Fig. 3

Phylogenetic analysis of the genus Protomyces. Phylogenetic tree built by ITS (a), D1D2 (b) and genome-wide sequences (c), with maximum likelihood method. a ITS and b D1D2 sequences were aligned with ClustalX2. Bootstraping (1000x) was conducted and best-scoring ML tree were produced with randomized axelerated maximum likelihood (RAxML) rapid bootstrapping program. Bootstrap support values (%) are indicated at each node. c RAxML with rapid bootstrapping (100x) were chosen for constructing the maximum likelihood tree utilizing 1670 concatenated single-copy conserved protein sequences from whole genome sequence data. Alignment quality control of single-copy conserved proteins was achieved by applying sequence scores > = 0.8 in MAFFT analysis using Guidance2. Multiple aligned sequences of each species/strain were concatenated using FASconCAT_V1.0 and bootstrap values (%) are indicated at the nodes. The output .tre files were viewed with online tool iTOL. In all phylogenies Schizosaccharomyces pombe was used as an outgroup. For the same phylogenies built using the Bayesian inference method, see Supplemental Fig. 1