Evolution of the ancestral mammalian karyotype and syntenic regions

• DOI: 10.1073/pnas.2209139119
• Publication Date: 2022-09-26T19:21:09Z
• Authors: Joana Damas; Marco Corbo; Jaebum Kim; Jason Turner-Maier; Marta Farré; Denis M. Larkin; Oliver A. Ryder; Cynthia Steiner; Marlys L. Houck; Shaune Hall; Lily Shiue; Stephen Thomas; Thomas Swale; Mark Daly; Jonas Korlach; Marcela Uliano-Silva; Camila J. Mazzoni; Bruce W. Birren; Diane P. Genereux; Jeremy Johnson; Kerstin Lindblad-Toh; Elinor K. Karlsson; Martin T. Nweeia; Rebecca N. Johnson; ; Harris A. Lewin; Gregory Andrews; Joel C. Armstrong; Matteo Bianchi; Bruce W. Birren; Kevin R. Bredemeyer; Ana M. Breit; Matthew J. Christmas; Hiram Clawson; Joana Damas; Federica Di Palma; Mark Diekhans; Michael X. Dong; Eduardo Eizirik; Kaili Fan; Cornelia Fanter; Nicole M. Foley; Karin Forsberg-Ni...; Carlos J. Garcia; John Gatesy; Steven Gazal; Diane P. Genereux; Linda Goodman; Jenna Grimshaw; Michaela K. Halsey; Andrew J. Harris; Glenn Hickey; Michael Hiller; Allyson G. Hindle; Robert M. Hubley; Graham M. Hughes; Jeremy Johnson; David Juan; Irene M. Kaplow; Elinor K. Karlsson; Kathleen C. Keough; Bogdan Kirilenko; Klaus-Peter Koepfli; Jennifer M. Korstian; Amanda Kowalczyk; Sergey V. Kozyrev; Alyssa J. Lawler; Colleen Lawless; Thomas Lehmann; Danielle L. Levesque; Harris A. Lewin; Xue Li; Abigail Lind; Kerstin Lindblad-Toh; Ava Mackay-Smith; Voichita D. Marin...; Tomas Marques-Bonet; Victor C. Mason; Jennifer R. S. Me...; Wynn K. Meyer; Jill E. Moore; Lucas R. Moreira; Diana D. Moreno-S...; Kathleen M. Morrill; Gerard Muntané; William J. Murphy; Arcadi Navarro; Martin Nweeia; Sylvia Ortmann; Austin Osmanski; Benedict Paten; Nicole S. Paulat; Andreas R. Pfenning; BaDoi N. Phan; Katherine S. Pollard; Henry E. Pratt; David A. Ray; Steven K. Reilly; Jeb R. Rosen; Irina Ruf; Louise Ryan; Oliver A. Ryder; Pardis C. Sabeti; Daniel E. Schäffer; Aitor Serres; Beth Shapiro; Arian F. A. Smit; Mark Springer; Chaitanya Srinivasan; Cynthia Steiner; Jessica M. Storer; Kevin A. M. Sullivan; Patrick F. Sullivan; Elisabeth Sundström; Megan A. Supple; Ross Swofford; Joy-El Talbot; Emma Teeling; Jason Turner-Maier; Alejandro Valenzuela; Franziska Wagner; Ola Wallerman; Chao Wang; Juehan Wang; Zhiping Weng; Aryn P. Wilder; Morgan E. Wirthlin; James R. Xue; Xiaomeng Zhang
• Keywords: Synteny; Chromosomal rearrangement; Ancestor

Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded 26 chromosome-scale genome assemblies representing 23/26 mammal orders, we computationally reconstructed ancestral karyotypes syntenic relationships at 16 nodes along phylogeny. Three different reference genomes (human, sloth, cattle) phylogenetically distinct superorders were used assess bias in expand number clades with genomes. The ancestor likely had 19 pairs autosomes, nine smallest chromosomes shared common all amniotes (three still conserved extant mammals), demonstrating a striking conservation synteny for ∼320 My vertebrate evolution. numbers types classified transitions between karyotype, descendent ancestors, species. For example, 94 inversions, fissions, 14 fusions occurred over 53 differentiated therian from eutherian ancestor. highest breakpoint rate was observed ancestors (3.9 breakpoints/My). Reconstructed found have evolutionary histories reflected their rates rearrangements. distributions genes, repetitive elements, topologically associating domains, actively transcribed regions multispecies homologous blocks indicate purifying selection acted millions years maintain developmentally important genes regulatory landscapes gene-dense chromosomes.