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Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations

Yann Bourgeois, Robert Ruggiero, Imtiyaz Hariyani, Stéphane Boissinot
doi: https://doi.org/10.1101/2020.04.12.037754
Yann Bourgeois
1School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
2New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
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  • For correspondence: yann.bourgeois@port.ac.uk stephane.boissinot@nyu.edu
Robert Ruggiero
2New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
3Department of Biology, Southeast Missouri State University, Cape Girardeau, MO, 63701, USA
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Imtiyaz Hariyani
1School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
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Stéphane Boissinot
1School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
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  • For correspondence: yann.bourgeois@port.ac.uk stephane.boissinot@nyu.edu
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Abstract

Background The interactions between transposable elements (TEs) and their hosts constitute one of the most profound co-evolutionary processes found in nature. The population dynamics of TEs depends on factors specific to each TE families, such as the rate of transposition and insertional preference, the demographic history of the host and the genomic landscape. How these factors interact has yet to be investigated holistically. Here we are addressing this question in the green anole (Anolis carolinensis) whose genome contains an extraordinary diversity of TEs (including non-LTR retrotransposons, SINEs, LTR-retrotransposons and DNA transposons).

Results We observe a positive correlation between recombination rate and TEs frequencies and densities for LINEs, SINEs and DNA transposons. For these elements, there was a clear impact of demography on TE frequency and abundance, with a loss of polymorphic elements and skewed frequency spectra in recently expanded populations. On the other hand, some LTR-retrotransposons displayed patterns consistent with a very recent phase of intense amplification. To determine how demography, genomic features and intrinsic properties of TEs interact we ran simulations using SLiM3. We determined that i) short TE insertions are not strongly counter-selected, but long ones are, ii) neutral demographic processes, linked selection and preferential insertion may explain positive correlations between average TE frequency and recombination, iii) TE insertions are unlikely to have been massively recruited in recent adaptation..

Conclusions We demonstrate that deterministic and stochastic processes have different effects on categories of TEs and that a combination of empirical analyses and simulations can disentangle the effects of these processes.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • E-mail addresses: Robert Ruggiero: rruggiero{at}semo.edu, Imtiyaz Hariyani: imtiyaz.hariyani{at}nyu.edu

  • https://github.com/YannBourgeois/SLIM_simulations_TEs

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 13, 2020.
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Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations
Yann Bourgeois, Robert Ruggiero, Imtiyaz Hariyani, Stéphane Boissinot
bioRxiv 2020.04.12.037754; doi: https://doi.org/10.1101/2020.04.12.037754
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Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations
Yann Bourgeois, Robert Ruggiero, Imtiyaz Hariyani, Stéphane Boissinot
bioRxiv 2020.04.12.037754; doi: https://doi.org/10.1101/2020.04.12.037754

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