Figure 5

Rooted phylogenic tree based on RT/RH amino acid sequences of DIRS1 -like retrotransposons. Tree performed on a core data set including representative amino acid consensus sequences of the RT/RH domains of the Ymur3 and Alvi1-5 families and 16 previously well-described DIRS1-like retrotransposons (see Table 1 for accession numbers). PAT-like sequences were used as outgroup as well as Ty3/gypsy-like elements according to the close phylogenic relationships of their RT/RH domains with those of DIRS-like retrotransposons: Clonorchis sinensis CsRn1, [GenBank:AAK07485]; Drosophila melanogaster 412, [GenBank:CAA27750.1]; Tetraodon nigroviridis TnGr1 available on Retrobase database [50];Takifugu rubripes sushi-ichi, [GenBank:AAC33526]; Caenorhabditis briggsae CbPAT1, [GenBank:XP_001664700.1] and Strongylocentrotus purpuratus SpPAT1 available on Retrobase database [50]. The tree was constructed using the Maximum Likelihood method and 100 bootstrap replicates. Only nodes with bootstrap value over 50% are indicated. Distances were calculated using WAG model with gamma distribution's correction for amino acids. The two previously described clades [41, 48], DrDIRS1-clade and TcDIRS1-clade, are indicated.