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

Osmanski, A. B.; Paulat, N. S.; Korstian, J.; Grimshaw, J. R.; Halsey, M.; Sullivan, K. A. M.; Moreno-Santillan, D. D.; Crookshanks, C.; Roberts, J.; Garcia, C.; Johnson, M. G.; Densmore, L. D.; Stevens, R. D.; Zoonomia Consortium,; Rosen, J.; Storer, J. M.; Hubley, R.; Smit, A. F. A.; Davalos, L. M.; Karlsson, E. K.; Lindblad-Toh, K.; Ray, D. A.

doi:10.1101/2022.12.28.522108

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bioRxiv · 10.1101/2022.12.28.522108

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

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Abstract

We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We find that while 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 LINEs, drive increases in genome size while DNA transposons are associated with smaller genomes. Mammals tend to accumulate only a few types of TE 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. One-Sentence SummaryA de novo assessment of TE content in 248 mammals finds informative trends in mammalian genome evolution.

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Osmanski, A. B., Paulat, N. S., Korstian, J., Grimshaw, J. R., Halsey, M., Sullivan, K. A. M., Moreno-Santillan, D. D., Crookshanks, C., Roberts, J., Garcia, C., Johnson, M. G., Densmore, L. D., Stevens, R. D., Zoonomia Consortium,, Rosen, J., Storer, J. M., Hubley, R., Smit, A. F. A., Davalos, L. M., Karlsson, E. K., Lindblad-Toh, K., Ray, D. A.. 2022-12-30. Insights into mammalian TE diversity via the curation of 248 mammalian genome assemblies. https://doi.org/10.1101/2022.12.28.522108

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