The subphylum Saccharomycotina is a lineage in the fungal phylum Ascomycota that exhibits levels of genomic diversity similar to those of plants and animals. The Saccharomycotina consist of more than ...1 200 known species currently divided into 16 families, one order, and one class. Species in this subphylum are ecologically and metabolically diverse and include important opportunistic human pathogens, as well as species important in biotechnological applications. Many traits of biotechnological interest are found in closely related species and often restricted to single phylogenetic clades. However, the biotechnological potential of most yeast species remains unexplored. Although the subphylum Saccharomycotina has much higher rates of genome sequence evolution than its sister subphylum, Pezizomycotina , it contains only one class compared to the 16 classes in Pezizomycotina . The third subphylum of Ascomycota , the Taphrinomycotina , consists of six classes and has approximately 10 times fewer species than the Saccharomycotina . These data indicate that the current classification of all these yeasts into a single class and a single order is an underappreciation of their diversity. Our previous genome-scale phylogenetic analyses showed that the Saccharomycotina contains 12 major and robustly supported phylogenetic clades; seven of these are current families ( Lipomycetaceae , Trigonopsidaceae , Alloascoideaceae , Pichiaceae , Phaffomycetaceae , Saccharomycodaceae , and Saccharomycetaceae ), one comprises two current families ( Dipodascaceae and Trichomonascaceae ), one represents the genus Sporopachydermia , and three represent lineages that differ in their translation of the CUG codon (CUG-Ala, CUG-Ser1, and CUG-Ser2). Using these analyses in combination with relative evolutionary divergence and genome content analyses, we propose an updated classification for the Saccharomycotina , including seven classes and 12 orders that can be diagnosed by genome content. This updated classification is consistent with the high levels of genomic diversity within this subphylum and is necessary to make the higher rank classification of the Saccharomycotina more comparable to that of other fungi, as well as to communicate efficiently on lineages that are not yet formally named.
ABSTRACT
In recent years, ‘multi-omic’ sciences have affected all aspects of fundamental and applied biological research. Yeast taxonomists, though somewhat timidly, have begun to incorporate ...complete genomic sequences into the description of novel taxa, taking advantage of these powerful data to calculate more reliable genetic distances, construct more robust phylogenies, correlate genotype with phenotype and even reveal cryptic sexual behaviors. However, the use of genomic data in formal yeast species descriptions is far from widespread. The present review examines published examples of genome-based species descriptions of yeasts, highlights relevant bioinformatic approaches, provides recommendations for new users and discusses some of the challenges facing the genome-based systematics of yeasts.
The cases in which genome data has accompanied the description of asomycetous and basidiomycetous yeasts are revised including the different methods and approaches used.
We describe the yeast genus Tortispora gen. nov., an early-diverging lineage in the Saccharomycetales that displays the formation of helical ascospores. The genus is based on 16 strains resembling ...Candida caseinolytica that were isolated from necrotic plant tissue in warm regions of the New World. Based on sequences of the D1/D2 domains of the nuclear large subunit rRNA gene, as well as other data, the strains are assigned to eight distinct species. The species are nutritionally specialized and share the unusual ability to hydrolyse casein and to grow on 1-butanol as sole carbon source. One species of the proposed new genus produces a simple ascus with a helical ascospore, whereas other species of the clade have failed to form ascospores. All species in the clade, including C. caseinolytica, are assigned to Tortispora gen. nov. The new binomials are Tortispora ganteri sp. nov., type species of the genus (SUB 86-469.5T = CBS 12581T = NRRL Y-17035T), Tortispora caseinolytica f.a., comb. nov. (UCD-FST 83-438.3T = CBS 7781T = NRRL Y-17796T), Tortispora mauiana f.a., sp. nov. (UWOPS 87-2430.3T = CBS 12803T = NRRL Y-48832T), Tortispora agaves f.a., sp. nov. (UWOPS 94-257.6T = CBS 12794T = NRRL Y-63662T), Tortispora sangerardonensis f.a., sp. nov. (UWOPS 00-157.1T = CBS 12795T = NRRL Y-63663T), Tortispora cuajiniquilana f.a., sp. nov. (UWOPS 99-344.4T = CBS 12796T = NRRL Y-63664T), Tortispora starmeri f.a., sp. nov. (G 91-702.5T = CBS 12793T = NRRL Y-63665T) and Tortispora phaffii f.a., sp. nov. (UWOPS 91-445.1T = CBS 12804T = NRRL Y-48833T). In addition, species formerly assigned to the genus Ascobotryozyma are reassigned to the genus Botryozyma. The genera Trigonopsis, Botryozyma and Tortispora are assigned to the family Trigonopsidaceae fam. nov.
1 Department of Pathobiology, Nihon University School of Veterinary Medicine, Kameino, Fujisawa, Kanagawa 252-8510, Japan
2 Teikyo University Institute of Medical Mycology, Otsuka, Hachioji, Tokyo ...192-0395, Japan
3 Department of Microbiology, Biological Science Institute, Federal University of Minas Gerais, Avenida Antonio Carlos, Belo Horizonte, Minas Gerais, 31270-901, Brazil
4 Department of Biology, University of Western Ontario, London, Ontario, Canada N6A 5B7
Correspondence Rui Kano kano{at}brs.nihon-u.ac.jp
Five isolates of a novel species of the yeast genus Malassezia were isolated from animals in Japan and Brazil. Phylogenetic trees based on the D1/D2 domains of the large-subunit (26S) rDNA sequences and nucleotide sequences of the internal transcribed spacer 1 region showed that the isolates were conspecific and belonged to the genus Malassezia . They were related closely to Malassezia dermatis and Malassezia sympodialis , but were clearly distinct from these two species and the other six species of Malassezia that have been reported, indicating that they should be classified as a novel species, Malassezia nana sp. nov. Morphologically and physiologically, M. nana resembles M. dermatis and M. sympodialis , but can be distinguished from these species by its inability to use Cremophor EL (Sigma) as the sole lipid source and to hydrolyse aesculin. The type strain of M. nana is NUSV 1003 T (=CBS 9557 T =JCM 12085 T ).
Abbreviations: ITS1, internal transcribed spacer 1
Published online ahead of print on 1 August 2003 as DOI 10.1099/ijs.0.02776-0.
The GenBank/EMBL/DDBJ accession numbers for the 26S rDNA sequences reported in this paper are AB075224 , AB105860 AB105862 and AY166596 , and the accession numbers for the ITS1 region sequences are AB075223 and AB105863 .
Gliomas account for approximately 80 % of all primary malignant brain tumors and, despite improvements in clinical care over the last 20 years, remain among the most lethal tumors, underscoring the ...need for gaining new insights that could translate into clinical advances. Recent genome-wide association studies (GWAS) have identified seven new susceptibility regions. We conducted a new independent GWAS of glioma using 1,856 cases and 4,955 controls (from 14 cohort studies, 3 case–control studies, and 1 population-based case-only study) and found evidence of strong replication for three of the seven previously reported associations at 20q13.33 (
RTEL
), 5p15.33 (
TERT
), and 9p21.3 (
CDKN2BAS
), and consistent association signals for the remaining four at 7p11.2 (
EGFR
both loci), 8q24.21 (
CCDC26
) and 11q23.3 (
PHLDB1
). The direction and magnitude of the signal were consistent for samples from cohort and case–control studies, but the strength of the association was more pronounced for loci rs6010620 (20q,13.33;
RTEL
) and rs2736100 (5p15.33,
TERT
) in cohort studies despite the smaller number of cases in this group, likely due to relatively more higher grade tumors being captured in the cohort studies. We further examined the 85 most promising single nucleotide polymorphism (SNP) markers identified in our study in three replication sets (5,015 cases and 11,601 controls), but no new markers reached genome-wide significance. Our findings suggest that larger studies focusing on novel approaches as well as specific tumor subtypes or subgroups will be required to identify additional common susceptibility loci for glioma risk.
Two new yeast species were isolated from flowers of Hibiscus species in Eastern and Northern Australia. Kodamaea kakaduensis is heterothallic, haploid, and similar to other Kodamaea species and to ...Candida restingae. Buds are often produced on short protuberances, and a true mycelium is formed. The new species differs from others by the assimilation of trehalose, melezitose, and xylitol, and is reproductively isolated. The cells of Candida tolerans are small and a pseudomycelium is formed. The carbon and nitrogen assimilation pattern is reminiscent of that of Zygosaccharomyces rouxii but the two are not closely related. Sequences of the D1/D2 domain of large subunit ribosomal DNA confirm the membership of K. kakaduensis in the genus Kodamaea and indicate that C. tolerans belongs to the Clavispora-Metschnikowia clade, with a moderate relatedness to Candida mogii. The type strains are: K. kakaduensis, UWO(PS)98-119.2 (h+, holotype, CBS 8611) and UWO(PS)98-117.1 (h-, isotype, CBS 8612); and C. tolerans, UWO(PS)98-115.5 (CBS 8613).
A snow model forced by temperature and precipitation is used to simulate the spatial distribution of snow water equivalent (SWE) over a 600 000 km² portion of the province ofQuebec, Canada. We ...propose to improve model simulations by assimilating SWE data from sporadic manual snow surveys with a particle filter. A temporally and spatially correlated perturbation of the meteorological forcing is used to generate the set of particles. The magnitude of the perturbations is fixed objectively. First, the particle filter and direct insertion were both applied on 88 sites for which measured SWE consisted of more or less five values per year over a period of 17 years. The temporal correlation of perturbations enables us to improve the accuracy and the ensemble dispersion of the particle filter, while the spatial correlation leads to a spatial coherence in the particle weights. The spatial estimates of SWE obtained with the particle filter are compared with those obtained through optimal interpolation of the snow survey data, which is the current operational practice in Quebec. Cross-validation results as well as validation against an independent dataset show that the proposed particle filter enables us to improve the spatial distribution of the snow water equivalent compared with optimal interpolation.
Celotno besedilo
Dostopno za:
BFBNIB, DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
We studied specific yeast communities vectored by beetles, drosophilids, and bees that visit ephemeral flowers, mostly in the genus
Hibiscus and in the families Convolvulaceae and Cactaceae, in the ...Neotropical, Nearctic, and Australian biogeographic regions. The communities consist mostly of yeasts in four clades centered around the genera
Metschnikowia,
Kodamaea,
Wickerhamiella, and
Starmerella. The largest geographic discontinuity occurs as a function of the nitidulid beetle species that dominate the non-pollinator insect visitors of the flowers. This partitions the New World, where the dominant beetle is in the genus
Conotelus, from the Australian biogeographic region, dominated by species of
Aethina. Distinct but sympatric insects may also carry radically different yeast communities.
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