Fig. 3

Visualisation of Class II DNA TIR Transposons and Class I LTR elements. A Multiple sequence alignment of Mariner3_CE family. The consensus sequence of Caenorhabditis elegans “Mariner3_CE” autonomous DNA transposon (Dfam accession DF0001435.1) was downloaded from Dfam [34] and used as query to search the C.elegans genome (accession GCF_000002985.6) for highly similar sequences - see Protocol 8 in Supplementary Methods. The MSA was generated with MUSCLE [25]. The resulting alignment is seen at the top, with dashed boxes marking the start (5’end) and end (3’end) of all family members. Bottom panels show respective magnified views of either end of the alignment. Arrows indicate first (5’end panel) and last (3’end panel) nucleotide of the alignment corresponding to start and end of the consensus sequence for DF0001435. Mariner DNA transposons show a TA dinucleotide TSD and this can be seen before and after the nucleotides indicated with the arrows. An MSA of full-length LTR element family has the same “shape” as for DNA TIR transposons, with two “blunt ends” of sequence similarity at either end of the alignment. B Class II DNA TIR transposon representative dot-plot. Terminal inverted repeats are shown in red and are perpendicular to the diagonal representing the self-alignment. The longer diagonal line represents matches between position 1 of sequence A and position 1 of sequence B, etc. For structural diagnostics of TEs, dot-plots are made entering the same sequence (i.e. the consensus TE) as sequence A and sequence B. C Class I LTR retrotransposon representative dot-plot. Long terminal repeats, sometimes referred to as “LTR subparts” and found at the 5′ and 3′ end of LTR elements, are shown in blue and are parallel to the diagonal showing the “self-alignment”. Contrary to TIRs in DNA transposons, where the sequence is inverted at either end of the TE, LTR subparts are terminal repeats with a tandem orientation