Patterns of selection in the evolution of a transposable element.pdf (453.86 kB)
Patterns of selection in the evolution of a transposable element
journal contribution
posted on 2023-06-10, 04:41 authored by Julie Jeannine Claude DAZENIEREJulie Jeannine Claude DAZENIERE, Alexandros BousiosAlexandros Bousios, Adam Eyre-WalkerAdam Eyre-WalkerTransposable elements are a major component of most eukaryotic genomes. Here, we present a new approach which allows us to study patterns of natural selection in the evolution of transposable elements over short time scales. The method uses the alignment of all elements with intact gag/pol genes of a transposable element family from a single genome. We predict that the ratio of nonsynonymous to synonymous variants in the alignment should decrease as a function of the frequency of the variants, because elements with nonsynonymous variants that reduce transposition will have fewer progeny. We apply our method to Sirevirus long-terminal repeat retrotransposons that are abundant in maize and other plant species and show that nonsynonymous to synonymous variants declines as variant frequency increases, indicating that negative selection is acting strongly on the Sirevirus genome. The asymptotic value of nonsynonymous to synonymous variants suggests that at least 85% of all nonsynonymous mutations in the transposable element reduce transposition. Crucially, these patterns in nonsynonymous to synonymous variants are only predicted to occur if the gene products from a particular transposable element insertion preferentially promote the transposition of the same insertion. Overall, by using large numbers of intact elements, this study sheds new light on the selective processes that act on transposable elements.
History
Publication status
- Published
File Version
- Published version
Journal
G3 (Bethesda, Md.)ISSN
2160-1836Publisher
Oxford University Press (OUP)External DOI
Volume
12Page range
jkac056 1-10Event location
EnglandDepartment affiliated with
- Biochemistry Publications
Full text available
- Yes
Peer reviewed?
- Yes
Legacy Posted Date
2022-09-09First Open Access (FOA) Date
2022-09-09First Compliant Deposit (FCD) Date
2022-09-08Usage metrics
Categories
No categories selectedKeywords
Licence
Exports
RefWorks
BibTeX
Ref. manager
Endnote
DataCite
NLM
DC