Fig 3.

Putative group I introns within 23S rRNA genes. Relatives of BOGUAY 0660_3609 were identified by BLASTN searches of the GenBank nr and JCVI IMG/ER databases; all are located within 23S rRNA genes. As shown, there were very few full-length or nearly full-length matches. Species which also have putative 23S homing endonucleases are indicated by black stars, and species whose close relatives do are indicated by open circles (compare to Fig. 2). Nucleic acid sequences were aligned in MEGA5 (10) using MUSCLE (11). Maximum-likelihood phylogenies were inferred in ARB (13) with RAxML rapid bootstrapping (14), using the GTRGAMMA rate distribution model and 1,000 bootstraps. Numbers at nodes represent bootstrap values for each node, and circles indicate uncertain branch points. The scale bar represents base changes per position.