Fig 4.

Inferred phylogeny of candidate BOGUAY group II catalytic introns and related sequences. Four sequences annotated as BOGUAY group II introns were used for BLASTN searches of the IMG/ER database (cutoff E value of 9e−06, cutoff score of 58 bits). For sequences not previously annotated (the majority), genome positions are indicated. Three Crocosphaera watsonii sequences were used to root the tree. Nucleic acid sequences were aligned in MEGA5 (10) using MUSCLE (11). Phylogenetic analysis was carried out in MrBayes 3.2 (15) (2 runs of 4 chains each, 1.5 million generations) using the GTR base substitution and invgamma rate variation models. With the first 25% of generations discarded, the final statistics indicated that convergence was reached between the two runs (data not shown). The scale bar represents base changes per position. See Fig. S5 in the supplemental material for the phylogeny inferred by neighbor joining.