Broadscale evolutionary analysis of eukaryotic DDE transposons

Abstract

DDE transposons are widespread selfish genetic elements, often comprising a large proportion of eukaryotic genomic content. DDE transposons have also made important contributions to varied host functions during eukaryotic evolution, and their transposases may be the most abundant and ubiquitous genes in nature. Yet much remains unknown about their basic biology. We employ a broadscale screen of DDE transposase diversity to characterise major evolutionary patterns for all 19 DDE transposon superfamilies. We identify considerable variation in DDE transposon superfamily size, and find a dominant association with animal hosts. While few DDE transposon superfamilies specialise in plants or fungi, the four largest superfamilies contain major plant-associated clades, at least partially underlying their relative success. We recover a pattern of host conservation among DDE transposon lineages, punctuated by occasional horizontal transfer to distantly related hosts. Host range and horizontal transfer are strongly positively correlated with DDE transposon superfamily size, arguing against variation in the capacity for generalism. We find that rates of horizontal transfer decrease sharply with increasing levels of host taxonomy, supporting the existence of host-associated barriers to DDE transposon spread. Overall, despite their relatively simple genetic structure, our results imply that trade-offs in host adaptation are important in defining DDE transposon-host relationships and evolution. In addition, our study provides a phylogenetic framework to facilitate the identification and further analysis of DDE transposons.

Migrators Within Migrators: Exploring Transposable Element Dynamics in the Monarch Butterfly, Danaus plexippus

“…The copyright holder for this preprint this version posted September 28, 2021. ; https://doi.org/10.1101/2021.09.28.462135 doi: bioRxiv preprint attributed to increases in non-autonomous copies [66]. In the meantime, however, these TEs are proliferating and dynamically altering the genomic landscape of D. plexippus, with potential connotations for ongoing genome structural and functional evolution [1][2][3]19].…”

“…2), has led to another wave of TE proliferation in the monarch genomes. These elements are closely related and located in Clade 130 in a recent phylogenetic study of Tc1/mariner diversity [78], which contains elements from diverse insect species, including butterflies, aphids and ants (Figure S6; Additional File 7). Ants and aphids are known to share environments with monarch larvae on milkweed plants [79], increasing the potential for HTT events [54,80].…”

“…There has been a recent burst of activity in two Tc1-Mariner elements: danPle_TcM-1 (499 new copies, from ~0.68Mya), and danPle_TcM-2 (275 new copies, from ~0.34Mya), with insertion rates of 733 insertions/My and 798 insertions/My, respectively (Tables S7 and S9; Additional File 3). The identified Tc1-Mariner elements are closely related and located in Clade 130 in a recent phylogenetic study of Tc1/mariner diversity [66], which contains elements from diverse insect species, including butterflies, aphids and ants (Figure S5;…”

“…To further classify the novel DNA elements in the monarch beyond homology to known elements, as used by RepeatModeler. DDE transposases were compared with curated alignments for all DDE TE superfamilies [66]. Specifically, dashes in curated alignments of all known DDE TE sequences for each of the 19 families were removed, and the resultant fasta file was used as the subject in a blastx search against the de novo monarch TE library, with an e-value threshold of 1x10 -20 and tabular output specified (evalue 1e-20 -outfmt 6) [111].…”

“…The copyright holder for this preprint this version posted September 28, 2021. ; https://doi.org/10.1101/2021.09.28.462135 doi: bioRxiv preprint described [66]. To estimate phylogenies for the two DDE superfamilies, we performed 1,000 ultra-fast bootstrap replicates in IQ-TREE (v1.6.12) [131] specifying the best fit amino acid model for each family as indicated by ModelFinder [132].…”