26 mammal orders, we computationally reconstructed ancestral karyotypes and syntenic relationships at 16 nodes along the mammalian phylogeny. Three different reference genomes (human, sloth, and cattle) representing phylogenetically distinct mammalian superorders were used to assess reference bias in the reconstructed ancestral karyotypes and to expand the number of clades with reconstructed genomes. The mammalian ancestor likely had 19 pairs of autosomes, with nine of the smallest chromosomes shared with the common ancestor of all amniotes (three still conserved in extant mammals), demonstrating a striking conservation of synteny for ∼320 My of vertebrate evolution. The numbers and types of chromosome rearrangements were classified for transitions between the ancestral mammalian karyotype, descendent ancestors, and extant species. For example, 94 inversions, 16 fissions, and 14 fusions that occurred over 53 My differentiated the therian from the descendent eutherian ancestor. The highest breakpoint rate was observed between the mammalian and therian ancestors (3.9 breakpoints/My). Reconstructed mammalian ancestor chromosomes were found to have distinct evolutionary histories reflected in their rates and types of rearrangements. The distributions of genes, repetitive elements, topologically associating domains, and actively transcribed regions in multispecies homologous synteny blocks and evolutionary breakpoint regions indicate that purifying selection acted over millions of years of vertebrate evolution to maintain syntenic relationships of developmentally important genes and regulatory landscapes of gene-dense chromosomes.
Publisher
Proceedings of the National Academy of Sciences
Subject
Multidisciplinary
Cited by
22 articles.
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