Phylogeny and Evolution of Medical Species of Candida and Related Taxa: a Multigenic Analysis

Abstract

Hemiascomycetes are species of yeasts within the order Saccharomycetales. The order encompasses disparate genera with a variety of life styles, including opportunistic human pathogens (e.g., Candida albicans), plant pathogens (e.g., Eremothecium gossypii), and cosmopolitan yeasts associated with water and decaying vegetation. To analyze the phylogeny of medically important species of yeasts, we selected 38 human pathogenic and related strains in the order Saccharomycetales. The DNA sequences of six nuclear genes were analyzed by maximum likelihood and Bayesian phylogenetic methods. The maximum likelihood analysis of the combined data for all six genes resolved three major lineages with significant support according to Bayesian posterior probability. One clade was mostly comprised of pathogenic species of Candida. Another major group contained members of the family Metschnikowiaceae as a monophyletic group, three species of Debaryomyces, and strains of Candida guilliermondii. The third clade consisted exclusively of species of the family Saccharomycetaceae. Analysis of the evolution of key characters indicated that both codon reassignment and coenzyme Q 9 likely had single origins with multiple losses. Tests of correlated character evolution revealed that these two traits evolved independently.The Ascomycota include three major groups, the monophyletic Euascomycetes (molds), the Hemiascomycetes (yeasts), and the Archiascomycetes, which contains taxa that likely arose before the other lineages (35). According to the taxonomic study of the yeasts by Kurtzman and Fell (23), the Hemiascomycetes comprise one large order, the Saccharomycetales, which was established in 1960 by Kudrjavzev (17). All members of this order are characterized by (i) no or only rudimentary hyphae, (ii) vegetative cells that proliferate by budding or fission, (iii) cell walls that lack chitin, and (iv) asci that are formed singly or in chains (17). Phylogenetic analyses of ribosomal DNA (rDNA) and RNA polymerase II (RPB2) gene sequences support a single evolutionary origin of the Saccharomycetales (1, 3, 29). However, to date, only a few representatives of the order have been included in molecular phylogenetic studies of the higher-level relationships among the Ascomycota.The order Saccharomycetales contains many species of practical importance and scientific interest, including several species that are pathogenic for humans, such as Candida parapsilosis, Candida tropicalis, and Candida albicans, which is the most common human pathogenic fungus (4). Other species of the Saccharomycetales are exploited by industry to produce secondary metabolites and fermentative by-products (23). During the translation of mRNA to polypeptides, several species of Candida exhibit alternative codon usage. The reassignment of the codon CUG from leucine to serine was first described by Kawaguchi et al. (16) for Candida cylindraceae. Sugita and Nakase (44) applied phylogenetic methods to investigate relationships among Candida species with alternative use of the CUG...

Reconstructing the Fungal Tree of Life Using Phylogenomics and a Preliminary Investigation of the Distribution of Yeast Prion-Like Proteins in the Fungal Kingdom

“…For example, there is substantial evidence that within the Ascomycota phylum, the Pezizomycotina and Saccharomycotina subphyla are sister groups (Fitzpatrick et al 2006;Kuramae et al 2006;Liu et al 2009;Philippe et al 2004;Robbertse et al 2006). However, there is conflicting evidence to suggest that the Taphrinomycotina and Saccharomycotina are sister clades (Baldauf et al 2000;Bullerwell et al 2003;Diezmann et al 2004). Similarly within the Basidiomycota phylum, a consensus regarding the phylogenetic relationships among the Ustilagomycotina, Pucciniomycotina, and Agaricomycotina subphyla is not yet available (Begerow et al 2004;Hibbett et al 2007;James et al 2006b).…”

“…1, 2, 3, and 4). Until recently the phylogenetic relationships between these three subphyla were uncertain with some analyses placing Saccharomycotina and Taphrinomycotina as sister clades (Baldauf et al 2000;Diezmann et al 2004) while others inferred a sister group relationship between Pezizomycotina and Saccharomycotina (Fitzpatrick et al 2006;Kuramae et al 2006;Philippe et al 2004;Robbertse et al 2006). Recently a comprehensive phylogenomic analysis of 113 nuclear genes by Liu et al (2009) has shown that the Taphrinomycotina are a monophyletic clade and branch as a sister group to a (Pezizomycotina, Saccharomycotina) clade.…”

MalasseziaversusCandidain Healthy Dogs

“…are also important pathogens in dogs, being related to: urinary infections [32], endophthalmitis [26], cutaneous lesions [28], and systemic infections [6]. The group with the most rel- [13,37].…”

Mode of vegetative reproduction of the bipolar budding yeast species Wickerhamomyces pijperi and related strains

“…The actin gene ACT1 and the elongation factor 2 gene EF2 were amplified with KOD FX polymerase (Toyobo Co.) using the primers ACT1 (59-TACCCAATTGAACACGGTAT-39) and ACT2 (59-TCTGAATCTTTCGTTACCAAT-39) for ACT1 and EFIIF1 (59-AAGTCTCCAAACAAAGCATAAC-39) and EFIIR2 (59-GGGAAA-GCTTGACCACCAGTAGC-39) for EF2. PCR was performed according to the method described by Diezmann et al (2004). The PCR products were purified with AMPure (Agencourt Bioscience Co.), according to the manufacturer's protocol.…”