Fig. 2
From: Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration
Genomic expansion and the expression of Harbinger DNA transposable elements pluripotency miRNAs and salamander-specific methyltransferases during adult limb regeneration in P. waltl. a Portion of Gypsy and Harbinger repeats (>1 kb) retaining a detectable protein domain. b Phylogeny of Gypsy and Harbinger elements. While the tree-based on Gypsy elements indicates a uniform expansion, the tree-based on Harbinger elements shows three branches (brown) resulting from a second distinct burst. The second Harbinger burst also results in a bimodal pairwise genomic distance distribution, compared to a unimodal distribution for the Gypsy elements. c Phylogenic tree of 361 mature P. waltl miRNAs with miR-427 and miR-93b expansion highlighted (top). Sequence logo based on multiple alignment of 155 miR-427 sequences and 66 miR-93b sequences (bottom). Note the embryonic stem cell-specific cell cycle regulating seed AAGUGC within the first eight nucleotides. d Split violin plot showing the tau score distribution of P. waltl genes that have non-salamander vertebrate orthologs (blue) and genes that only have salamander orthologs (beige). e RNAseq quantification of five Harbinger orthology groups encoding Myb or Harbi domain-bearing proteins (top), four Gypsy orthology groups encoding reverse transcriptase domain-bearing proteins (middle) and mir-427 and mir-93b primary transcripts (bottom). In parentheses are the number of transcripts and gene models belonging to each group. The groups chosen were significantly upregulated in the regenerating limb 3 days post amputation (dpa). Differential expression calculated by DESeq2 (Supplementary Table 9). TPM transcripts per million. f Eleven orthology groups of salamander methyltransferase are expressed specifically in appendages of the adult animal. In parentheses are the number of transcripts and gene models belonging to each group
