Fig. 6

Group II intron superfamilies defined by maturase similarities. Two selected subclades of the comprehensive maturase phylogeny shown in Additional file 7: Figure S5 for group II intron superfamilies SF01-03-22 (A) and SF10-11-17-28 (B). The eukaryote maturase phylogeny contains samples from nuclear encoded maturases of embryophytes (dark green with underline), streptophyte mitochondria (green and bold), fungal mitochondria (orange), metazoan mitochondria (blue) and organelles of chlorophytes (light green), stramenopiles (purple), cryptophytes (beige), rhodophytes (red) and oomycetes (black). A SF01-03-22 contains solitary-type streptophyte mitochondrial maturase mat-cox1i769g2 and mat-cox1i652g2, which forms a joint clade with orthologs from fungal Termitomyces mitochondria. The free-standing mitochondrial maturases of liverworts (“mat-free”) cluster with the nuclear encoded mat-nuc1 of P. patens and with maturases of algal F01 paralogs while no F01 intron paralogues are present in liverwort mitogenomes. Extended family eF03 supports a close relation of F03 paralogs and the well-characterized nuclear-encoded maturases nmat1 and nmat2 of angiosperms together with nuclear maturase paralogs in the lycophyte S. moellendorffii and, more distantly, with mitochondrial maturase paralogs in fungi and a chloroplast paralogue in a rhodophyte. B Superfamily SF10-11-17-28 contains F17 mat-nad1i728g2 (or matR), the only mitochondrial encoded maturase in euphyllophytes together with the maturases in the S-type intron cox1i44g2 and mat-atp9i95g2. Angiosperm nuclear encoded nmat3 and nmat4 form a joint clade with maturases of F10 paralogs including the pseudogenized (PSX) mat-nad1i669g2 in the fern Osmunda regalis indicating the ancestral presence of a maturase in this intron paralogue conserved also in angiosperms. Maturases of S-type introns mat-atp1i1050g2 and mat-atp1i989g2 form a well-supported “maturase family” clade mF28 with mat-cobi787g2 as sister group