Troyka represents a unique lineage of virus-like retroelements

Eukaryotic reverse transcriptase genes are mostly incorporated into viruses or transposons. Among the six reported families of reverse-transcribing viruses, three families (<i>Metaviridae</i>/<i>Gypsy</i>, <i>Belpaoviridae</i>/<i>BEL</i> and <i>Pseudoviridae</i>/<i>Copia</i>) have proliferated mostly as transposons, collectively known as LTR retrotransposons. <i>Troyka</i> was reported as a unique lineage of the <i>Metaviridae</i>/<i>Gypsy</i> family. While most LTR retrotransposons generate 4 to 6 bp target site duplications (TSDs) upon integration and contain 5'-TG. CA-3' termini, <i>Troyka</i> generates 3 bp TSDs and contains 5'-CG.CG-3' termini. Here, the distribution and diversity of <i>Troyka</i> were extensively investigated from the available genome sequences. In addition to the six animal phyla reported previously, <i>Troyka</i> was characterized for the first time in Hemichordata, Priapulida, Annelida, Phoronida and Brachiopoda. The unique terminal nucleotides of <i>Troyka</i> are very well conserved. The phylogenetic analysis with various combinations of conserved domains supported the independent position of <i>Troyka</i> from any established retroelement groups, most likely as the sister lineage of the group including <i>Metaviridae</i>/<i>Gypsy</i>, <i>Retroviridae</i>, <i>Caulimoviridae</i>, Lokiretroviruses and <i>Odin</i> LTR retrotransposons. <i>Troyka</i> is here proposed as a new superfamily of LTR retrotransposons.