Network-based visualisation reveals new insights into transposable element diversity

Lisa Schneider, Yi-Ke Guo, David Birch, Peter Sarkies*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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 non-conventional 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.
Original languageEnglish
Article numbere9600
Number of pages12
JournalMolecular Systems Biology
Volume17
Issue number6
DOIs
Publication statusPublished - 1 Jun 2021

Scopus Subject Areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Agricultural and Biological Sciences(all)
  • Applied Mathematics

User-Defined Keywords

  • epigenetics
  • evolution
  • networks
  • piRNAs
  • transposable elements

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