Malassezia is a unique lipophilic genus in class Malasseziomycetes in Ustilaginomycotina, (Basidiomycota, fungi) that otherwise consists almost exclusively of plant pathogens. Malassezia are ...typically isolated from warm-blooded animals, are dominant members of the human skin mycobiome and are associated with common skin disorders. To characterize the genetic basis of the unique phenotypes of Malassezia spp., we sequenced the genomes of all 14 accepted species and used comparative genomics against a broad panel of fungal genomes to comprehensively identify distinct features that define the Malassezia gene repertoire: gene gain and loss; selection signatures; and lineage-specific gene family expansions. Our analysis revealed key gene gain events (64) with a single gene conserved across all Malassezia but absent in all other sequenced Basidiomycota. These likely horizontally transferred genes provide intriguing gain-of-function events and prime candidates to explain the emergence of Malassezia. A larger set of genes (741) were lost, with enrichment for glycosyl hydrolases and carbohydrate metabolism, concordant with adaptation to skin's carbohydrate-deficient environment. Gene family analysis revealed extensive turnover and underlined the importance of secretory lipases, phospholipases, aspartyl proteases, and other peptidases. Combining genomic analysis with a re-evaluation of culture characteristics, we establish the likely lipid-dependence of all Malassezia. Our phylogenetic analysis sheds new light on the relationship between Malassezia and other members of Ustilaginomycotina, as well as phylogenetic lineages within the genus. Overall, our study provides a unique genomic resource for understanding Malassezia niche-specificity and potential virulence, as well as their abundance and distribution in the environment and on human skin.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
A collection of 48 clinical Cryptococcus neoformans isolates from Croatia was investigated retrospectively using in vitro antifungal susceptibility testing and molecular biological techniques to ...determine mating type and serotype by PCR and amplified fragment length polymorphism (AFLP) genotyping. These isolates were obtained from 15 patients: ten were human immunodeficiency virus (HIV)-negative (66.7 %) and five were HIV-positive (33.3 %). From five patients, only one isolate was available, whilst from the other ten patients, two to 11 isolates were isolated sequentially. Antifungal susceptibility was tested by a broth microdilution method. Serotype A (genotype AFLP1) and serotype D (genotype AFLP2) were both found in six patients (40 % each), and serotype AD (genotype AFLP3) in three (20.0 %) patients. Mating type α (n = 12; 80.0 %) predominated and α/a hybrids were identified in 20.0 % of patients diagnosed with cryptococcosis. Two AFLP genotypes of C. neoformans were isolated during a single episode from one patient. The in vitro antifungal MIC(90) and susceptibility ranges for C. neoformans isolates were 0.5 µg ml(-1) (range 0.031-0.5 µg ml(-1)) for amphotericin B, 4 µg ml(-1) (range 1-4 µg ml(-1)) for flucytosine and fluconazole, 0.25 µg ml(-1) (range 0.031-0.5 µg ml(-1)) for itraconazole and 0.062 µg ml(-1) (range 0.031-0.25 µg ml(-1)) for voriconazole.
Acetic acid is one of the major inhibitors in lignocellulose hydrolysates used for the production of second-generation bioethanol. Although several genes have been identified in laboratory yeast ...strains that are required for tolerance to acetic acid, the genetic basis of the high acetic acid tolerance naturally present in some Saccharomyces cerevisiae strains is unknown. Identification of its polygenic basis may allow improvement of acetic acid tolerance in yeast strains used for second-generation bioethanol production by precise genome editing, minimizing the risk of negatively affecting other industrially important properties of the yeast.
Haploid segregants of a strain with unusually high acetic acid tolerance and a reference industrial strain were used as superior and inferior parent strain, respectively. After crossing of the parent strains, QTL mapping using the SNP variant frequency determined by pooled-segregant whole-genome sequence analysis revealed two major QTLs. All F1 segregants were then submitted to multiple rounds of random inbreeding and the superior F7 segregants were submitted to the same analysis, further refined by sequencing of individual segregants and bioinformatics analysis taking into account the relative acetic acid tolerance of the segregants. This resulted in disappearance in the QTL mapping with the F7 segregants of a major F1 QTL, in which we identified HAA1, a known regulator of high acetic acid tolerance, as a true causative allele. Novel genes determining high acetic acid tolerance, GLO1, DOT5, CUP2, and a previously identified component, VMA7, were identified as causative alleles in the second major F1 QTL and in three newly appearing F7 QTLs, respectively. The superior HAA1 allele contained a unique single point mutation that significantly improved acetic acid tolerance under industrially relevant conditions when inserted into an industrial yeast strain for second-generation bioethanol production.
This work reveals the polygenic basis of high acetic acid tolerance in S. cerevisiae in unprecedented detail. It also shows for the first time that a single strain can harbor different sets of causative genes able to establish the same polygenic trait. The superior alleles identified can be used successfully for improvement of acetic acid tolerance in industrial yeast strains.
A molecular taxonomic investigation performed on basidiomycetous yeast strains isolated from plant leaves collected in two areas of China revealed two novel species, Cryptococcus foliicola sp. nov. ...(type strain HS 23.3T = AS 2.2471T= CBS 9920T) and Cryptococcus taibaiensis sp. nov. (type strain ST 7.9T = AS 2.2444T= CBS 9919T), among the non ballistoconidium-forming strains producing cream-colored colonies. These new species differed markedly from closely related species in the internal transcribed spacer (ITS) and 26S rRNA D1/D2 region sequences. They clustered in a strongly supported clade represented by Cryptococcus victoriae in the Tremellales group in the phylogenetic trees drawn from ITS and D1/D2 sequences.
The distinction and monophyletic property of the basidiomycetous yeast species in the Bulleribasidium clade of the order Tremellales was resolved by molecular phylogenetic analysis based on the ...combined sequences of the 18S rRNA gene, internal transcribed spacer (ITS) region including 5.8S rRNA gene and 26S rRNA gene D1/D2 domain. The addition to the clade of new anamorphic species identified among ballistoconidium-forming yeasts isolated from China confirmed and strengthened the separation of this clade from other clades or lineages in the order Tremellales. A new anamorphic genus, Mingxiaea gen. nov. (type species Mingxiaea variabilis comb. nov.) is therefore proposed to accommodate the anamorphic species in the Bulleribasidium clade. Six new combinations are proposed for the described species of this clade which were formerly assigned to the genus Bullera. Four novel species in the new genus were identified among 16 ballistoconidium-forming yeast strains isolated from plant leaves collected in Hainan province, southern China, by D1/D2 and ITS sequence analyses. The novel species are described as Mingxiaea sanyaensis sp. nov. (type strain SY-3.23(T) =AS 2. 3623(T) =CBS 11408(T)), Mingxiaea hainanensis (type strain WZS-8.13(T) =AS 2.4161(T) =CBS 11409(T)), Mingxiaea foliicola (type strain WZS-8.14(T) =AS 2.3518(T) =CBS 11407(T)) and Mingxiaea wuzhishanensis (type strain WZS-29.8(T) =AS 2.4163(T) =CBS 11411(T)).
The aim of the present multicenter study was to assess quality of life of Dutch dialysis patients 3 months after the start of chronic dialysis treatment. The quality of life was compared with the ...quality of life of a general population sample, and the impact of demographic, clinical, renal function, and dialysis characteristics on patients' quality of life was studied. New end-stage renal disease (ESRD) patients who were started on chronic hemodialysis or peritoneal dialysis in 13 dialysis centers in The Netherlands were consecutively included. Patients' self-assessment of quality of life was measured by the SF-36, a 36-item Short Form Health Survey Questionnaire encompassing eight dimensions: physical functioning, social functioning, role-functioning physical, role-functioning emotional, mental health, vitality, bodily pain, and general health perceptions. One hundred twenty hemodialysis and 106 peritoneal dialysis patients completed the SF-36. Quality of life of hemodialysis and peritoneal dialysis patients was substantially impaired in comparison to the general population sample, particularly with respect to role-functioning physical and general health perceptions. Mean role-functioning physical and general health perceptions scores of the hemodialysis patients corresponded with the lowest scoring 8% and 12%, respectively, of the reference group. Mean role-functioning physical and general health perceptions scores of the peritoneal dialysis patients corresponded with the lowest scoring 10% and 12%, respectively, of the reference group. Hemodialysis patients showed lower levels of quality of life than peritoneal dialysis patients on physical functioning, role-functioning emotional, mental health, and pain. However, on the multivariate level, we could only demonstrate an impact of dialysis modality on mental health. A higher number of comorbid conditions, a lower hemoglobin level, and a lower residual renal function were independently related to poorer quality of life. The variability of the SF-36 scores explained by selected demographic, clinical, renal function, and dialysis characteristics was highest for physical functioning (29.7%). Explained variability of the other SF-36 dimensions ranged from 6.9% for general health perceptions to 15.4% for vitality. We conclude that quality of life of new ESRD patients is substantially impaired. Comorbid conditions, hemoglobin, and residual renal function could explain poor quality of life only to a limited extent. Further research exploring determinants and indices of quality of life in ESRD patients is warranted. From a clinical perspective, we may conclude that quality of life should be considered in the monitoring of dialysis patients.
Cryptococcus gattii is a primary pathogenic basidiomycetous yeast comprising four genotypic groups. Here we present data on two mitochondrial loci (MtLrRNA and ATP6). Two of the genotypic groups, ...namely amplified fragment length polymorphism (AFLP)5/VGIII and AFLP6/VGII, formed monophyletic lineages. The AFLP4/VGI genotypic group, however, possessed five different mitochondrial genotypes that did not form a monophyletic lineage. The majority of these isolates contained mitochondrial genomes that are partially identical to those found in isolates belonging to AFLP6/VGII, which is causing the ongoing and expanding Vancouver Island outbreak. Two out of four AFLP7/VGIV isolates contained an AFLP4/VGI allele of MtLrRNA. These observations are best explained by assuming a process of mitochondrial recombination. If this is true, mitochondrial recombination seems possible between cells belonging to different genotypic groups of C. gattii, especially between AFLP6/VGII or AFLP7/VGIV and AFLP4/VGI. We also have to assume that mitochondria, most likely, were transferred from cells belonging to AFLP6/VGII to AFLP4/VGI. As such a process of mitochondrial recombination is only possible after cell-cell conjugation, this may also allow the further exchange of genetic material, for example nuclear or plasmid in nature, between different genotypes of C. gattii. This may be relevant as it may provide a possible mechanism contributing to the modulation of virulence attributes of isolates, such as has been observed in the ongoing Vancouver Island outbreak of C. gattii.
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