A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina.

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. Taxonomic novelties: New classes: Alloascoideomycetes M. Groenew., Hittinger, Opulente & A. Rokas, Dipodascomycetes M. Groenew., Hittinger, Opulente & A. Rokas, Lipomycetes M. Groenew., Hittinger, Opulente, A. Rokas, Pichiomycetes M. Groenew., Hittinger, Opulente & A. Rokas, Sporopachydermiomycetes M. Groenew., Hittinger, Opulente & A. Rokas, Trigonopsidomycetes M. Groenew., Hittinger, Opulente & A. Rokas. New orders: Alloascoideomycetes: Alloascoideales M. Groenew., Hittinger, Opulente & A. Rokas; Dipodascomycetes: Dipodascales M. Groenew., Hittinger, Opulente & A. Rokas; Lipomycetes: Lipomycetales M. Groenew., Hittinger, Opulente & A. Rokas; Pichiomycetes: Alaninales M. Groenew., Hittinger, Opulente & A. Rokas, Pichiales M. Groenew., Hittinger, Opulente & A. Rokas, Serinales M. Groenew., Hittinger, Opulente & A. Rokas; Saccharomycetes: Phaffomycetales M. Groenew., Hittinger, Opulente & A. Rokas, Saccharomycodales M. Groenew., Hittinger, Opulente & A. Rokas; Sporopachydermiomycetes: Sporopachydermiales M. Groenew., Hittinger, Opulente & A. Rokas; Trigonopsidomycetes: Trigonopsidales M. Groenew., Hittinger, Opulente & A. Rokas. New families: Alaninales: Pachysolenaceae M. Groenew., Hittinger, Opulente & A. Rokas; Pichiales: Pichiaceae M. Groenew., Hittinger, Opulente & A. Rokas; Sporopachydermiales: Sporopachydermiaceae M. Groenew., Hittinger, Opulente & A. Rokas. Citation: Groenewald M, Hittinger CT, Bensch K, Opulente DA, Shen X-X, Li Y, Liu C, LaBella AL, Zhou X, Limtong S, Jindamorakot S, Gonçalves P, Robert V, Wolfe KH, Rosa CA, Boekhout T, Cadez N, Péter G, Sampaio JP, Lachance M-A, Yurkov AM, Daniel H-M, Takashima M, Boundy-Mills K, Libkind D, Aoki K, Sugita T, Rokas A (2023). A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina. Studies in Mycology 105: 1-22. doi: 10.3114/sim.2023.105.01 This study is dedicated to the memory of Cletus P. Kurtzman (1938-2017), a pioneer of yeast taxonomy.

Towards yeast taxogenomics: lessons from novel species descriptions based on complete genome sequences.

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.

Diversity and phylogeny of basidiomycetous yeasts from plant leaves and soil: Proposal of two new orders, three new families, eight new genera and one hundred and seven new species.

Nearly 500 basidiomycetous yeast species were accepted in the latest edition of The Yeasts: A Taxonomic Study published in 2011. However, this number presents only the tip of the iceberg of yeast species diversity in nature. Possibly more than 99 % of yeast species, as is true for many groups of fungi, are yet unknown and await discovery. Over the past two decades nearly 200 unidentified isolates were obtained during a series of environmental surveys of yeasts in phyllosphere and soils, mainly from China. Among these isolates, 107 new species were identified based on the phylogenetic analyses of nuclear ribosomal DNA (rDNA) [D1/D2 domains of the large subunit (LSU), the small subunit (SSU), and the internal transcribed spacer region including the 5.8S rDNA (ITS)] and protein-coding genes [both subunits of DNA polymerase II (RPB1 and RPB2), the translation elongation factor 1-α (TEF1) and the mitochondrial gene cytochrome b (CYTB)], and physiological comparisons. Forty-six of these belong to 16 genera in the Tremellomycetes (Agaricomycotina). The other 61 are distributed in 26 genera in the Pucciniomycotina. Here we circumscribe eight new genera, three new families and two new orders based on the multi-locus phylogenetic analyses combined with the clustering optimisation analysis and the predicted similarity thresholds for yeasts and filamentous fungal delimitation at genus and higher ranks. Additionally, as a result of these analyses, three new combinations are proposed and 66 taxa are validated.

New yeasts-new brews: modern approaches to brewing yeast design and development.

The brewing industry is experiencing a period of change and experimentation largely driven by customer demand for product diversity. This has coincided with a greater appreciation of the role of yeast in determining the character of beer and the widespread availability of powerful tools for yeast research. Genome analysis in particular has helped clarify the processes leading to domestication of brewing yeast and has identified domestication signatures that may be exploited for further yeast development. The functional properties of non-conventional yeast (both Saccharomyces and non-Saccharomyces) are being assessed with a view to creating beers with new flavours as well as producing flavoursome non-alcoholic beers. The discovery of the psychrotolerant S. eubayanus has stimulated research on de novo S. cerevisiae × S. eubayanus hybrids for low-temperature lager brewing and has led to renewed interest in the functional importance of hybrid organisms and the mechanisms that determine hybrid genome function and stability. The greater diversity of yeast that can be applied in brewing, along with an improved understanding of yeasts' evolutionary history and biology, is expected to have a significant and direct impact on the brewing industry, with potential for improved brewing efficiency, product diversity and, above all, customer satisfaction.

Serum levels of YKL-40 and hyaluronic acid as noninvasive markers of liver fibrosis in haemodialysis patients with chronic hepatitis C virus infection.

Hepatitis C virus (HCV) infection is highly prevalent among end-stage renal disease (ESRD) patients undergoing haemodialysis and it is an important cause of morbidity and mortality in this population. The aim of this study was to evaluate the diagnostic value of YKL-40 and hyaluronic acid (HA) as noninvasive markers of liver fibrosis in 185 ESRD HCV-infected patients. Significant liver fibrosis was defined as METAVIR F2, F3 or F4 stages. Significant fibrosis was observed in 45 patients (24%). By univariate analysis, higher levels of YKL-40, HA, aspartate aminotransferase (AST), alanine aminotransferase (ALT) and gamma-glutamyltransferase (GGT) as well as reduced platelet count were associated with fibrosis. However, by multivariate analysis, only AST (P = 0.001), platelet count (P = 0.004) and HA (P = 0.042) were independently associated with significant fibrosis. For the prediction of significant fibrosis, the areas under receiver operating characterictic curve (AUROC) of the regression model (0.798) was significantly higher than the AUROC of YKL-40 (0.607) and HA (0.650). No difference was noted between the AUROC of the regression model and AST to platelet ratio index (APRI) (0.787). Values <8.38 of the regression model showed a negative predictive value of 94% and scores >or=9.6 exhibited a positive predictive value of 65%. If biopsy indication was restricted to scores in the intermediate range of the regression model, it could have been correctly avoided in 61% of the cases. In conclusion, APRI and a model based on AST, platelet count and HA showed better accuracy than YKL-40 and HA (when used solely) for the prediction of significant fibrosis in ESRD HCV-infected patients.

Kurtzmanomyces insolitus sp. nov., a new anamorphic heterobasidiomycetous yeast species.

A new anamorphic heterobasidiomycetous yeast species, Kurtzmanomyces insolitus, is described using a polyphasic taxonomic approach. The new species has the salient characteristics of the genus Kurtzmanomyces and, additionally, the ability to produce ballistoconidia. Data derived from comparative micromorphological studies, physiological characterisation, ultrastructure and nucleic acid analyses led to assigning the new species to Kurtzmanomyces rather than to the currently accepted genera of ballistoconidia-forming fungi. An emendation of the genus Kurtzmanomyces is proposed to allow the inclusion of the new species.

New taxa in the Tremellales: Bulleribasidium oberjochense gen. et sp. nov., Papiliotrema bandonii gen. et sp. nov. and Fibulobasidium murrhardtense sp. nov.

Two new genera, Bulleribasidium and Papiliotrema, and three new species, B. oberjochense, P. bandonii and Fibulobasidium murrhardtense are described. An integrated analysis of morphological, ultrastructural, physiological, and molecular data indicates that the new taxa belong to the Tremellales (Basidiomycota). Relevant characteristics of the new genera and species are discussed and compared with those of closely related taxa.

O papel terapêutico do Programa Farmácia Viva e das plantas medicinais / The therapeutic role of the Program Farmacia Viva and the medicinal plants in the center-south of Piauí

RESUMOEste trabalho realizou um levantamento sobre o uso de plantas medicinais na cidade de Picos-PI, identificou as plantas cultivadas no horto pertencente ao Laboratório Fitoterápico de Picos (LAFIPI), e analisou o uso de fitoterápicos dispensados pelo Programa Farmácia Viva no triênio 2008-2010. Do total dos 750 entrevistados, 37,6% foram homens e 62,4 % mulheres, dentre os quais a maioria não concluiu o segundo grau (69,2%) e 77,2% possuíam renda mensal de até dois salários mínimos. Com relação ao consumo de plantas medicinais, 76,3% afirmaram utilizá-las para tratar doenças, principalmente por considerá-las mais saudáveis (84,8%). A indicação do uso foi orientada, sobretudo, por familiares (82,2%), embora a maioria adquira as plantas em feiras livres (32,8%). Das 127 plantas relatadas, as mais citadas foram erva-cidreira, boldo e hortelã, sendo as folhas a parte mais utilizada (42,3%), predominantemente por infusão (39,4%). As aplicações mais lembradas foram para tratar dores em geral (17%), distúrbios respiratórios (16,5%) e digestivos (16%). As espécies mais cultivadas no horto são chambá (Justicia pectoralis), alecrim pimenta (Lippia sidoides), malva santa (Plectranthus barbatus) e erva cidreira (Lippia alba). O lambedor de chambá foi o fitoterápico mais procurado pela população entre 2008 e 2010. Esse estudo descreveu, pela primeira vez, o uso tradicional de plantas medicinais no município de Picos e demonstrou, também de forma inédita, a relevância de investimentos do Programa Farmácia Viva no município de Picos e sua inclusão no Programa Saúde da Família como forma de disponibilizar à população de baixa renda fitoterápicos produzidos localmente a custos reduzidos.

ABSTRACTThis study performed a research about the use of medicinal plants in Picos city, identifying the plants grown in the garden belonging to the Laboratory of Phytotherapics in Picos (LAFIPI) and analying the use of phytotherapics distributed by the Farmácia Viva Project between 2008-2010. From the total of 750 interviewed participants, 37.6% were men and 62.4 % women. Most of them do not have secondary education (69.2%) and 77.2% had an income of up until two minimum wages. Regarding consumption of medicinal plants, 76.3 % used them to treat diseases, mainly because they considered them to be healthier (84.8%). The indication of use of the plants was mainly suggested by relatives (82.2%), even though the majority of the participants acquires plants in open markets (32.8%). From the 127 plants mentioned, the most cited ones were balm, boldo and mint, and leaves were the most utilized parts (42.3%), predominantly by infusion (39.4%). The most common reasons for the usewere to treat pain in general (17%), and respiratory (16.5%) and digestive disorders (16%). The most cultivated species in the garden were chambá (Justicia pectoralis), alecrim pimenta (Lippia sidoides), malva santa (Plectranthus barbatus) and erva cidreira (Lippia alba). The "chambá licker" was the most herbal medicine searched by the population between 2008 and 2010. This investigation described, for the first time, the traditional use of medicinal plants in Picos and demonstrated,alsounprecedentedly, the relevance of investments in the Farmácia Viva Project in Picos city and its inclusion in the Family Health Program as a strategyin order to provide locally producedphytotherapics for low-income population at low costs.

Utilization of low molecular weight aromatic compounds by heterobasidiomycetous yeasts: taxonomic implications.

The utilization of low molecular weight aromatic compounds implies the operation of complex metabolic pathways. In order to investigate the taxonomic relevance of this property among heterobasidiomycetous yeasts, both at the species level and at higher taxonomic ranks, the capacity to assimilate twenty such compounds was tested in a total of 332 strains representing approximately 200 species. The substrates most frequently utilized were protocatechuic, caffeic, and p-hydroxybenzoic acids, whereas cinnamic, sinapic, and syringic acids and guaiacol were never assimilated. The assimilation of the majority of the aromatic compounds investigated correlated with the utilization of protocatechuic acid. Among the Urediniomycetes, the members of the Sporidiales and those of the Naohidea-Rhodotorula minuta clade showed a good ability to utilize aromatic compounds, whereas the members of the Agaricostilbum-Kondoa group were more heterogeneous, in agreement with the four subclades known. Among the Tremellomycetidae, the members of the Cystofilobasidium and Tremella clades showed a reduced or null ability to utilize aromatic compounds. In contrast, the members of the Trichosporon clade were able to utilize phenol and similar substrates, and the representatives of the Filobasidium clade assimilated various aromatic compounds, including those requiring more complex catabolic routes. Assimilation tests using, as sole carbon and energy sources, low molecular weight aromatic compounds appear to be potentially useful in taxonomic studies of basidiomycetous yeasts. In those species in which a considerable number of strains was investigated, variable assimilation patterns were frequently observed. The possibility that such discrepant results indicate an incorrect species delimitation is discussed.

Polyphasic taxonomy of the basidiomycetous yeast genus Rhodosporidium: R. azoricum sp. nov.

This report presents the description of a new heterothallic Rhodosporidium species, R. azoricum sp. nov. The new species is based on two strains previously identified as Rhodotorula glutinis, which were isolated from soil in São Miguel island, Azores, Portugal. Evidence that the two strains were conspecific and distinct from Rhodotorula glutinis was obtained in DNA fingerprinting experiments using the microsatellite-primed PCR approach (MSP-PCR) and the primers M13 and (GTG)5. In order to determine the phylogenetic position of the new species, the nucleotide sequence of the D1/D2 region of the 26S rDNA was analysed and Rhodosporidium azoricum was found to belong to a cluster including R. fluviale, R. lusitaniae, Sporidiobolus microsporus, and S. ruineniae. The life cycle of R. azoricum was investigated and comparisons integrating physiological, morphological, and molecular data were made with related species.

Taxonomic studies on the genus Cystofilobasidium: description of Cystofilobasidium ferigula sp. nov. and clarification of the status of Cystofilobasidium lari-marini.

A new species of the genus Cystofilobasidium is described as Cystofilobasidium ferigula sp. nov. The new taxon represents the teleomorphic stage of Cryptococcus ferigula and was obtained in mating experiments using three strains deposited in the Portuguese Yeast Culture Collection (mating types A1) and a recent isolate (mating type A2). Cystofilobasidium ferigula is characterized using an integrated approach encompassing morphological studies, investigation of the ultrastructure of the septal pore, a comparative study of physiological traits, determination of the DNA base composition, DNA reassociation experiments and PCR fingerprinting. During the course of this study, a close similarity of microsatellite-primed PCR fingerprints was detected between Cystofilobasidium lari-marini and Cystofilobasidium capitatum. DNA-DNA reassociation experiments gave high homology values, which indicates that Cystofilobasidium lari-marini must be regarded as a synonym of Cystofilobasidium capitatum.

Emendation of the basidiomycetous yeast genus Kondoa and the description of Kondoa aeria sp. nov.

The genus Kondoa Y. Yamada, Nakagawa & Banno was erected to accommodate a single taxon, K. malvinella (Fell & Hunter) Y. Yamada, Nakagawa & Banno, which was transferred from the teliospore-forming genus Rhodosporidium Banno based on pronounced differences in the 5S and 26S ribosomal RNA (rRNA) nucleotide sequences to R. toruloides Banno. In contrast with the original description, reinvestigation of K. malvinella revealed the formation of transversely septate (auricularioid) basidia that did not arise on teliospores, but formed directly on the dikaryotic mycelium. The four-celled basidia developed sterigmata on which forcibly discharged asymmetric basidiospores (ballistospores) were produced. Additionally, a new taxon emerged from the study of recent isolates, for which the name K. aeria sp. nov. is proposed. This new species produced two-celled auricularioid basidia on hyphae with incomplete clamp connections. Ballistospores arose on the basidia at the tip of sterigmata and, after ejection, germinated by budding. These observations led us to present an emended diagnosis for the genus Kondoa. Analysis of the sequence data from the D1/D2 region of the 26S rRNA gene showed a very close resemblance between K. aeria and K. malvinella in a cluster that also contained several Bensingtonia species. Taxa in this cluster share specific physiological traits and produce characteristic pinkish-cream to mauve colonies; in contrast, formation of ballistoconidia is only observed in the Bensingtonia species. Sequence data supported placement of K. malvinella and K. aeria in the 'Agaricostilbum clade' of the Urediniomycetes.

Cuniculitrema polymorpha (Tremellales, gen. nov. and sp. nov.), a heterobasidiomycete vectored by bark beetles, which is the teleomorph of Sterigmatosporidium polymorphum.

In a study of the mycobiota associated with bark beetles, a dimorphic fungus producing longitudinally septate basidia of the Tremella-type and yeast cells budding off from stalks, was collected. Detailed morphological, physiological and molecular studies revealed that this fungus represents the teleomorph of Sterigmatosporidium polymorphum. Consequently, a new genus, Cuniculitrema gen. nov., and a new species, C. polymorpha sp. nov., are proposed. Comparative morphological and molecular studies indicated that the new taxon belongs to a group that also comprises species of the stalk-forming anamorphic genera Fellomyces and Kockovaella. The new family Cuniculitremaceae is proposed for this group.

Polyphasic taxonomy of the basidiomycetous yeast genus Rhodosporidium: Rhodosporidium kratochvilovae and related anamorphic species.

The phenotypic and genetic heterogeneity of the basidiomycetous yeast species Rhodosporidium kratochvilovae was investigated in a group of recent isolates and collection strains. A polyphasic taxonomic approach was followed which included micromorphological studies, nuclear staining, determination of sexual compatibility, physiological characterization, comparison of electrophoretic isoenzyme patterns, PCR fingerprinting, determination of mol% G+C, DNA-DNA reassociation experiments and 26S and ITS rDNA sequence analysis. The results allowed a more natural circumscription of the species, both from the genetic and phenotypic perspectives. The relationships with anamorphic species of the genus Rhodotorula were studied and isolates previously identified as Rhodotorula glutinis were found to belong to Rhodosporidium kratochvilovae. Other isolates included in the study were found to represent members of Rhodotorula glutinis var. dairenensis. Rhodosporidium kratochvilovae was found to include heterothallic strains, besides those already known to be self-sporulating. A total of 17 isolates, which were found to belong to this species, were heterothallic, self-sporulating and anamorphic strains. It is anticipated that integrated polyphasic studies of basidiomycetous yeasts will provide a more coherent classification system and the basis for accurate identification schemes, which in turn are essential for detailed ecological studies.