Troyka represents a unique lineage of virus-like retroelements

Supplementary Material for 'Troyka represents a unique lineage of virus-like retroelements' as described in Journal of General Virology. In this data repository, the supplementary material (3 figures, 3 tables and 11 text-based data) of the study entitled "Troyka represents a unique lineage of virus-like retroelements" is available.Eukaryotic reverse transcriptase (RT) genes are mostly incorporated into viruses or transposons. Among the 6 reported families of reverse transcribing viruses, 3 families (Metaviridae/Gypsy, Belpaoviridae/BEL, Pseudoviridae/Copia) have proliferated mostly as transposons, called long terminal repeat (LTR) retrotransposons altogether. Troyka was reported as a unique lineage of Metaviridae/Gypsy. 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 6 animal phyla reported previously, Troyka was characterized for the first time in Hemichordata, Priapulida, Annelida, Phoronida, and Branchiopoda. The unique terminal nucleotides of Troyka are very well conserved. The phylogenetic analysis with various combination 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.