Horizontal transfer of a retrotransposon between parasitic nematodes and the common shrew

BACKGROUND: As the genomes of more metazoan species are sequenced, reports of horizontal transposon transfers (HTT) have increased. Our understanding of the mechanisms of such events is at an early stage. The close physical relationship between a parasite and its host could facilitate horizontal transfer. To date, two studies have identified horizontal transfer of RTEs, a class of retrotransposable elements, involving parasites: ticks might act as vector for BovB between ruminants and squamates, and AviRTE was transferred between birds and parasitic nematodes. RESULTS: We searched for RTEs shared between nematode and mammalian genomes. Given their physical proximity, it was necessary to detect and remove sequence contamination from the genome datasets, which would otherwise distort the signal of horizontal transfer. We developed an approach that is based on reads instead of genomic sequences to reliably detect contamination. From comparison of 43 RTEs across 197 genomes, we identified a single putative case of horizontal transfer: we detected RTE1_Sar from Sorex araneus, the common shrew, in parasitic nematodes. From the taxonomic distribution and evolutionary analysis, we show that RTE1_Sar was horizontally transferred. CONCLUSION: We identified a new horizontal RTE transfer in host-parasite interactions, which suggests that it is not uncommon. Further, we present and provide the workflow a read-based method to distinguish between contamination and horizontal transfer. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13100-019-0166-3) contains supplementary material, which is available to authorized users.