Partial sequence analysis of the actin gene and its potential for studying the phylogeny of Candida species and their teleomorphs.

Abstract

The actin gene has been studied as a potential phylogenetic marker for selected members of the anamorphic genus Candida and seven related teleomorphic genera (Debaryomyces, Issatchenkia, Kluyveromyces, Saccharomyces and Pichia from the Saccharomycetaceae ; Clavispora and Metschnikowia from the Metschnikowiaceae). The nucleotide sequences of 36 fungal taxa were analysed with respect to their molecular evolution and phylogenetic relationships. A total of 460 bp (47 %) of the coding 979 bp were variable and 396 bp (40 %) of these were found to be phylogenetically informative. Further analysis of the sequences showed that the genic GMC contents were higher than the nuclear GMC contents for most of the taxa. A strong positive correlation was found between GMC content over all codon positions and third positions. First and second codon positions were considered to be independent of the genic GMC content. The expected transition/transversion bias was detected only for third positions. Pairwise comparisons of transitional and transversional changes (substitutions) with total percentage sequence divergences revealed that the third position transitions showed no saturation for ingroup comparisons. A specific weighting scheme was set up, combining codon-position weights with changefrequency weights to enable the inclusion of distant outgroup taxa. Parsimony analyses of the investigated taxa showed four groups, three of which corresponded to major clusters that had been established previously in Candida by rDNA analysis. Interrelationships among the species groups in this heterogeneous anamorphic genus were determined. The polyphyletic origin of the selected Candida species and their close associations with several ascomycete genera were verified and known anamorph/teleomorph pairs confirmed. The actin gene was established as a valuable phylogenetic marker with the particular advantage of an unambiguous alignment.

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

“…Previous studies also concluded that these families are monophyletic, albeit with low statistical support (7,21). The combi- (23) were uncertain about the placement of the genera Issatchenkia and Debaryomyces within the Saccharomycetaceae.…”

“…(i) Previous studies analyzed single genes and failed to define the relationships among C. albicans, C. viswanathii, C. tropicalis, and C. parapsilosis with significant statistical support (7,14,21,50). This investigation resolved the phylogeny of these species.…”

“…Because of a lack of distinctive morphological characters, molecular methods are invaluable for clarifying the phylogenetic relationships among ascomycetous yeast species. Previous phylogenies were based on single genes (7,21,22), sampled only one family (25), or were restricted to the most common pathogenic species of Candida (14,30,31,50). The single-gene studies have focused on the actin gene (ACT1) (7) or the large (26S rDNA) or small (18S rDNA) ribosomal subunit (21) and generally lacked good statistical support, especially for relationships along the backbone of the trees.…”

Species reassignment of Geotrichum bryndzae, Geotrichum phurueaensis, Geotrichum silvicola and Geotrichum vulgare based on phylogenetic analyses and mating compatibility

“…Primers V9G (de Hoog & Gerrits van den Ende, 1998) and LR5 (Vilgalys & Hester, 1990) were used to amplify the region of the nrRNA gene operon that includes the 39 end of the small-subunit rRNA gene, the ITS regions (ITS 1, ITS 2 and the intervening 5S rRNA gene), and the D1/D2 domain of the large-subunit (LSU) rRNA gene, as described by Knutsen et al (2007). Primers CA14 and CA5R (Daniel et al, 2001) were used to amplify part of the actin gene using the method described by Daniel et al (2001). The PCR products were separated by electrophoresis at 80 V for 40 min on a 0.8 % (w/v) agarose gel containing 0.1 mg ethidium bromide ml 21 in 16 TAE buffer (0.4 M Tris, 0.05 M sodium acetate, and 0.01 M EDTA, pH 7.85) and examined under UV light.…”

Delimitation of the species of the Debaryomyces hansenii complex by intron sequence analysis

“…Unlike in euascomycetes, for which a phylogenetic definition of species, phylogenetic species recognition or PSR (Taylor et al, 2000), prevails, the delineation of hemiascomycetous yeasts species has recently been based, in many cases, on the use of rDNA sequence comparison of type strains. A first attempt at using nuclear sequences for this purpose revealed that diversity was much more pronounced than previously thought (Daniel et al, 2001;Daniel & Meyer, 2003). Multigene approaches combining rDNA, housekeeping genes and mitochondrial cytochrome-c oxidase subunit II (COX2) gene sequences have been developed (Kurtzman, 2003;Kurtzman & Robnett, 2003).…”