  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.

Populations and Evolution;Genomics