Transposable elements as genetic accelerators of evolution: contribution to genome size, gene regulatory network rewiring and morphological innovation

Abstract

In the current era, as a growing number of genome sequence assemblies have been reported in animals, an in-depth analysis of transposable elements (TEs) is one of the most fundamental and essential studies for evolutionary genomics. Although TEs have, in general, been regarded as non-functional junk/selfish DNA, parasitic elements or harmful mutagens, studies have revealed that TEs have had a substantial and sometimes beneficial impact on host genomes in several ways. First, TEs are themselves diverse and thus provide lineage-specific characteristics to the genomes. Second, because TEs constitute a substantial fraction of animal genomes, they are a major contributing factor to evolutionary changes in genome size and composition. Third, host organisms have co-opted many repetitive sequences as genes, cis-regulatory elements and chromatin domain boundaries, which alter gene regulatory networks and in addition are partly involved in morphological evolution, as has been well documented in mammals. Here, I review the impact of TEs on various aspects of the genome, such as genome size and diversity in animals, as well as the evolution of gene networks and genome architecture in mammals. Given that a number of TE families probably remain to be discovered in many non-model organisms, unknown TEs may have contributed to gene networks in a much wider variety of animals than considered previously.

Comparative genomic analyses illuminate the distinct evolution of megabats within Chiroptera

“…S2 ). Consistent with the previous observations, it is also interesting that the proportion of TEs is generally correlated with the genome size in mammals 51 , 52 ( Supplementary Fig. S2 ).…”

“…In general, different types of SINE families are distributed for each mammalian clade, such as order, sub-order, or family. 52 In megabats, the only known active SINEs are the 5S rRNA-derived MEG SINEs. 54 It should be noted that Rousettus genomes contain no more than 23,000 copies of the MEG-related SINEs, which cover 0.21% of the genome.…”

Comprehensive genomic analysis reveals dynamic evolution of endogenous retroviruses that code for retroviral-like protein domains

“…It has been reported that up to 70%, of the human genome originates from TEs [1][2][3]. Generally, TEs are categorized as junk DNA [4]; however, many studies have shown that they have, in fact, contributed greatly to mammalian evolution [5][6][7]. Furthermore, TEs promote rearrangement of chromosomal DNA [8], and can become sources of both coding and regulatory sequences during the evolution of host genomes [9][10][11][12].…”

The plastic genome: The impact of transposable elements on gene functionality and genomic structural variations

“…In plants, transposons play a key role in characters of agronomic interest and in their domestication. TEs contribute to genome evolution is through TE exaptation, a process whereby TEs, which usually persist by replicating in the genome, are integrated as novel host genes, which thereafter persist by conferring phenotypic benefits (Joly‐Lopez & Bureau, 2018; Nishihara, 2020; Schrader & Schmitz, 2019). Many TE‐induced mutations have been selected during plant domestication.…”

“…To understand the role that TEs have played during evolution, it is necessary to consider both history of their discovery and their genomic activity (Lisch, 2013). In plants, as in most organisms, TEs are by far the most variable sequences of the genome; TEs are DNA sequences capable of changing their position within a genome and being mobilized between different species (Bourque et al, 2018; Huang, Burns, & Bok, 2012; Nishihara, 2020; Slotkin & Martienssen, 2007). Expansion and contraction in the number of TEs can lead to dramatic differences in chromosomes rearrangement and in genome size, especially in species where TEs constitute the most conspicuous part of DNA (Kojima, 2020; Larsen, 2018; Vicient & Casacuberta, 2017).…”