Ancient persistence and newfound diversity of CR1-group retrotransposons across vertebrates

Abstract

Retrotransposons are mobile, repetitive DNA sequences that are ubiquitous across eukaryotes and widely recognised as key drivers of both gene and genome evolution. The CR1 group of retrotransposons is thought to have been present in the most recent common ancestor of vertebrates ∼560 mya, and is the dominant retrotransposon in the majority of vertebrate species. The advent of long-read sequencing technologies has enabled the assembly of high-quality genomes from representatives of almost all major vertebrate orders, enabling comparative analysis with deeply divergent species. To better understand the composition of CR1-group elements (CGEs) in vertebrates, we systematically characterised transposable elements across representative species from every available extant order of vertebrate. Our analysis uncovered previously unknown phylogenetic relationships of CGEs within and between species and has pushed back the origin of certain CR1-group subclades by tens of millions of years. Additionally, entirely novel elements with no close relatives in existing databases were uncovered within several of the species analysed. We also detected numerous putative horizontal transfer events, many of which had not been previously documented. Overall, this investigation has provided the first vertebrate-wide analysis of an element that is historically understudied yet plays a pivotal role in genome biology and evolution.