Fig. 6

Sequence similarity network reveals inteins cluster by exteins and shows dynamic movement. a Eukaryotic intein clustering. The eukaryotic intein network shows relationships between nDNA (red), cpDNA (green), and vDNA (blue) inteins. Network indicates the presence of multiple intein lineages, which mostly correspond to clustering by exteins. Clear examples are Prp8i (1a, 1b) and VMA1i (2), and many viral inteins also cluster by exteins (7, 8, 9, 10). Cases where this pattern is broken represent possible horizontal transfer events (1b, 1c, 3, 6). Some inteins cluster phylogenetically, such as DnaBi from Rhodophyta (5a) or Heterokonta (5b). Hedgehog proteins (black; HhC) do not cluster with any eukaryotic inteins (11), indicating no phylogenetic relationship between Hedgehog and inteins based on sequence, although they are structurally and functionally similar. Hint-containing mating type switching proteins (yellow, HO Hop) cluster with VMA1i (2). Some inteins do not form connections to anything at all (12). b Nuclear intragenomic intein transfer. Selected intein pairs were further examined by calculating pairwise similarity percentages and are shown in the box plot. The GLTi and CHSi pair shows an average similarity above 50%, indicative of intragenomic transfer. c Endosymbiotic intein transfer. A phylonetwork tree was built in SplitsTree after alignment of cpDNA DnaBi (green) and bacterial DnaBi (pink). A branch of clustering of cpDNA DnaBi and bacterial DnaBi (shaded) suggests that DnaBi in chloroplasts might have been inherited from a cyanobacterial progenitor. Since bacteria also have inteins in ClpP, cpDNA ClpPi were included as a control and they cluster separately (6)