Evolutionary impacts of alternative transposition

Abstract

With the development of rapid DNA-sequencing techniques, more and more eukaryotic genomes are sequenced, assembled, and annotated. Now, we know that many eukaryotic genomes are large, highly repetitive, and very complex. One question that remains is what evolutionary forces generate the complexity of eukaryotic genomes? In this chapter, we discuss one of the possible answers to this question: the capacity of transposable elements to induce diverse genomic recombinations through various transposition reactions. Transposable elements (TEs or transposons) are DNA sequences that can move from one genomic location to another, and they are highly represented in most eukaryotic genomes. TEs are often called "junkDNA" because most copies are silenced and have no obvious function; however, various studies have indicated that TEs have made major contributions to shaping eukaryotic genomes and regulating gene expression.We show that TE transpositions can induce a variety of genome rearrangements including deletion, inversion, duplication, and translocation. These occur as direct products of alternative transposition pathways. Unlike standard transposition which involves only one transposon, alternative transposition involves two distinct TEs, undergoes more complicated movements, and generates more significant genome structure variations. Here, we describe various types of alternative transposition pathways, the diverse genome rearrangements they generate, and their potential role in the process of genome evolution.