Metabolic pathways phylogenies / Photosynthesis phylogenies

Phylogenetic reconstructions of 30 enzymes for plastid metabolic pathways (isoprenoid, heme, iron-sulfur cluster and fatty acid biosynthesis) and 8 photosynthetic complex subunits as pdf figure (*.tre.pdf) and in newick format (*.tre). Trees were inferred using IQ-TREE, using the best model identified for each alignment separately, node support was calculated using 1000 ultrafast bootstrap (UFBoot) replicates. In the pdf figures: groups are indicated by colored taxon names: green, Viridiplantae; red, rhodophytes; grey, glaucophytes; turquoise, cryptophytes; pink, stramenopiles; dark blue, haptophytes; yellow, dinoflagellates; light green, RSD; orange, chrompodellids/Apicomplexa; brown, Opisthokonta/Amoebozoa/Apusozoa/Ancyromonadida/ciliates; black, prokaryotes. Selected clades are collapsed for increased clarity, see corresponding newick files for full trees. Filenames contain, in that order, the pathway/photosynthetic complex, the query ID, the name of the gene, the e-value used for parsing the BLASTP result (if deviating from the default of ≤1e-25 = 1E25) and the model used for tree reconstruction. See Fig. 2 and Table S2 in the manuscript for overview of the enzymes/subunits.