Squamate reptiles challenge paradigms of genomic repeat element evolution set by birds and mammals

Nature Communications
Giulia I M PasquesiTodd A Castoe

Abstract

Broad paradigms of vertebrate genomic repeat element evolution have been largely shaped by analyses of mammalian and avian genomes. Here, based on analyses of genomes sequenced from over 60 squamate reptiles (lizards and snakes), we show that patterns of genomic repeat landscape evolution in squamates challenge such paradigms. Despite low variance in genome size, squamate genomes exhibit surprisingly high variation among species in abundance (ca. 25-73% of the genome) and composition of identifiable repeat elements. We also demonstrate that snake genomes have experienced microsatellite seeding by transposable elements at a scale unparalleled among eukaryotes, leading to some snake genomes containing the highest microsatellite content of any known eukaryote. Our analyses of transposable element evolution across squamates also suggest that lineage-specific variation in mechanisms of transposable element activity and silencing, rather than variation in species-specific demography, may play a dominant role in driving variation in repeat element landscapes across squamate phylogeny.

References

Sep 15, 1994·Nature·B CharlesworthW Stephan
Sep 2, 1998·Proceedings of the National Academy of Sciences of the United States of America·D Kordis, F Gubensek
Oct 29, 1998·Toxicon : Official Journal of the International Society on Toxinology·D Kordis, F Gubensek
May 24, 2001·Molecular Biology and Evolution·S BoissinotA V Furano
Oct 30, 2001·Evolution; International Journal of Organic Evolution·B D Neff, M R Gross
Aug 9, 2002·Theoretical Population Biology·Dmitri A Petrov
Apr 19, 2003·Proceedings of the National Academy of Sciences of the United States of America·Brook BrouhaHaig H Kazazian
Apr 30, 2003·Molecular Biology and Evolution·Dmitri A PetrovAaron E Hirsh
Nov 25, 2003·Science·Michael Lynch, John S Conery
Jan 22, 2004·Bioinformatics·Emmanuel ParadisKorbinian Strimmer
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Sep 3, 2004·Molecular Biology and Evolution·Daniel E NeafseyDaniel L Hartl
Nov 13, 2004·Molecular Biology and Evolution·Karl J Fryxell, Won-Jong Moon
Oct 19, 2006·Molecular Biology and Evolution·Michael J Benton, Philip C J Donoghue
Feb 27, 2007·Genome Research·William J MurphyWebb Miller
Jul 12, 2007·Proceedings of the National Academy of Sciences of the United States of America·Oliver Piskurek, Norihiro Okada
Sep 12, 2007·Bioinformatics·M A LarkinD G Higgins
Nov 13, 2007·BMC Evolutionary Biology·Alexei J Drummond, Andrew Rambaut
Nov 28, 2007·Proceedings of the National Academy of Sciences of the United States of America·Arnaud Le RouzicPierre Capy
Apr 29, 2008·Nucleic Acids Research·Mark JohnsonThomas L Madden
Feb 12, 2009·Molecular Ecology·Rasmus Nielsen, Mark A Beaumont
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Apr 13, 2010·Nature Methods·J Gregory CaporasoRob Knight
Dec 22, 2010·Molecular Biology and Evolution·Dmitri A PetrovJosefa González
May 17, 2011·Genome Biology and Evolution·Todd A CastoeDavid D Pollock
Aug 19, 2011·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·J Arvid Ågren, Stephen I Wright
Dec 7, 2011·PLoS Genetics·A P Jason de KoningDavid D Pollock
Feb 10, 2012·Molecular Biology and Evolution·Robert LanfearStephane Guindon
Apr 27, 2012·Genome Biology and Evolution·Eryn BlassStéphane Boissinot
Sep 18, 2012·Molecular Phylogenetics and Evolution·Matthias BerntPeter F Stadler
Nov 14, 2012·Annual Review of Genetics·Cheng Ran Lisa HuangJef D Boeke
Jan 1, 2013·Genome Biology and Evolution·Arnaud Le RouzicAurélie Hua-Van
Jan 2, 2013·Proceedings of the National Academy of Sciences of the United States of America·Ali Morton WalshDavid L Adelson
May 1, 2013·BMC Evolutionary Biology·R Alexander PyronJohn J Wiens
May 30, 2013·PeerJ·Elizabeth Hb Hellen, John Fy Brookfield

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Citations

Apr 10, 2020·Genome Biology and Evolution·Giulia I M PasquesiTodd A Castoe
Jan 12, 2020·Molecular Biology and Evolution·Drew R SchieldTodd A Castoe
Jul 6, 2020·Nature Communications·Tiago R SimõesStephanie E Pierce
Aug 8, 2020·Nature·Neil J GemmellUNKNOWN Ngatiwai Trust Board
Oct 7, 2020·Proceedings of the National Academy of Sciences of the United States of America·Asier Ullate-AgoteAthanasia C Tzika
Nov 5, 2020·Cells·Worapong SingchatKornsorn Srikulnath
Sep 22, 2020·Annual Review of Genetics·Jonathan N Wells, Cédric Feschotte
Oct 7, 2020·Genome Biology and Evolution·James D GalbraithDavid L Adelson
Nov 11, 2020·Molecular Ecology·Alastair J Ludington, Kate L Sanders
Mar 7, 2021·International Journal of Molecular Sciences·Anna Maria PappalardoTeresa Capriglione
Apr 11, 2021·Proceedings of the National Academy of Sciences of the United States of America·Sangeet LamichhaneyTariq Ezaz
May 12, 2021·Proceedings of the National Academy of Sciences of the United States of America·Diego Dantas AlmeidaInácio L M Junqueira-de-Azevedo
Jun 5, 2021·PloS One·Brenna A LevineWarren Booth
Mar 8, 2021·Genomics, Proteomics & Bioinformatics·Jie WangRachel Lockridge Mueller
Aug 28, 2021·Molecular Ecology·Alexander Ochoa, H Lisle Gibbs
Sep 24, 2021·Annual Review of Genetics·Daren C CardScott V Edwards

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Datasets Mentioned

BETA
PRJNA413172
PRJNA413201

Methods Mentioned

BETA
454 shotgun sequencing

Software Mentioned

finder
psmc
BLAST
ProcessRepeat
pegas
multi
BEAST
Phytools
R 79 custom script
plot

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