FIG 1.

Phylogenetic relationships and ortholog conservation for Pneumocystis and related fungi. The maximum likelihood tree was inferred from 248 single-copy core orthologs. Ortholog conservation patterns highlighted include core orthologs found in all genomes (CORE), ascomycete-specific orthologs found in all ascomycetes but not in Microsporidia (ASCOM), basidiomycete-specific orthologs found in both Cryptococcus neoformans and Ustilago maydis but not in all other fungi (BASIDIO), Pneumocystis-specific orthologs (PNEUMO), orthologs shared in any two or more genomes (SHARED), and orthologs unique to only one genome (UNIQUE). Numbers on the branches of the tree indicate bootstrap support values. The phyla and subphyla are indicated on the main branches as follows: Ta, Taphrinomycotina; Sa, Saccharomycotina; Pe, Pezizomycotina; Ba, Basidiomycota; and Mi, Microsporidia.