Phylogenomic Analysis of Peronosporales Genomes

A dataset of 33 Peronosporales genomes (Supplementary Table S1) was used for phylogenomic analysis. We also included Pythium ultimum as an outgroup. BUSCO analysis revealed 208 BUSCO families that are present and single copy in at least 90% of the species (i.e., at least 31 of the 34 species). Each BUSCO family was individually aligned with MUSCLE (v3.8.31) [79 (link)] and trimmed using trimAl (v1.4) [80 (link)] with the parameter “-automated1” to remove poorly aligned regions. Trimmed alignments were concatenated together resulting in a final supermatrix alignment of 106,315 amino acids. Maximum-likelihood (ML) phylogenetic reconstruction was performed using IQ-TREE (v1.6.12) [81 (link)] with the JTT+F+R5 model, which was the best fit model according to ModelFinder [82 (link)], and 100 bootstrap replicates were undertaken to infer branch support values. Bayesian analysis was also performed using PhyloBayes MPI (v1.8) [83 (link)] with the CAT model. Two independent chains were run for 10,000 cycles and convergence was assessed using bpcomp and tracecomp. A consensus Bayesian phylogeny was generated with a burn-in of 10%. The phylogeny was visualised and annotated using the Interactive Tree of Life (iTOL) [84 (link)].