A Maximum-Likelihood Approach to Estimating the Insertion Frequencies of Transposable Elements from Population Sequencing Data

Abstract

Transposable elements (TEs) contribute to a large fraction of the expansion of many eukaryotic genomes due to the capability of TEs duplicating themselves through transposition. A first step to understanding the roles of TEs in a eukaryotic genome is to characterize the population-wide variation of TE insertions in the species. Here, we present a maximum-likelihood (ML) method for estimating allele frequencies and detecting selection on TE insertions in a diploid population, based on the genotypes at TE insertion sites detected in multiple individuals sampled from the population using paired-end (PE) sequencing reads. Tests of the method on simulated data show that it can accurately estimate the allele frequencies of TE insertions even when the PE sequencing is conducted at a relatively low coverage (=5normalX). The method can also detect TE insertions under strong selection, and the detection ability increases with sample size in a population, although a substantial fraction of actual TE insertions under selection may be undetected. Application of the ML method to genomic sequencing data collected from a natural Daphnia pulex population shows that, on the one hand, most (>90normal%) TE insertions present in the reference D. pulex genome are either fixed or nearly fixed (with allele frequencies >0.95); on the other hand, among the nonreference TE insertions (i.e., those detected in some individuals in the population but absent from the reference genome), the majority (>70normal%) are still at low frequencies (<0.1). Finally, we detected a substantial fraction (∼9%) of nonreference TE insertions under selection.

Nucleic acids movement and its relation to genome dynamics of repetitive DNA

“…The first papers on this topic supported rather the view that the selection is the most important factor, for example, in gathering TEs in regions of low or no recombination, [24,25] while more recent papers also demonstrated the role of TE targeting into specific regions (centromeres, heterochromatin, changed DNA conformation, higher transcription, etc.). [26,27] Nevertheless, the present study detecting selection on TE insertion confirms the general expectation that the majority of TE insertions are fixed [28] and thus, that TEs are more likely neutral and/or deleterious to the host. [29] TEs not only move from one site to another one in a genome and reshape the primary genomic structure but they can also contribute to dynamic changes of 3D nuclear architecture as was recently exemplified by the separate clustering of L1 and Alu/B1 retrotransposons in human and mouse genomes.…”

“…The first papers on this topic supported rather the view that the selection is the most important factor, for example, in gathering TEs in regions of low or no recombination, [ 24,25 ] while more recent papers also demonstrated the role of TE targeting into specific regions (centromeres, heterochromatin, changed DNA conformation, higher transcription, etc.). [ 26,27 ] Nevertheless, the present study detecting selection on TE insertion confirms the general expectation that the majority of TE insertions are fixed [ 28 ] and thus, that TEs are more likely neutral and/or deleterious to the host. [ 29 ]…”

Taming transposable elements in livestock and poultry: a review of their roles and applications

“…However, recent studies have demonstrated that TE play important roles in driving the evolution of genomes [ 8 ]. Transposable elements can promote genetic diversity through insertion [ 9 ] and regulate other factors such as genome size expansion [ 10 ], 3D organization [ 11 ], chromatin modifications [ 12 ], gene regulatory networks [ 13 ], and DNA methylation [ 14 ]. Transposable elements can be considered as a source of raw material for primitive genomes, tools of genetic innovation, and ancestors of modern genes (e.g., ncRNA) [ 15 ].…”