Fig. 5.

Maximum-likelihood tree of single-LAGLIDADG homing endonucleases carried by group I introns. The 23 first hits to single-LAGLIDADG homing endonucleases in blast-x searches, with the Thermotoga sequences as probes, was selected to build the phylogeny. Chloroplast and mitochondrial introns are indicated by a “c” or an “m,” respectively. Double-LAGLIDADG homing endonucleases were excluded because they have a higher rate of divergence (26). The tree was estimated by using a JTT+Γ model in phylip version 3.6 (17) with a substitution matrix provided by E. Tillier (personal communication), with 10 random additions of the sequences and global rearrangements. The α-parameter was estimated in puzzle version 4.0 (18). Values at nodes indicate number of times the node was recovered in 100 bootstrap replicates (bold numbers) or puzzle support (italic numbers). Insertion position in the 23S rRNA of the group I intron carrying the endonuclease is indicated where this was given in the GenBank entry or available at www.rna.icmb.utexas.edu (21). Specific insertion positions were not available for m. Chlorella vulgaris, m2. Chlorella vulgaris, m. Acanthamoeba castellanii, m2. Acanthamoeba castellanii, and m. Chaetosphaeridium globosum.