Figure 3.

Phylogenetic analysis of HDP1. (A) Upper panel: schematic representation of HDP1 domain structure. Lower panel: MSA of HDP1 and selected Harbinger transposases from BLAST hits. Red arrows indicate the residues critical for nuclease enzymatic activity. (B) Phylogenetic tree of HDP1 homologous sequences and Harbinger transposases. Black nodes are HDP1 homologous sequences from BLAST search on NCBI nr database, and they are named using their genus name and gi ID in NCBI. Sequences from Arabidopsis are labeled in blue with gene ID. Red nodes are sequences of Harbinger transposases from Repbase, with their original names in Repbase. The orthologous clades of HDP1 (at1g72270), at3g63270, at3g55350, at4g29780, at5g12010 and at3g19120 are labeled in green, yellow, red, purple, orange and grey, respectively. Several clades of Harbinger transposases intermingled with host sequences are labeled in blue. Possible branching points of host proteins and transposases are labeled with red stars. See also Supplementary information, Table S2.