Fig. 6

Phylogeny of the subphylum Taphrinomycotina. Maximum likelihood phylogenetic tree of representative species in the subphylum Taphrinomycotina. Tree was built using 636 single-copy protein sequences that were common to all species used. Alignment quality control of single-copy conserved proteins was achieved by applying sequence scores > = 0.8 in MAFFT analysis using Guidance2. Saccharomyces cerevisiae was used as an outgroup. Multiple aligned sequences of each species were concatenated into a single long sequence using FASconCAT_V1.0. The randomized axelerated maximum likelihood method (RAxML) and rapid Bootstrapping (100x) were applied for constructing the maximum-likelihood phylogenetic tree. Bootstrap support values (%) are shown at each node. The output files were viewed with online tool iTOL. For the same phylogeny built using the Bayesian inference method, see Supplemental Fig. 2