Impact of a horizontally transferred Helitron family on genome evolution in Xenopus laevis

Within eukaryotes, most horizontal transfer of genetic material involves mobile DNA sequences and such events are called horizontal transposable element transfer (HTT). Although thousands of HTT examples have been reported, the transfer mechanisms and their impacts on host genomes remain elusive.

In this work, we carefully annotated three Helitron families within several Xenopus frog genomes. One of the Helitron family, Heli1Xen1, is recurrently involved in capturing and shuffling Xenopus laevis genes required in early embryonic development. Remarkably, we found that Heli1Xen1 is seemingly expressed in X. laevis and has produced multiple genomic polymorphisms within the X. laevis population. To identify the origin of Heli1Xen1, we searched its consensus sequence against available genome assemblies. We found highly similar copies in the genomes of another 13 vertebrate species from divergent vertebrate lineages, including reptiles, ray-finned fishes and amphibians. Further phylogenetic analysis provides evidence showing that Heli1Xen1 invaded these lineages via HTT quite recently, around 0.58-10.74 million years ago.

The frequently Heli1Xen1-involved HTT events among reptiles, fishes and amphibians could provide insights into possible vectors for transfer, such as shared viruses across lineages. Furthermore, we propose that the Heli1Xen1 sequence could be an ideal candidate for studying the mechanism and genomic impact of Helitron transposition.