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

Zoonomia Consortium

doi:10.1126/SCIENCE.ABN1430

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

Zoonomia Consortium

Ecology and Evolution

Texas Tech University
Institute for Systems Biology
University of Massachusetts Medical School
University of California at Santa Cruz
Uppsala University
Broad Institute
Texas A&M University
University of Maine
University of California at Davis
Genome British Columbia
University of East Anglia
Pontifícia Universidade Católica do Rio Grande do Sul
University of Nevada, Las Vegas
University of Nottingham
American Museum of Natural History
University of Southern California
Fauna Bio Incorporated
Goethe University Frankfurt
LOEWE Centre for Translational Biodiversity Genomics
Senckenberg Gesellschaft für Naturforschung
University College Dublin
Pompeu Fabra University
Carnegie Mellon University
University of California at San Francisco
Glad-stone Institutes

Research output: Contribution to journal › Article › peer-review

75 Scopus citations

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 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.

Original language	English
Article number	eabn1430
Journal	Science
Volume	380
Issue number	6643
DOIs	https://doi.org/10.1126/SCIENCE.ABN1430
State	Published - Apr 28 2023

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10.1126/SCIENCE.ABN1430

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@article{ac1d36d9dc9847d594e8f00e9614e48d,

title = "Insights into mammalian TE diversity through the curation of 248 genome assemblies",

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 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.",

author = "\{Zoonomia Consortium\} and Osmanski, \{Austin B.\} and Jenny Korstian and Grimshaw, \{Jenna R.\} and Michaela Halsey and Moreno-Santill{\'a}n, \{Diana D.\} and Claudia Crookshanks and Jacquelyn Roberts and Carlos Garcia and Johnson, \{Matthew G.\} and Densmore, \{Llewellyn D.\} and Stevens, \{Richard D.\} and Jeb Rosen and Robert Hubley and D{\'a}valos, \{Liliana M.\} and Ray, \{David A.\} and Gregory Andrews and Armstrong, \{Joel C.\} and Matteo Bianchi and Birren, \{Bruce W.\} and Bredemeyer, \{Kevin R.\} and Breit, \{Ana M.\} and Christmas, \{Matthew J.\} and Hiram Clawson and Joana Damas and \{Di Palma\}, Federica and Mark Diekhans and Dong, \{Michael X.\} and Eduardo Eizirik and Kaili Fan and Cornelia Fanter and Foley, \{Nicole M.\} and Karin Forsberg-Nilsson and Garcia, \{Carlos J.\} and John Gatesy and Steven Gazal and Genereux, \{Diane P.\} and Linda Goodman and Jenna Grimshaw and Halsey, \{Michaela K.\} and Harris, \{Andrew J.\} and Glenn Hickey and Michael Hiller and Hindle, \{Allyson G.\} and Hubley, \{Robert M.\} and Hughes, \{Graham M.\} and Jeremy Johnson and David Juan and Kaplow, \{Irene M.\} and Karlsson, \{Elinor K.\} and Keough, \{Kathleen C.\}",

year = "2023",

month = apr,

day = "28",

doi = "10.1126/SCIENCE.ABN1430",

language = "English",

volume = "380",

journal = "Science",

issn = "0036-8075",

number = "6643",

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T1 - Insights into mammalian TE diversity through the curation of 248 genome assemblies

AU - Zoonomia Consortium

AU - Osmanski, Austin B.

AU - Korstian, Jenny

AU - Grimshaw, Jenna R.

AU - Halsey, Michaela

AU - Moreno-Santillán, Diana D.

AU - Crookshanks, Claudia

AU - Roberts, Jacquelyn

AU - Garcia, Carlos

AU - Johnson, Matthew G.

AU - Densmore, Llewellyn D.

AU - Stevens, Richard D.

AU - Rosen, Jeb

AU - Hubley, Robert

AU - Dávalos, Liliana M.

AU - Ray, David A.

AU - Andrews, Gregory

AU - Armstrong, Joel C.

AU - Bianchi, Matteo

AU - Birren, Bruce W.

AU - Bredemeyer, Kevin R.

AU - Breit, Ana M.

AU - Christmas, Matthew J.

AU - Clawson, Hiram

AU - Damas, Joana

AU - Di Palma, Federica

AU - Diekhans, Mark

AU - Dong, Michael X.

AU - Eizirik, Eduardo

AU - Fan, Kaili

AU - Fanter, Cornelia

AU - Foley, Nicole M.

AU - Forsberg-Nilsson, Karin

AU - Garcia, Carlos J.

AU - Gatesy, John

AU - Gazal, Steven

AU - Genereux, Diane P.

AU - Goodman, Linda

AU - Grimshaw, Jenna

AU - Halsey, Michaela K.

AU - Harris, Andrew J.

AU - Hickey, Glenn

AU - Hiller, Michael

AU - Hindle, Allyson G.

AU - Hubley, Robert M.

AU - Hughes, Graham M.

AU - Johnson, Jeremy

AU - Juan, David

AU - Kaplow, Irene M.

AU - Karlsson, Elinor K.

AU - Keough, Kathleen C.

PY - 2023/4/28

Y1 - 2023/4/28

N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/85163029203

U2 - 10.1126/SCIENCE.ABN1430

DO - 10.1126/SCIENCE.ABN1430

M3 - Article

AN - SCOPUS:85163029203

SN - 0036-8075

VL - 380

JO - Science

JF - Science

IS - 6643

M1 - eabn1430

ER -

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

Abstract

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