Giant Transposons in Eukaryotes: Is Bigger Better?

Abstract

Transposable elements (TEs) are ubiquitous in both prokaryotes and eukaryotes, and the dynamic character of their interaction with host genomes brings about numerous evolutionary innovations and shapes genome structure and function in a multitude of ways. In traditional classification systems, TEs are often being depicted in simplistic ways, based primarily on the key enzymes required for transposition, such as transposases/recombinases and reverse transcriptases. Recent progress in whole-genome sequencing and long-read assembly, combined with expansion of the familiar range of model organisms, resulted in identification of unprecedentedly long transposable units spanning dozens or even hundreds of kilobases, initially in prokaryotic and more recently in eukaryotic systems. Here, we focus on such oversized eukaryotic TEs, including retrotransposons and DNA transposons, outline their complex and often combinatorial nature and closely intertwined relationship with viruses, and discuss their potential for participating in transfer of long stretches of DNA in eukaryotes.

Eukaryotic transposable elements as “cargo carriers”: the forging of metal resistance in the fungusPaecilomyces variotii

“…These include helitrons in maize capable of capturing up to nine gene fragments and totaling up to 39 kb 54 , and the tetratorn elements of fish that are well over 150 kb 21 . The discovery of these large transposable elements in eukaryotes has prompted the hypothesis that such transposons might be capable of carrying greater amounts of useful “cargo” including entire gene clusters 22 .…”

“…How such clusters are transferred between species is not understood. Although it has recently been hypothesized that gene clusters are horizontally transferred between eukaryotic species on large transposable elements 21,22 , transposons carrying large regions of host-beneficial DNA have not been reported.…”

Long Tandem Arrays of Cassandra Retroelements and Their Role in Genome Dynamics in Plants

“…Repetitive sequences are extensively distributed throughout the genomes of many organisms [1][2][3][4][5][6]. A repetitive sequence refers to highly similar DNA fragments that are present in multiple copies in the genome.…”

High-throughput retrotransposon-based genetic diversity of maize germplasm assessment and analysis

“…The long terminal repeat (LTR) retrotransposons (RLX) [1,2] are a large class of transposable elements that propagate in the genome by a "copy-and-paste" mechanism that is essentially identical to the intracellular phase of retrovirus replication [1][2][3][4][5], in contrast to the "cut-and-paste" mobility of DNA transposons. The RLX lifecycle involves transcription of an integrated copy, reverse transcription of the transcript into cDNA, and integration of the new copy.…”

“…Complete understanding of the genome and the relationship between genotype and phenotype requires knowledge of both the role and function of the genes as well as of the repetitive component, particularly regarding RLX dynamics [3]. Most eukaryotic genomes comprise over 70% repetitive DNA, with gene numbers, ranging from 10,000 to 50,000, showing much less variation at the monoploid level [4][5][6][7]. Particularly in higher plants, RLXs compose more than half of the repetitive DNA; they not only facilitate homologous recombination, but also can undergo intra-and inter-RLX recombination that is part of their dynamism [4,[8][9][10].…”