Insights into mammalian TE diversity through the curation of 248 genome assemblies

• DOI: 10.1126/science.abn1430
• Publication Date: 2023-04-27T17:59:00Z
• Authors: Austin B. Osmanski; Nicole S. Paulat; Jenny Korstian; Jenna R. Grimshaw; Michaela Halsey; Kevin A. M. Sullivan; Diana D. Moreno-S...; Claudia Crookshanks; Jacquelyn Roberts; Carlos Garcia; Matthew G. Johnson; Llewellyn D. Dens...; Richard D. Stevens; ; Jeb Rosen; Jessica M. Storer; Robert Hubley; Arian F. A. Smit; Liliana M. Dávalos; Elinor K. Karlsson; Kerstin Lindblad-Toh; David A. Ray; 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: Evolution, Molecular; Long Interspersed Nucleotide Elements; Evolution; Pregnancy; Eutheria; DNA Transposable Elements; Molecular; Animals; Datasets as Topic; Genetic Variation; Female; Feeding Behavior

We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We found that although mammals resemble one another in total TE content and diversity, they show substantial differences with regard to recent TE accumulation. This includes multiple recent expansion and quiescence events across the mammalian tree. Young TEs, particularly long interspersed elements, drive increases in genome size, whereas DNA transposons are associated with smaller genomes. Mammals tend to accumulate only a few types of TEs at any given time, with one TE type dominating. We also found association between dietary habit and the presence of DNA transposon invasions. These detailed annotations will serve as a benchmark for future comparative TE analyses among placental mammals.