Network‐based visualisation reveals new insights into transposable element diversity

Abstract

Transposable elements (TEs) are widespread across eukaryotic genomes, yet their content varies widely between different species. Factors shaping the diversity of TEs are poorly understood. Understanding the evolution of TEs is difficult because their sequences diversify rapidly and TEs are often transferred through nonconventional means such as horizontal gene transfer. We developed a method to track TE evolution using network analysis to visualise TE sequence and TE content across different genomes. We illustrate our method by first using a monopartite network to study the sequence evolution of Tc1/mariner elements across focal species. We identify a connection between two subfamilies associated with convergent acquisition of a domain from a protein-coding gene. Second, we use a bipartite network to study how TE content across species is shaped by epigenetic silencing mechanisms. We show that the presence of Piwi-interacting RNAs is associated with differences in network topology after controlling for phylogenetic effects. Together, our method demonstrates how a network-based approach can identify hitherto unknown properties of TE evolution across species.

The curious case of the disappearing piRNAs

“…The “richness” of TEs is therefore higher in piRNA‐containing species. This fits with the idea that piRNAs enable the accumulation of many different types of TEs, but prevent them from spreading (Schneider et al, 2021). Whether this difference would act as an evolutionary force promoting loss of piRNAs in certain lineages, though, is far from obvious.…”

“…Interestingly, analysis of TE content in animal genomes using networks rather than more linear measures such as TE coverage or family distribution, provided some evidence in support of this idea. Species with piRNAs were found to have a larger variety of TEs in their genome than species without: TE networks had a higher degree when constructed using piRNA‐containing species only (Schneider et al, 2021). The overall content, however, measured by the weighted degree, was not significantly different between species with piRNAs and those without.…”

Evolutionary dynamics of the LTR-retrotransposon crapaud in the Podospora anserina species complex and the interaction with repeat-induced point mutations

“…An alternative example of a method for understanding TE family relationships is the use of sequence similarity networks (SSN) [ 33 ]. In this study, we explore the use of SSNs to classify LTR-retrotransposons in the species complex of the filamentous ascomycete Podospora anserina , and subsequently study their evolution.…”

Overview of methods for characterization and visualization of a protein–protein interaction network in a multi-omics integration context

“…Visual representation allows to understanding PPIs and to analyze networks ( Iranzo, Krupovic and Koonin, 2016 ; Armanious et al, 2020 ; Schneider et al, 2021 ; Sejdiu and Tieleman, 2021 ). However, due to complexity of proteomes of different organisms, visualization is a challenge ( Crowther, Wipat and Goñi-Moreno, 2021 ).…”