Eisosomal proteins in the subphylum Pezizomycotina. Phylogenetic unrooted tree, including the Pil1 (YGR086C) and Lsp1 (YPL004C) proteins of S. cerevisiae; the two putative eisosomal proteins of the second member of the Saccharomycotina, Kluvermyces lactis (KLLA); a member of the Taphrinomycotina, S. pombe (SPAC3C7.02c, SPCC736.15); and the PilA and PilB homologues (see text) of a number of representative fungi of the Pezizomycotina. The proteins of A. nidulans (Euriotiomycetes) referred to are PilA (ANID_05217.1) and PilB (ANID_03931.1) Other species referred to are Botritis cynerea (BC) (Leotiomycetes), Coccidioides immitis (CIGH; Euriotiomycetes), Magnaporthe grisae (MGG), Neurospora crassa (NCU; Sordariomycetes), and Stegonospora nodorum (SNOG; Dothideomycetes), followed by their systematic numbers in the relevant databases. Alignments were carried out with T-Coffee, curated with the Phylogeny site internal curation program (see Materials and Methods), and the tree was obtained with the maximum-likelihood program alLRT-PhyML (; http://www.phylogeny.fr/version2_cgi/alacarte.cgi) and redrawn after a Drawtree image. The digits at the nodes represent the results of the approximate likelihood ratio test and are nonparametric branch support values (http://atgc.lirmm.fr/alrt/). The PilA clade is clustered with all the homologues of the Saccharomycotina (approximate likelihood ratio test value = 1), but note the weak support (approximate likelihood ratio test value = 0.25) of the node where the PilA clade branches out from the homologues in the Saccharomycotina; in trees (data not shown) where many more species of Saccharomycotina and Pezizomycotina are included, the topology is maintained and the approximate likelihood ratio test value increases to >0. 80. For reasons of space, we do not show the branch support approximate likelihood ratio test values within the PilA clade; all nodes with the exception of the node where PilA branches out have strong support (approximate likelihood ratio test value > 0.80); the node where PilA branches out has an approximate likelihood ratio test value of 0.43. While we show only representative species in this tree, the topology of a tight cluster of PilA homologues and a looser cluster of PilB homologues is maintained in a tree that was constructed with the same or other algorithms and that includes at least one species of every genus of the Pezizomycotina for which there is an available sequence. Arrows show the nodes corresponding to the three independent duplications that gave origin to the PilA and PilB clades of the Pezizomycotina, the Pil1 and Lsp1 clades of the Saccharomycotina, and the two clades of the Taphrinomycotina.