Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations
Autoři:
Yann Bourgeois aff001; Robert Ruggiero aff002; Imtiyaz Hariyani aff001; Stéphane Boissinot aff001; Robert P. Ruggiero aff002; Imtiyaz Hariyani aff002; Stéphane Boissinot aff002
Působiště autorů:
School of Biological Sciences, University of Portsmouth, Portsmouth, United Kingdom
aff001; New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
aff002; Department of Biology, Southeast Missouri State University, Cape Girardeau, MO, United States of America
aff003
Vyšlo v časopise:
Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations. PLoS Genet 16(10): e32767. doi:10.1371/journal.pgen.1009082
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pgen.1009082
Souhrn
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). We observed a positive correlation between recombination rate and frequency of TEs 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. 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 these mechanisms.
Klíčová slova:
DNA recombination – Effective population size – Florida – Genomics – Heterozygosity – Population genetics – Transposable elements – DNA transposons
Zdroje
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