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The unambiguous application of fungal names is important to communicate scientific findings. Names are critical for (clinical) diagnostics, legal compliance, and regulatory controls, such as biosafety, food security, quarantine regulations, and industrial applications. Consequently, the stability of the taxonomic system and the traceability of nomenclatural changes is crucial for a broad range of users and taxonomists. The unambiguous application of names is assured by the preservation of nomenclatural history and the physical organisms representing a name. Fungi are extremely diverse in terms of ecology, lifestyle, and methods of study. Predominantly unicellular fungi known as yeasts are usually investigated as living cultures. Methods to characterize yeasts include physiological (growth) tests and experiments to induce a sexual morph; both methods require viable cultures. Thus, the preservation and availability of viable reference cultures are important, and cultures representing reference material are cited in species descriptions. Historical surveys revealed drawbacks and inconsistencies between past practices and modern requirements as stated in the International Code of Nomenclature for Algae, Fungi, and Plants (ICNafp). Improper typification of yeasts is a common problem, resulting in a large number invalid yeast species names. With this opinion letter, we address the problem that culturable microorganisms, notably some fungi and algae, require specific provisions under the ICNafp. We use yeasts as a prominent example of fungi known from cultures. But viable type material is important not only for yeasts, but also for other cultivable Fungi that are characterized by particular morphological structures (a specific type of spores), growth properties, and secondary metabolites. We summarize potential proposals which, in our opinion, will improve the stability of fungal names, in particular by protecting those names for which the reference material can be traced back to the original isolate.

Although sugarcane produces a large amount of energy per hectare, its ensiled storage leads to losses, which makes it one of the most expensive options for animal feeding. These losses occur due to fermentation of sugars and organic acids by yeasts, producing alcohol and gas. Inoculants containing Lactobacillus buchneri increase acetic acid production, which has effect against yeast. In this study, we produced egg yolk antibodies (IgY) against yeasts that ferment lactate (Candida glabrata, Pichia kudriavzevii, and Pichia manshurica) and sugar (Saccharomyces cerevisiae, Torulospora delbrueckii, Schizosaccharomyces pombe and Debaryomyces etchellsii) isolated in sugarcane silage. Shortly before ensiling, doses of 0, 175, 350, and 700 g/t IgY, and Lactobacillus buchneri were applied to chopped forage. Gas losses were calculated using experimental silos in triplicate, according to the equation: G = (PCf - PCa)/(MFf) × 100, in which: G = gas losses (kg/t); PCf = weight of full silo (equipped with a Bunsen valve to allow gas outflow) at sealing (kg); PCa = weight of full bucket at opening (kg); MFf = forage mass at sealing (kg). The data were analyzed as a completely randomized design and submitted to analysis of variance and regression using the SAS (SAS, 1998), which was chosen because of the significance of the regression parameters, tested by Tukey’s test (P < 0.05) and the values of the coefficients of determination. Thirty days after sealing the L. buchneri inoculant and doses of 350 and 700 g/t IgY promoted less gas losses than control that had no any product (12.74; 15.59 and 15.28 versus 27.74, respectively, P < 0.05) and the L. buchneri did not differ from IgY doses. The gas losses decreased quadratically with the anti-yeast addition, estimating maximum of 530 g/t fresh forage. We conclude that anti-yeast use reduces gas production during fermentation. With continuity of this research, we may obtain a roughage with higher nutritional value, as its mode of action in yeast control does not involve consumption of sugars or organic acids.

Phaffia is an orange-colored basidiomycetous yeast genus of the order Cystofilobasidiales that contains a single species, P. rhodozyma. This species is the only fungus known to produce the economically relevant carotenoid astaxanthin. Although Phaffia was originally found in the Northern hemisphere, its diversity in the southern part of the globe has been shown to be much greater. Here we analyze the genomes of two Australasian lineages that are markedly distinct from P. rhodozyma. The two divergent lineages were investigated within a comprehensive phylogenomic study of representatives of the Cystofilobasidiales that supported the recognition of two novel Phaffia species, for which we propose the names of P. australis sp. nov. and P. tasmanica sp. nov. Comparative genomics and other analyses confirmed that the two new species have the typical Phaffia hallmark&mdash, the six genes necessary for the biosynthesis of astaxanthin could be retrieved from the draft genome sequences, and this carotenoid was detected in culture extracts. In addition, the organization of the mating-type (MAT) loci is similar to that of P. rhodozyma, with synteny throughout most regions. Moreover, cases of trans-specific polymorphism involving pheromone receptor genes and pheromone precursor proteins in the three Phaffia species, together with their shared homothallism, provide additional support for their classification in a single genus.

Background: Lignocellulosic biomass is a common resource across the globe, and its fermentation offers a promising option for generating renewable liquid transportation fuels. The deconstruction of lignocellulosic biomass releases sugars that can be fermented by microbes, but these processes also produce fermentation inhibitors, such as aromatic acids and aldehydes. Several research projects have investigated lignocellulosic biomass fermentation by the baker's yeast Saccharomyces cerevisiae. Most projects have taken synthetic biological approaches or have explored naturally occurring diversity in S. cerevisiae to enhance stress tolerance, xylose consumption, or ethanol production. Despite these efforts, improved strains with new properties are needed. In other industrial processes, such as wine and beer fermentation, interspecies hybrids have combined important traits from multiple species, suggesting that interspecies hybridization may also offer potential for biofuel research. Results: To investigate the efficacy of this approach for traits relevant to lignocellulosic biofuel production, we generated synthetic hybrids by crossing engineered xylose-fermenting strains of S. cerevisiae with wild strains from various Saccharomyces species. These interspecies hybrids retained important parental traits, such as xylose consumption and stress tolerance, while displaying intermediate kinetic parameters and, in some cases, heterosis (hybrid vigor). Next, we exposed them to adaptive evolution in ammonia fiber expansion-pretreated corn stover hydrolysate and recovered strains with improved fermentative traits. Genome sequencing showed that the genomes of these evolved synthetic hybrids underwent rearrangements, duplications, and deletions. To determine whether the genus Saccharomyces contains additional untapped potential, we screened a genetically diverse collection of more than 500 wild, non-engineered Saccharomyces isolates and uncovered a wide range of capabilities for traits relevant to cellulosic biofuel production. Notably, Saccharomyces mikatae strains have high innate tolerance to hydrolysate toxins, while some Saccharomyces species have a robust native capacity to consume xylose. Conclusions: This research demonstrates that hybridization is a viable method to combine industrially relevant traits from diverse yeast species and that members of the genus Saccharomyces beyond S. cerevisiae may offer advantageous genes and traits of interest to the lignocellulosic biofuel industry. Fil: Peris, David. University of Wisconsin; Estados Unidos Fil: Moriarty, Ryan V.. University of Wisconsin; Estados Unidos Fil: Alexander, William G.. University of Wisconsin; Estados Unidos Fil: Baker, EmilyClare. University of Wisconsin; Estados Unidos Fil: Sylvester, Kayla. University of Wisconsin; Estados Unidos Fil: Sardi, Maria. University of Wisconsin; Estados Unidos Fil: Langdon, Quinn K.. University of Wisconsin; Estados Unidos Fil: Libkind Frati, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales. Universidad Nacional del Comahue. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales.; Argentina Fil: Wang, Qi-Ming. University of Wisconsin; Estados Unidos. Institute Of Microbiology Chinese Academy Of Sciences; China Fil: Bai, Feng-Yan. Institute Of Microbiology Chinese Academy Of Sciences; China Fil: Leducq, Jean Baptiste. University of Montreal; Canadá. Laval University; Canadá Fil: Charron, Guillaume. Laval University; Canadá Fil: Landry, Christian R.. Laval University; Canadá Fil: Sampaio, José Paulo. New University Of Lisbon; Portugal Fil: Gonçalves, Paula. New University Of Lisbon; Portugal Fil: Hyma, Katie E.. Washington University in St. Louis; Estados Unidos Fil: Fay, Justin C.. Washington University in St. Louis; Estados Unidos Fil: Sato, Trey K.. University of Wisconsin; Estados Unidos Fil: Hittinger, Chris Todd. University of Wisconsin; Estados Unidos

During a survey of yeast populations associated with grape and apple musts used for wine and cider fermentation, respectively, six pink-coloured ballistoconidia-forming yeasts belonging to the order Sporidiobolales (Basidiomycota) were isolated. Phylogenetic analysis inferred using sequences of the internal transcribed spacer (ITS), the D1/D2 domain of the large subunit rRNA gene, the small subunit (SSU) rRNA gene and DNA-directed RNA polymerase II subunit (RPB2) indicated that the six isolates were separated in two novel species. One of the new species, Sporobolomyces agrorum sp. nov., isolated from grape must, had Sporobolomyces roseus and Sporobolomyces metaroseus as its closest relatives, but showed four/two and 16 nucleotide substitutions in the D1/D2 and ITS regions, respectively, to these two species. The other novel species, Sporobolomyces sucorum sp. nov., was found in apple must and was closely related to Sporobolomyces pararoseus and Sporobolomyces patagonicus, but showed two/three and five substitutions in those two regions for its closest relatives. We detected additional representatives of this species, most of them isolated from grapes whose sequences were already available on public databases. A sexual stage could not be observed for the novel species. publishersversion published

Fundacao para a Ciencia e a Tecnologia (Portugal) grants PTDC/BIA-MIC/30785/2017. SFRH/BD/136462/2018. Slovenian Research Agency Grants P4-0116 and MRIC-ULZIM, IP-0510 (NC). The adaptation of the yeast Saccharomyces cerevisiae to man-made environments for the fermentation of foodstuffs and beverages illustrates the scientific, social, and economic relevance of microbe domestication. Here we address a yet unexplored aspect of S. cerevisiae domestication, that of the emergence of lineages harboring some domestication signatures but that do not fit completely in the archetype of a domesticated yeast, by studying S. cerevisiae strains associated with processed olives, namely table olives, olive brine, olive oil, and alpechin. We confirmed earlier observations that reported that the Olives population results from a hybridization between S. cerevisiae and S. paradoxus. We concluded that the olive hybrids form a monophyletic lineage and that the S. cerevisiae progenitor belonged to the wine population of this species. We propose that homoploid hybridization gave rise to a diploid hybrid genome, which subsequently underwent the loss of most of the S. paradoxus sub-genome. Such a massive loss of heterozygosity was probably driven by adaptation to the new niche. We observed that olive strains are more fit to grow and survive in olive brine than control S. cerevisiae wine strains and that they appear to be adapted to cope with the presence of NaCl in olive brine through expansion of copy number of ENA genes. We also investigated whether the S. paradoxus HXT alleles retained by the Olives population were likely to contribute to the observed superior ability of these strains to consume sugars in brine. Our experiments indicate that sugar consumption profiles in the presence of NaCl are different between members of the Olives and Wine populations and only when cells are cultivated in nutritional conditions that support adaptation of their proteome to the high salt environment, which suggests that the observed differences are due to a better overall fitness of olives strains in the presence of high NaCl concentrations. Although relic olive hybrids exhibit several characteristics of a domesticated lineage, tangible benefits to humans cannot be associated with their phenotypes. These strains can be seen as a case of adaptation without positive or negative consequences to humans, that we define as a quasi-domestication. publishersversion published

The most common fermented beverage, lager beer, is produced by interspecies hybrids of the brewing yeast Saccharomyces cerevisiae and its wild relative S. eubayanus. Lager-brewing yeasts are not the only example of hybrid vigour or heterosis in yeasts, but the full breadth of interspecies hybrids associated with human fermentations has received less attention. Here we present a comprehensive genomic analysis of 122 Saccharomyces hybrids and introgressed strains. These strains arose from hybridization events between two to four species. Hybrids with S. cerevisiae contributions originated from three lineages of domesticated S. cerevisiae, including the major wine-making lineage and two distinct brewing lineages. In contrast, the undomesticated parents of these interspecies hybrids were all from wild Holarctic or European lineages. Most hybrids have inherited a mitochondrial genome from a parent other than S. cerevisiae, which recent functional studies suggest could confer adaptation to colder temperatures. A subset of hybrids associated with crisp flavour profiles, including both lineages of lager-brewing yeasts, have inherited inactivated S. cerevisiae alleles of critical phenolic off-flavour genes and/or lost functional copies from the wild parent through multiple genetic mechanisms. These complex hybrids shed light on the convergent and divergent evolutionary trajectories of interspecies hybrids and their impact on innovation in lager brewing and other diverse fermentation industries., Work supported by the National Science Foundation (grant nos. DEB-1253634 to C.T.H. and DGE-1256259 (Graduate Research Fellowship to Q.K.L.), the USDA National Institute of Food and Agriculture Hatch Project (nos. 1003258 and 1020204 to C.T.H.) and in part by the DOE Great Lakes Bioenergy Research Center (DOE BER Office of Science nos. DE-SC0018409 and DE-FC02-07ER64494). Q.K.L. was also supported by the Predoctoral Training Program in Genetics, funded by the National Institutes of Health (grant no. 5T32GM007133). D.P. is a Marie Sklodowska-Curie fellow of the European Union’s Horizon 2020 research and innovation programme (grant no. 747775).

Horizontal gene transfer (HGT) and introgression are increasingly recognized as a prominent source of adaptation in eukaryotes. Over the past decade, several cases of HGT from prokaryotes to the yeast Saccharomyces strains have been demonstrated. In addition, we have recently identified eukaryote-to-eukaryote gene transfers and some of them have been shown to be involved in the adaptation of the yeast S. cerevisiae to environmental conditions (1;2;3). Three large genomic regions, (A, B and C), were acquired by wine yeasts strains from more distant yeast species (1;3). The yeasts Zygosaccharomyces bailii and Torulaspora microellipsoides, species found in wine fermentations, were identified as the donors of regions B and C, respectively (1;3). We obtained evidence for the amplification of the region B (17 kb) in the genome of S. cerevisiae wine strains (4). The organization of this region differ considerably between strains and the identification of an autonomously replicating sequence functional in S. cerevisiae strongly suggest an expansion mechanism in yeast genomes involving an extrachromosomal circular DNA molecule. We also showed that region C have undergone several rearrangements and carries genes playing a key role in the adaptation of wine yeasts to the nitrogen-limited wine fermentation environment (3). The analysis of 82 S. cerevisiae strains from various ecological origins allowed identification of 33 HGT or introgression for which we have proposed potential donors using phylogenetic topology test. Among these events, we observed, the replacement of a GAL cluster in cheese strains which enables a faster switch from glucose to galactose and improves growth speed in a media containing a mix of the two hexoses such as fermented milk products. These data support the vision of customized yeast genomes associated to specific ecological niches and highlight the key role of HGT in the adaptation of fungal species to their environments.1. Novo et al. 2009, PNAS, 106: 16333-16338.2. Damon et al 2011, ISME Journal 9: 67.3. Marsit et al 2015, Mol. Biol. Evol., 32:1695–1707 4. Galeote et al 2011, PLoS One 6: e17872.

Multiple isolates belonging to the ascomycetous genus Zygotorulaspora were obtained from forest soils and tree bark in Shiba Prefecture in Japan, and Lake Daniels, Lewis Pass, in New Zealand. Phylogenetic analyses employing combined sequences of the D1/D2 domain and ITS region support the recognition of two new species:Zygotorulaspora chibaensis sp. nov. (type strain PYCC 6970T =CBS 15364T) and Zygotorulaspora danielsina sp. nov. (type strain PYCC 6984T =CBS 15365T). Both species are able to grow on D-xylose and L-arabinose and at 35° C, unlike Zygotorulaspora florentina and Zygotorulaspora mrakii, the other two species in the genus. Fil: Carvalho, Cláudia. Universidad Nova de Lisboa; Portugal Fil: Tomás, André. Universidad Nova de Lisboa; Portugal Fil: Libkind Frati, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales. Universidad Nacional del Comahue. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales.; Argentina Fil: Imanishi, Yumi. Kanto Gakuin University; Japón Fil: Sampaio, José Paulo. Universidad Nova de Lisboa; Portugal

International audience; During a survey of the yeast community associated with the phylloplane of corn in Thailand, a basidiomycetous yeast strain belonging to the genus Papiliotrema was isolated. Analyses of the D1/D2 domains of the 26S (LSU) rRNA gene and complete ITS region supported the recognition of a novel species, for which the name Papiliotrema plantarum sp. nov. is proposed (type strain DMKU-CP801(T) =CBS 15220(T) =PYCC 7257(T)). Another strain of P. plantarum sp. nov., isolated in French Guiana, was found to be sexually compatible with the Thai isolate and mycelium with clamp connections, basidia and basidiospores were observed in culture. The basidial morphology of P. plantarum combined features previously observed for Papiliotrema bandonii and Papiliotrema fuscus, which represent the only sexual species hitherto known in the genus, i.e. transversely septate basidia, with sexual structures of the Tremella type.

Adaptation of Yeast to Anthropogenic Environments Using Comparative Genomics. 27. International Conference on Yeast Genetics and Molecular Biology (ICYGMB)

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. Fil: Gibson, B.. Vtt Technical Research Centre Of Finland; Finlandia Fil: Geertman, J. M. A.. Heineken Supply Chain; Países Bajos Fil: Hittinger, C. T.. University of Wisconsin; Estados Unidos Fil: Krogerus, K.. Vtt Technical Research Centre Of Finland; Finlandia. Aalto University; Finlandia Fil: Libkind Frati, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales. Universidad Nacional del Comahue. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales.; Argentina Fil: Louis, E. J.. University of Leicester; Reino Unido Fil: Magalhães, F.. Vtt Technical Research Centre Of Finland; Finlandia. Aalto University; Finlandia Fil: Sampaio, J.P.. Universidade Nova de Lisboa; Portugal

Horizontal Gene Transfer is a key mechanism permitting adaptation of [i]S. cerevisiae[/i][i][/i] to its ecological niches. Reunión anual conjunta genética y evolución

In fungi belonging to the phylum Basidiomycota, sexual compatibility is usually determined by two genetically unlinked MAT loci, one of which encodes one or more pheromone receptors (P/R) and pheromone precursors, and the other comprehends at least one pair of divergently transcribed genes encoding homeodomain (HD) transcription factors. Most species are heterothallic, meaning that sexual reproduction requires mating between two sexually compatible individuals harboring different alleles at both MAT loci. However, some species are known to be homothallic, one individual being capable of completing the sexual cycle without mating with a genetically distinct partner. While the molecular underpinnings of the heterothallic life cycles of several basidiomycete model species have been dissected in great detail, much less is known concerning the molecular basis for homothallism. Following the discovery in available draft genomes of the homothallic basidiomycetous yeast Phaffia rhodozyma of P/R and HD genes, we employed available genetic tools to determine their role in sexual development. Two P/R clusters, each harboring one pheromone receptor and one pheromone precursor gene were found in close vicinity of each other and were shown to form two redundant P/R pairs, each receptor being activated by the pheromone encoded by the most distal pheromone precursor gene. The HD locus is apparently genetically unlinked to the P/R locus and encodes a single pair of divergently transcribed HD1 and HD2 transcription factors, both required for normal completion of the sexual cycle. Given the genetic makeup of P. rhodozyma MAT loci, we postulate that it is a primarily homothallic organism and we propose a model for the interplay of molecular interactions required for sexual development in this species. Phaffia rhodozyma is considered one of the most promising microbial source of the carotenoid astaxanthin. Further development of this yeast as an industrial organism will benefit from new insights regarding its sexual reproduction system., Author Summary Some fungi are capable of sexual reproduction without the need for a sexually compatible partner, a behavior called homothallism. For some of these fungi, it was observed that they carried in a single individual all the genes normally determining sexual identity in two distinct sexually compatible individuals, but in most cases the role of these genes is still unclear. Here we examined in detail the homothallic sexual cycle of the yeast Phaffia rhodozyma that belongs to the Basidiomycota, which is the fungal lineage that also includes the mushrooms. Phaffia rhodozyma produces astaxanthin, a pigment with antioxidant properties used in the food and cosmetic industries and is accessible to genetic modifications, so far aimed mainly at improving astaxanthin production. Here we harnessed these genetic tools to dissect the self-fertile life cycle of this yeast and found that all genes normally involved in two-partner sexual reproduction are also required for self-fertile sex in P. rhodozyma and propose a model describing molecular interactions required to trigger sexual development. We also generated preferably outcrossing strains, which are potentially useful for further improvement of P. rhodozyma as an industrial organism.

The yeast Saccharomyces cerevisiae is one of the most important microorganisms for food and drink production and it is as well a model for biology. Surprisingly, the bases of yeast population structure have been unraveled only recently [1, 2] and the first genomic population approaches have failed to point adaptation to ecological niches. However, as many groups present highly contrasted lifestyle (e.g. anaerobic growth on grape must for wine yeast, aerobic growth as a biofilm on ethanol and glycerol for flor strains, growth on low amount of sugars for oak strains) different adaptations are expected. In this project we have obtained high quality genome sequences of 82 yeast strains: 35 from wine environment (27 wine strains, 8 flor strains) as well as 47 other strains from rum, fermented dairy product, bakery including 8 from oaks trees. Our genomic data enable us to delineate specific genetic groups corresponding to the different ecological niches, and indicate different life cycles. We first detected the amplification of several genes with critical function in their environment (e.g. CUP1 for wine yeast, IMA2 and SUC2 for bakery yeast…). We then established a catalog of genes potentially impacted per population. Several tests revealed a non-neutral evolution at several loci, and especially the presence of selective sweep for wine yeast, suggesting positive selection. The comparison of flor and wine yeast revealed allelic variation associated to growth under velum, as well as the fructophily of flor strains, or a specific metal homeostasis. Last among the three large chromosomal regions originated from horizontal gene transfer (HGT) from distant yeasts first discovered in EC1118 [3] were encountered mainly in wine or flor yeasts but the complete region C was only found among flor strains. These genomic data represent a unique resource for understanding the adaptation of yeast to wine making niches and thus for elucidating the bases of technological properties.

Exploring the adaptation of yeast to wine making environment using comparative genomics . SMBE Satellite meeting SMBEBA 2015 "Investigating biological adaptation with NGS: data and models"

Deciphering the adaptation of yeast to anthropic environment using comparative genomics. ESF-EMBO Symposium, Exploring the genomic complexity and diversity of eukaryotes

The domestication of the wine yeast Saccharomyces cerevisiae is thought to be contemporary with the development and expansion of viticulture along the Mediterranean basin. Until now, the unavailability of wild lineages prevented the identification of the closest wild relatives of wine yeasts. Here, we enlarge the collection of natural lineages and employ whole-genome data of oak-associated wild isolates to study a balanced number of anthropic and natural S. cerevisiae strains. We identified industrial variants and new geographically delimited populations, including a novel Mediterranean oak population. This population is the closest relative of the wine lineage as shown by a weak population structure and further supported by genomewide population analyses. A coalescent model considering partial isolation with asymmetrical migration, mostly from the wild group into the Wine group, and population growth, was found to be best supported by the data. Importantly, divergence time estimates between the two populations agree with historical evidence for winemaking. We show that three horizontally transmitted regions, previously described to contain genes relevant to wine fermentation, are present in the Wine group but not in the Mediterranean oak group. This represents a major discontinuity between the two populations and is likely to denote a domestication fingerprint in wine yeasts. Taken together, these results indicate that Mediterranean oaks harbour the wild genetic stock of domesticated wine yeasts.

In addition to Saccharomyces cerevisiae, the cryotolerant yeast species S. uvarum is also used for wine and cider fermentation but nothing is known about its natural history. Here we use a population genomics approach to investigate its global phylogeography and domestication fingerprints using a collection of isolates obtained from fermented beverages and from natural environments on five continents. South American isolates contain more genetic diversity than that found in the Northern Hemisphere. Moreover, coalescence analyses suggest that a Patagonian sub-population gave rise to the Holarctic population through a recent bottleneck. Holarctic strains display multiple introgressions from other Saccharomyces species, those from S. eubayanus being prevalent in European strains associated with humandriven fermentations. These introgressions are absent in the large majority of wild strains and gene ontology analyses indicate that several gene categories relevant for wine fermentation are overrepresented. Such findings constitute a first indication of domestication in S. uvarum. Fil: Almeida, Pedro. Universidade Nova de Lisboa; Portugal Fil: Goncalves, Carla. Universidade Nova de Lisboa; Portugal Fil: Teixeira, Sara. Universidade Nova de Lisboa; Portugal Fil: Libkind Frati, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Patagonia Norte. Instituto de Investigación en Biodiversidad y Medioambiente; Argentina. Universidad Nacional del Comahue; Argentina Fil: Bontrager, Martín. University Of Wisconsin; Estados Unidos Fil: Masneuf Pomarede, Isabelle. Bordeaux Sciences agro; Francia Fil: Albertin, Warren. Universite de Bordeaux; Francia Fil: Durrens, Pascal. Universite de Bordeaux; Francia Fil: Sherman, David James. Universite de Bordeaux; Francia Fil: Marullo, Philippe. Universite de Bordeaux; Francia. BIOLAFFORT; Francia Fil: Hittinger, Chris Todd. University Of Wisconsin; Estados Unidos Fil: Gonçalves, Paula. Universidade Nova de Lisboa; Portugal Fil: Sampaio, José Paulo . Universidade Nova de Lisboa; Portugal

Nine yeast species belonging to genera Candida , Cryptococcus , Phaffomyces , Rhodotorula and Wickerhamomyces , and one species of Aureobasidium genus were isolated from the cloaca of migratory birds. Candida glabrata and C. inconspicua were the species most frequently isolated and Wickerhamomyces sylviae , which has recently been described as a new species isolated from bird cloaca, was again found. The majority of isolates showed the ability to grow up to 40 °C and/or at pH 3.0, two environmental conditions typical of the digestive tract of birds. The phylogenetic analysis of the D1/D2 domain of 26S rRNA gene placed the cultures of Phaffomyces in a new lineage that differed from the closest species, P. opuntiae , by 13 nucleotide substitutions. The new species was able to grow at 40 °C and at pH 2.5, which suggests a possible adaptation to the bird cloaca. Moreover, the ability to grow in the presence of digitonin at pH 3.7 and the assimilation of ethyl acetate indicates a potential cactophilic origin. For the first time, the presence of yeasts belonging to the Phaffomyces clade in Europe and also in non-cactus environments is reported. The new species is formally described as P. usticensis sp. nov. (PYCC 6346T = CBS 12958T).

Comparative genomics revealed in the last decade a scenario of rampant horizontal gene transfer (HGT) among prokaryotes, but for fungi a clearly dominant pattern of vertical inheritance still stands, punctuated however by an increasing number of exceptions. In the present work, we studied the phylogenetic distribution and pattern of inheritance of a fungal gene encoding a fructose transporter (FSY1) with unique substrate selectivity. 109 FSY1 homologues were identified in two sub-phyla of the Ascomycota, in a survey that included 241 available fungal genomes. At least 10 independent inter-species instances of horizontal gene transfer (HGT) involving FSY1 were identified, supported by strong phylogenetic evidence and synteny analyses. The acquisition of FSY1 through HGT was sometimes suggestive of xenolog gene displacement, but several cases of pseudoparalogy were also uncovered. Moreover, evidence was found for successive HGT events, possibly including those responsible for transmission of the gene among yeast lineages. These occurrences do not seem to be driven by functional diversification of the Fsy1 proteins because Fsy1 homologues from widely distant lineages, including at least one acquired by HGT, appear to have similar biochemical properties. In summary, retracing the evolutionary path of the FSY1 gene brought to light an unparalleled number of independent HGT events involving a single fungal gene. We propose that the turbulent evolutionary history of the gene may be linked to the unique biochemical properties of the encoded transporter, whose predictable effect on fitness may be highly variable. In general, our results support the most recent views suggesting that inter-species HGT may have contributed much more substantially to shape fungal genomes than heretofore assumed., Author Summary Genes are commonly vertically inherited, meaning that they share the evolutionary history of the organisms in which they are found. However, they can also be transmitted between species with overlapping niches, a phenomenon known as horizontal gene transfer (HGT) that can occur between closely related species but also between organisms belonging to different domains of life. While HGT is very common in prokaryotes, it has been less frequently reported in eukaryotes, including eukaryotic microbes. In fungi, several instances of genes acquired by HGT from bacteria have been reported, but gene exchange between fungal species is thought to be rare. Here, we describe our findings concerning a single fungal gene that seems to have been transferred between fungi very often. We believe this may be related to the fact that the gene can be both very useful and detrimental for the host, depending on genetic background and environment. Our results suggest that exchange of genes between fungi may happen much more frequently than assumed so far.

New insights into the adaptation of yeast to anthropic niches using comparative genomics. Focus on flor yeast genome. ESF-EMBO Comparative Genomics of Eukaryotic Microorganisms: Complexity Patterns in Eukaryotic Genomes

Background The red yeasts are an early diverged group of basidiomycetes comprising sexual and asexual species. Sexuality is based on two compatible mating types and sexual identity is determined by MAT loci that encode homeodomain transcription factors, peptide pheromones and their receptors. The objective of the present study was to investigate the presence and integrity of MAT genes throughout the phylogenetic diversity of red yeasts belonging to the order Sporidiobolales. Results We surveyed 18 sexual heterothallic and self-fertile species and 16 asexual species. Functional pheromone receptor homologues (STE3.A1 and STE3.A2) were found in multiple isolates of most of the sexual and asexual species. For each of the two mating types, sequence comparisons with whole-genome data indicated that synteny tended to be conserved along the pheromone receptor region. For the homeodomain transcription factor, likelihood methods suggested that diversifying selection acting on the self/non-self recognition region promotes diversity in sexual species, while rapid evolution seems to be due to relaxed selection in asexual strains. Conclusions The majority of both sexual and asexual species of red yeasts have functional pheromone receptors and homeodomain homologues. This and the frequent existence of asexual strains within sexual species, makes the separation between sexual and asexual species imprecise. Events of loss of sexuality seem to be recent and frequent, but not uniformly distributed within the Sporidiobolales. Loss of sex could promote speciation by fostering the emergence of asexual lineages from an ancestral sexual stock, but does not seem to contribute to the generation of exclusively asexual lineages that persist for a long time.

The genus Saccharomyces currently includes eight species in addition to the model yeast Saccharomyces cerevisiae, most of which can be consistently isolated from tree bark and soil. We recently found sympatric pairs of Saccharomyces species, composed of one cryotolerant and one thermotolerant species in oak bark samples of various geographic origins. In order to contribute to explain the occurrence in sympatry of Saccharomyces species, we screened Saccharomyces genomic data for protein divergence that might be correlated to distinct growth temperature preferences of the species, using the dN/dS ratio as a measure of protein evolution rates and pair-wise species comparisons. In addition to proteins previously implicated in growth at suboptimal temperatures, we found that glycolytic enzymes were among the proteins exhibiting higher than expected divergence when one cryotolerant and one thermotolerant species are compared. By measuring glycolytic fluxes and glycolytic enzymatic activities in different species and at different temperatures, we subsequently show that the unusual divergence of glycolytic genes may be related to divergent evolution of the glycolytic pathway aligning its performance to the growth temperature profiles of the different species. In general, our results support the view that growth temperature preference is a trait that may have undergone divergent selection in the course of ecological speciation in Saccharomyces.

Here we report on the results of a survey of the yeast populations occurring on submerged leaves (alder, eucalyptus and oak) in a natural mountain stream, during different phases of their decomposition and through two consecutive years. Leaf litter mass loss, total yeast counts, Shannon-Weiner index (H'), yeast community structure and physiologic abilities were analyzed to evaluate the dynamics of yeast communities during decay. Seventy-two yeast taxa were recorded, and in all litter types, species of basidiomycetous affinity predominated over ascomycetous ones. Discriminant analysis of presence/absence data (yeast species) showed significant differences both among substrate types (P

Phaffia rhodozyma (sexual form, Xanthophyllomyces dendrorhous ) is a basidiomycetous yeast that has been found in tree exudates in the Northern Hemisphere at high altitudes and latitudes. This yeast produces astaxanthin, a carotenoid pigment with biotechnological importance because it is used in aquaculture for fish pigmentation. We isolated X. dendrorhous from the Southern Hemisphere (Patagonia, Argentina), where it was associated with fruiting bodies of Cyttaria hariotii , an ascomycetous parasite of Nothofagus trees. We compared internal transcribed spacer (ITS)-based phylogenies of P. rhodozyma and its tree host (Betulaceae, Corneaceae, Fagaceae, and Nothofagaceae) and found them to be generally concordant, suggesting that different yeast lineages colonize different trees and providing an explanation for the phylogenetic distance observed between the type strains of P. rhodozyma and X. dendrorhous . We hypothesize that the association of Xanthophyllomyces with Cyttaria derives from a previous association of the yeast with Nothofagus , and the sister relationship between Nothofagaceae and Betulaceae plus Fagaceae correlates with the phylogeny of X. dendrorhous strains originating from these three plant families. The two most basal strains of X. dendrorhous are those isolated from Cornus , an ancestral genus in the phylogenetic analysis of the host trees. Thus, we question previous conclusions that P. rhodozyma and X. dendrorhous represent different species since the polymorphisms detected in the ITS and intergenic spacer sequences can be attributed to intraspecific variation associated with host specificity. Our study provides a deeper understanding of Phaffia biogeography, ecology, and molecular phylogeny. Such knowledge is essential for the comprehension of many aspects of the biology of this organism and will facilitate the study of astaxanthin production within an evolutionary and ecological framework.

A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community. The classification includes 195 taxa, down to the level of order, of which 16 are described or validated here: Dikarya subkingdom nov.; Chytridiomycota, Neocallimastigomycota phyla nov.; Monoblepharidomycetes, Neocallimastigomycetes class. nov.; Eurotiomycetidae, Lecarioromycetidae, Mycocaliciomycetidae subclass. nov.; Acarosporales, Corticiales, Baeomycetales, Candelariales, Gloeophyllales, Melanosporales, Trechisporales, Umbilicariales ords. nov. The clade containing Ascomycota and Basidiomycota is classified as subkingdom Dikarya, reflecting the putative synapomorphy of dikaryotic hyphae. The most dramatic shifts in the classification relative to previous works concern the groups that have traditionally been included in the Chytridiomycota and Zygomycota. The Chytridiomycota is retained in a restricted sense, with Blastocladiomycota and Neocallimastigomycota representing segregate phyla of flagellated Fungi. Taxa traditionally placed in Zygomycota are distributed among Glomeromycota and several subphyla incertae sedis, including Mucoromycotina, Entomophthoromycotina, Kickxellomycotina, and Zoopagomycotiria. Microsporidia are included in the Fungi, but no further subdivision of the group is proposed. Several genera of 'basal' Fungi of uncertain position are not placed in any higher taxa, including Basidiobolus, Caulochytrium, Olpidium, and Rozella. (c) 2007 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

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.