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