Analyzing Horizontal Transfer of Transposable Elements on a Large Scale: Challenges and Prospects

Abstract

Whoever compares the genomes of distantly related species might find aberrantly high sequence similarity at certain loci. Such anomaly can only be explained by genetic material being transferred through other means than reproduction, that is, a horizontal transfer (HT). Between multicellular organisms, the transferred material will likely turn out to be a transposable element (TE). Because TEs can move between loci and invade chromosomes by replicating themselves, HT of TEs (HTT) profoundly impacts genome evolution. Yet, very few studies have quantified HTT at large taxonomic scales. Indeed, this task currently faces difficulties that range from the variable quality of available genome sequences to limitations of analytical procedures, some of which have been overlooked. Here we review the many challenges that an extensive analysis of HTT must overcome, we expose biases and limits of current methods, suggest solutions or workarounds, and reflect upon approaches that could be developed to better quantify this phenomenon.

Horizontal transfer and evolution of transposable elements in vertebrates

“…Frequent horizontal transfers of transposable elements. We investigated HTT involving most TE types among 307 vertebrate species whose genome sequences are publicly available on Gen-Bank (Supplementary Data 1), following principles developed in earlier studies 18,24 . To avoid detection biases that could have arisen from the use of available TE databases of varying quality across species, TEs were de novo characterized with the same procedure for all genomes.…”

“…Clearly, filters designed to select homologies resulting from HTT might pick up the few vertically inherited TEs copies that happened to have diverged at the slowest pace. As a result, HTT among species that are not sufficiently divergent on a molecular level will remain difficult to reliably ascertain 18 . This risk precluded the detection of HTT within mammals and birds.…”

“…We further assessed whether the Ks distribution of hits within each group was visibly truncated to the right by our filter involving Ks thresholds. In such case, retained hits in a group might represent pairs of TE copies that happened to have diverged much more slowly than average after a speciation event, i.e., the Ks of the hit group might constitute the left tail of a larger Ks distribution that represents vertical inheritance rather than HTT 18 . To account for this risk, any hit group was removed if the modal class of its Ks distribution did not contain at least 20 more hits than the rightmost class, or if its maximum Ks was higher than the Ks threshold used to select hits, minus 0.2.…”

“…In particular, the frequency and impact of HTT that have occurred during the evolution of large clades, and the factors governing these transfers, are poorly known. This limited understanding is due in part from the reliance on manual curation of TEs and individual detection and validation of transfer events, which has restricted the scope of studies on HTT 18 . The lack of global quantification of HTT echoes the limited knowledge about the selective constraints acting on TEs during vertical versus horizontal transmission (but see ref.…”

New environment, new invaders - repeated horizontal transfer of LINEs to sea snakes

“…Whilst transposons are normally vertically transmitted (parent to offspring) there have been many instances of horizontal transfer of transposons (HTT) observed between distantly related species. While HTT of DNA transposons and LTR retrotransposons appears to be more common, many examples of HTT of non-LTR retrotransposons (LINEs) have been described (6) . These include transfers of RTE-BovBs between ticks and distant vertebrate lineages (7) , of AviRTEs between birds and parasitic nematodes (8) , and of Rex1 elements between teleost fish (9) .…”