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Fig. 3 | BMC Biology

Fig. 3

From: Group II intron and repeat-rich red algal mitochondrial genomes demonstrate the dynamic recent history of autocatalytic RNAs

Fig. 3

Maximum likelihood phylogeny of group II intron ORFs. a Maximum likelihood tree of group II intronic ORFs was identified using BLASTp (e-value cutoff = 1.0e−5). The taxa corresponding to red algal mitochondria are marked in red. The taxa corresponding to red algal plastids are marked in blue. Among the red algal taxa, Porphyridium species are marked with a colored circle (P. purpureum MT; red circle, P. aerugineum MT; green circle, Porphyridium PT; red circle). The taxa corresponding to fungi are in purple, cyanobacteria are in cyan, non-cyanobacterial bacteria are in black, non-red algal mitochondria are in orange, and non-red algal plastids are in green text. The clades described in the main text are indicated by black-filled and white-numbered circles. The clades corresponding to the contents in Fig. 5a are presented in colored circles in alphabetical order. The location of the intron (i.e., rnl-i1 = intron 1 in rnl) is shown after the gene name. We used the previously proposed nomenclature [37] to identify the Porphyridium mitochondrial introns. Bootstrap values below 50% were removed. b The distribution of red algal mitochondrial group II introns based on the phylogenetic tree. The origins of IEPs present in each intron are shown using triangles of different colors (fungus-related: purple; stramenopiles-related: orange; both-related: mixed with purple and orange). c A simplified tree indicating the number of mitochondrial genes with group II introns based on clades (PT clade and MT clades 1, 2, and 3)

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