Figure 5. Mutational dynamics in group II introns.

a) Schematic consensus structure of plastid group II introns based on Michel et al. (1989). Roman numbers indicate the six domains. B) Alignment and predicted RNA secondary structure for domain IV of the atpF intron in Cymbidium, Pyrus, Oenothera and Olea. The apparently non-homologous sequence blocks are placed separately in the alignment. There are no substitutions or length mutations in Pyrus and Cymbidium, the structures shown are therefore identical in the two species compared. The shown secondary structures of Oenothera and Olea are consensus structures. Two conserved nucleotide blocks at the 3′ and 5′ ends, indicated by thick blue bars, are conserved across all taxa and homologous in primary sequence and secondary structure. These conserved sequence blocks form the stem of the domain while variation occurs in the terminal stem-loops part of the domain. c) Alignment and predicted secondary RNA structures of domain IV of the rpl16 intron. For clarity, only the part of the domain with positions variable within genera are shown; “[-]” mark the omitted stem-loop elements. The apparently non-homologous sequence blocks are placed separately in the alignment. Those positions where variation occurs within a genus are marked with arrows. See text for more explanation.