Horizontal transfer and subsequent explosive expansion of a DNA transposon in sea kraits (Laticauda)

Abstract

Transposable elements (TEs) are self replicating genetic sequences and are often described as important “drivers of evolution”. This driving force is because TEs promote genomic novelty by enabling rearrangement, and through exaptation as coding and regulatory elements. However, most TE insertions will be neutral or harmful, therefore host genomes have evolved machinery to supress TE expansion. Through horizontal transposon transfer (HTT) TEs can colonise new genomes, and since new hosts may not be able to shut them down, these TEs may proliferate rapidly. Here we describe HTT of the Harbinger-Snek DNA transposon into sea kraits (Laticauda), and its subsequent explosive expansion within Laticauda genomes. This HTT occurred following the divergence of Laticauda from terrestrial Australian elapids ~15-25 Mya. This has resulted in numerous insertions into introns and regulatory regions, with some insertions into exons which appear to have altered UTRs or added sequence to coding exons. Harbinger-Snek has rapidly expanded to make up 8-12% of Laticauda spp. genomes; this is the fastest known expansion of TEs in amniotes following HTT. Genomic changes caused by this rapid expansion may have contributed to adaptation to the amphibious-marine habitat.

Dataset

The deposited dataset contains scripts used in analysis, GFFs of the Laticauda genome gene annotations produced using Liftoff, repeat sequences of all Harbinger-Snek variants and Harbinger-Snek-like TEs, repeat library used in RepeatMasker repeat annotation, repeat annotation of Laticauda, Notechis and Pseudonaja genomes, screenshots of IGV showing RNASeq reads mapped to gene exons and UTRs containing Harbinger-Snek insertions, and all phylogenetic trees and the sequence data used in generating them.