Bacterial RT phylogeny.
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Unrooted phylogenetic trees based on the alignment of the RT-domain (domains 0–7) of the 742 sequences used as the dataset. The group II intron ORF classes and varieties are designated according to the most recent proposals from Toro et al. in 2013 and Simon et al. in 2008 , . Additional group II intron ORF varieties are also annotated here (g5 and g6, see the results and discussion section). Other RT groups are named as previously reported  and suggested in this work. (A) A consensus unrooted tree estimated by FastTree method. The main groups were color-coded to improve visualization and collapsed at the internal nodes with local support values ≧0.96, with the exceptions of UG4 (0.84) and UG5 (0.87). Local support values ≧0.95 at inner nodes are also indicated. (B) A consensus unrooted tree estimated by the RAxML method. The main groups were collapsed at the internal nodes with strong support (bootstrap values ≧75%), with the exception of class ML (55%), subgroup CL1B (34%) and variety g3 (71%); UG10 (G2L3) (39%); and DGRs (17%). Inner nodes with strong statistical support (bootstrap values ≧80%) are also indicated.