The evolution of tyrosine-recombinase elements in Nematoda

TL;DR

This study explores the diversity and evolution of tyrosine-recombinase transposable elements in Nematoda, revealing previously unrecognized elements and emphasizing the need for phylogenetically-based classification methods.

Contribution

Developed a new workflow for classifying YREs in Nematoda, uncovering novel elements and demonstrating the diversity is broader than in model species.

Findings

Detected Dirs1-like YREs in Nematoda classes Enoplia and Dorylaimia.

Found Pat1-like YREs to be a derived form with wider distribution.

Highlighted homoplasious features in YRE classification, advocating phylogenetic methods.

Abstract

Transposable elements can be categorised into DNA and RNA elements based on their mechanism of transposition. Tyrosine recombinase elements (YREs) are relatively rare and poorly understood, despite sharing characteristics with both DNA and RNA elements. Previously, the Nematoda have been reported to have a substantially different diversity of YREs compared to other animal phyla: the Dirs1-like YRE retrotransposon was encountered in most animal phyla but not in Nematoda, and a unique Pat1-like YRE retrotransposon has only been recorded from Nematoda. We explored the diversity of YREs in Nematoda by sampling broadly across the phylum and including 34 genomes representing the three classes within Nematoda. We developed a method to isolate and classify YREs based on both feature organization and phylogenetic relationships in an open and reproducible workflow. We also ensured that our phylogenetic approach to YRE classification identified truncated and degenerate elements, informatively increasing the number of elements sampled. We identified Dirs1-like elements (thought to be absent from Nematoda) in the nematode classes Enoplia and Dorylaimia indicating that nematode model species do not adequately represent the diversity of transposable elements in the phylum. Nematode Pat1-like elements were found to be a derived form of another pat1-like element that is present more widely in animals. Several sequence features used widely for the classification of YREs were found to be homoplasious, highlighting the need for a phylogenetically-based classification scheme. Nematode model species do not represent the diversity of transposable elements in the phylum.