Transposable elements (TEs) are prevalent genomic components which can replicate as a function of mobilization in eukaryotes. Not only do they alter genome structure, they also play regulatory functions or organize chromatin structure. In addition to vertical parent-to-offspring inheritance, TEs can also horizontally "jump" between species, known as horizontal transposon transfer (HTT). This can rapidly alter the course of genome evolution. In this chapter, we provide a practical framework to detect HTT events. Our HTT detection framework is based on the use of sequence alignment to determine the divergence/conservation profiles of TE families to determine the history of expansion events. In summary, it includes (a) workflow of HTT detection from Ab initio identified TEs; (b) workflow for detecting HTT for specific, curated TEs; and (c) workflow for validating detected HTT candidates. Our framework covers two common scenarios of HTT detection in the modern omics era, and we believe it will serve as a valuable toolbox for the TE and genomics research community.
Keywords: Horizontal transfer; LINE; Retrotransposon; Transposable element; Transposon.
© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.