Birth, School, Work, Death, and Resurrection: The Life Stages and Dynamics of Transposable Element Proliferation

Abstract

Transposable elements (TEs) can be maintained in sexually reproducing species even if they are harmful. However, the evolutionary strategies that TEs employ during proliferation can modulate their impact. In this review, I outline the different life stages of a TE lineage, from birth to proliferation to extinction. Through their interactions with the host, TEs can exploit diverse strategies that range from long-term coexistence to recurrent movement across species boundaries by horizontal transfer. TEs can also engage in a poorly understood phenomenon of TE resurrection, where TE lineages can apparently go extinct, only to proliferate again. By determining how this is possible, we may obtain new insights into the evolutionary dynamics of TEs and how they shape the genomes of their hosts.

Telomere‐Specialized Retroelements in Drosophila: Adaptive Symbionts of the Genome, Neutral, or in Conflict?

“…Only when proteins and telomeric RNA are not part of the same TE (i.e., domesticated TE proteins acting in trans on domesticated TE sequences) can one be certain of their domestication [85] because the potential of a TE to strengthen the conflict at any point through mutation or gene conversion between TEs is possible. [10] 6. Why is reverse transcription a recurrent theme for telomere elongation?…”

“…Mutation and gene conversion allow the LINE elements to strengthen or "resurrect" the conflict at any point. [10] This article is protected by copyright. All rights reserved.…”

Evolution of genome structure in theDrosophila simulansspecies complex

“…(Daborn et al 2002;Aminetzach et al 2005;Montchamp-Moreau et al 2006;Tao et al 2007bTao et al , 2007aFishman and Saunders 2008;Larracuente and Presgraves 2012;Ellison and Bachtrog 2013;Van't Hof et al 2016;Battlay et al 2018;Chakraborty et al 2018Chakraborty et al , 2019 ). The selfish proliferation of repetitive sequences can alter protein coding genes (Lipatov et al 2005) , create intragenomic conflicts (Doolittle and Sapienza 1980;Orgel and Crick 1980) and trigger evolutionary arms races within and between genomes (Werren et al 1988;Aravin et al 2007;Ellis et al 2011;Cocquet et al 2012;Lindholm et al 2016;Blumenstiel 2019;Parhad and Theurkauf 2019;Rathje et al 2019) . For example, centromeric repeats can drive through female meiosis, causing rapid evolution of centromere proteins to restore equal segregation (Henikoff et al 2001) .…”

Engines of change: Transposable element mutation rates are high and vary widely among genotypes and populations ofDaphnia magna

“…It is now known that transposable elements (TEs) make up a significant proportion of the genome in most eukaryotes, and in some cases even represent the majority of the sequence (e.g., Bennetzen Because TEs are mobile and far outnumber 'regular' protein-coding genes in most eukaryotic genomes, elucidating their patterns of replication, transposition, and excision/deletion is a major task that spans subdisciplines from molecular biology to population genetics (Hickman and Dyda 2015, Bourgeois and Boissinot 2019). The dynamics of TE proliferation includes 1) how TEs jump between lineages initially (horizontal transfer of TEs; HTT; Zhang et al 2020), 2) differential success among TE families in various host lineages (e.g., Lu et al 2017), and 3) when and where TEs are repressed and/or go extinct, and become resurrected (e.g., Blumenstiel 2019). Indeed, the idea that genomes are like habitats and that TEs are like individuals (and TE families like species) has gained popularity as a way of better characterizing the complexities of TE movement in different host genomes (e.g., Kremer et al 2020) and the notion that TEs and their host genomes co-evolve is now widely acknowledged (Koonin et al 2020).…”