Additional file 1 of Intruder (DD38E), a recently evolved sibling family of DD34E/Tc1 transposons in animals

Additional file 1: Fig. S1. Copy number estimation by BLASTN search against the cat RefSeq genome with the identified IT sequence. Fig. S2. IT elements (> 80% identity and 40% coverage) were identified in the cat genome. Fig. S3. Representative PCR products of IT motifs from the cat genome. (A) Primer sequences for transposon amplification. Nested PCR was used to amplify the transposase gene with two pairs of primers flanking the transposon or matching the CDS. Three pairs of primers were used for TIRs. (B) Schematic diagram of primer locations in the cat genome. These primers were designed using Primer 3. (C) Gel electrophoresis image of PCR products. Fig. S4. Alignment of the cat IT sequence to the nucleotide collection (nr/nt) database at NCBI. Fig. S5. Full phylogenetic tree of entire IT elements based on the alignment of DDE domains. The phylogenetic tree was inferred using the maximum likelihood method with the IQ-TREE program. Species with incomplete DD38E motifs were excluded from this analysis. Fig. S6. Motifs prediction for IT transposases. This analysis was performed using multiple alignment with Bioedit and with modifications in Genedoc. Fig. S7. Phylogenetic tree based on the alignment of the nucleotide sequence of IT transposons. The phylogenetic tree was inferred using the maximum likelihood method with the IQ-TREE program based on the alignment of transposon consensus or representative sequences. Fig. S8. Insertion ages of ITs. All sequences have consensus or representative sequences. The y-axis represents the mutation rate of each IT element in the genome, and the x-axis represents the age of transposon insertion. This analysis was performed using RepeatMasker. Fig. S9. Sequence identity matrix of IT elements. The sequence identities were measured by pairwise comparisons of the transposon consensus sequences or representative sequences. Fig. S10. Multiple alignments of the TIRs of copies 1 and 2 with the consensus sequence were performed using Bioedit.