Extensive remodeling of sugar metabolism through gene loss and horizontal gene transfer in a eukaryotic lineage.

BACKGROUND: In yeasts belonging to the subphylum Saccharomycotina, genes encoding components of the main metabolic pathways, like alcoholic fermentation, are usually conserved. However, in fructophilic species belonging to the floral Wickerhamiella and Starmerella genera (W/S clade), alcoholic fermentation was uniquely shaped by events of gene loss and horizontal gene transfer (HGT). RESULTS: Because HGT and gene losses were first identified when only eight W/S-clade genomes were available, we collected publicly available genome data and sequenced the genomes of 36 additional species. A total of 63 genomes, representing most of the species described in the clade, were included in the analyses. Firstly, we inferred the phylogenomic tree of the clade and inspected the genomes for the presence of HGT-derived genes involved in fructophily and alcoholic fermentation. We predicted nine independent HGT events and several instances of secondary loss pertaining to both pathways. To investigate the possible links between gene loss and acquisition events and evolution of sugar metabolism, we conducted phenotypic characterization of 42 W/S-clade species including estimates of sugar consumption rates and fermentation byproduct formation. In some instances, the reconciliation of genotypes and phenotypes yielded unexpected results, such as the discovery of fructophily in the absence of the cornerstone gene (FFZ1) and robust alcoholic fermentation in the absence of the respective canonical pathway. CONCLUSIONS: These observations suggest that reinstatement of alcoholic fermentation in the W/S clade triggered a surge of innovation that goes beyond the utilization of xenologous enzymes, with fructose metabolism playing a key role.

Phylogenomic delineation of two new species of ascomycetous yeasts, Wickerhamiella koratensis sp. nov. and Wickerhamiella limtongiae sp. nov., and proposal of two synonyms, Wickerhamiella infanticola and Wickerhamiella tropicalis.

Two novel ascomycetous yeast species of the genus Wickerhamiella are proposed based on isolates obtained in Thailand from food waste and the fruiting body of a polypore fungus, and on a combination of conventional DNA-barcode sequence analyses and whole-genome phylogenies. We focus on a particular subclade of the genus Wickerhamiella that contains species found in anthropic environments and describe Wickerhamiella limtongiae sp. nov. (DMKU-FW31-5T=PYCC 9022T=TBRC 15055T), found on food waste samples. In an adjacent clade, we describe Wickerhamiella koratensis sp. nov. (DMKU-KO16T=PYCC 8908T=TBRC 14869T), which represents the closest relative of Wickerhamiella slavikovae and was isolated from the fruiting body of Bjerkandera sp. In the subclade of W. limtongiae sp. nov., we propose that Wickerhamiella infanticola should be regarded as a synonym of Wickerhamiella sorbophila and that Wickerhamiella tropicalis should be regarded as a synonym of Wickerhamiella verensis.

Taxogenomic analyses of Starmerella gilliamiae f.a, sp. nov. and Starmerella monicapupoae f.a., sp. nov., two novel species isolated from plant substrates and insects.

Four yeast isolates collected from flowers from different ecosystems in Brazil, one from fruit of Nothofagus alpina in Argentina, three from flowers of Neltuma chilensis in Chile and one obtained from the proventriculus of a female bumblebee in Canada were demonstred, by analysis of the sequences of the internal transcribed spacer (ITS) region and D1/D2 domains of the large subunit rRNA gene, to represent two novel species of the genus Starmerella. These species are described here as Starmerella gilliamiae f.a, sp. nov. (CBS 16166T; Mycobank MB 851206) and Starmerella monicapupoae f.a., sp. nov. (PYCC 8997T; Mycobank MB 851207). The results of a phylogenomic analysis using 1037 single-copy orthogroups indicated that S. gilliamiae is a member of a subclade that contains Starmerella opuntiae, Starmerella aceti and Starmerella apicola. The results also indicated that S. monicapupoae is phylogenetically related to Starmerella riodocensis. The two isolates of S. monicapupoae were obtained from flowers in Brazil and were probably vectored by insects that visit these substrates. Starmerella gilliamiae has a wide geographical distribution having been isolated in flowers from Brazil and Chile, fruit from Argentina and a bumblebee from Canada.

Barriers to research in family medicine-interviews with Portuguese family physician researchers.

BACKGROUND: There is a need for a deeper understanding of the barriers to research in family medicine (FM) and to consider the perceptions and perspectives of professionals. Our study aims to provide a strategic view for research capacity building in FM. We included the perspective of family physician researchers (FPR) on the existing barriers to investigation in this context. OBJECTIVES: To understand and characterize the barriers to research in FM (personal and structural), from the perspective of Portuguese family physicians who are researchers. METHODS: A qualitative study, of phenomenological nature, was performed, through the conduction of semi-structured interviews with FPR, from 2019 to 2022. Data analysis and thematic coding were done on MAxQDA®, with inductive and deductive approaches, until data saturation was reached. RESULTS: A total of 12 family physicians/researchers were interviewed. Seven main themes were identified as barriers to research: time, professional valorization, funding, ethics committees, infrastructure, management/institutions, and participants. Each theme is divided into subthemes that make it possible to assess how a barrier can affect researchers in performing research activities. CONCLUSION: Our study highlights the identification of 7 main barriers. Structuring them into sub-themes not only improved the organization of our results but also provided robust support for the next phase, namely the application of a survey with the aim of gaining a deeper insight into the repercussions that these barriers to FPR have at a national level. This research is crucial to laying the foundations for a policy document that offers well-defined and tailored recommendations to address the barriers we have uncovered.

Oxysomatium brevispiculum n. sp. (Nematoda: Cosmocercidae) from Amphisbaena alba Linnaeus (Squamata, Amphisbaenidae) in the Cerrado Biome from Brazil.

In the present study, we describe Oxysomatium brevispiculum n. sp. (Ascaridida: Cosmocercidae) parasitizing Amphisbaena alba Linnaeus (Squamata: Amphisbaenidae) in the municipality of Uberlândia, Cerrado Biome, Minas Gerais, Brazil. Oxysomatium brevispiculum n. sp. differs from its congeners by having shorter spicules and by the number and arrangement of caudal papillae. The males of the new species have a precloacal unpaired papilla and can be easily distinguished from O. caucasicum in which this morphological trait is absent. Oxysomatium brevispiculum n. sp. differs from the other three species of the genus by the number and arrangement of caudal papillae, with 13 pairs + 1 unpaired precloacal papilla, arrangement 8+1:2:3, while O. brevicaudatum has 14-16 pairs +1 unpaired papilla, and 7-9+1:1:6 arrangement, O. petrolinensis has 16 pairs +1 unpaired papilla, and 8+1:1:7 arrangement, and O. dollfusi with 15-16 pairs +1 unpaired papilla, and 8-9+1:1:6 arrangement. Oxysomatium brevispiculum n. sp. is the fifth species of this genus, the second species in a Neotropical host, and the first species of this genus described in amphisbaenid hosts. In addition, the present study provides an identification key for the species of this genus.

Yeasts from tropical forests: Biodiversity, ecological interactions, and as sources of bioinnovation.

Tropical rainforests and related biomes are found in Asia, Australia, Africa, Central and South America, Mexico, and many Pacific Islands. These biomes encompass less than 20% of Earth's terrestrial area, may contain about 50% of the planet's biodiversity, and are endangered regions vulnerable to deforestation. Tropical rainforests have a great diversity of substrates that can be colonized by yeasts. These unicellular fungi contribute to the recycling of organic matter, may serve as a food source for other organisms, or have ecological interactions that benefit or harm plants, animals, and other fungi. In this review, we summarize the most important studies of yeast biodiversity carried out in these biomes, as well as new data, and discuss the ecology of yeast genera frequently isolated from tropical forests and the potential of these microorganisms as a source of bioinnovation. We show that tropical forest biomes represent a tremendous source of new yeast species. Although many studies, most using culture-dependent methods, have already been carried out in Central America, South America, and Asia, the tropical forest biomes of Africa and Australasia remain an underexplored source of novel yeasts. We hope that this review will encourage new researchers to study yeasts in unexplored tropical forest habitats.

Clinical Characterization of Congenital Anophthalmic and Microphthalmic Cavities in Inidviduals With Craniofacial Anomalies.

OBJECTIVE: Measure the frequency of anophthalmic and microphthalmic patients with craniofacial anomalies (FCAs). DESIGN: Descriptive, cross-sectional, retrospective study. SETTING: Hospital for Rehabilitation of Craniofacial Anomalies of the University of São Paulo (HRAC-USP). The medical records of patients treated at HRAC from 2000 to 2012 with a diagnosis of congenital anophthalmia or microphthalmia were examined. Patients were excluded for secondary anophthalmia, incomplete medical records, or information that could not be accessed. OUTCOME MEASURES: Frequency of anophthalmia and microphthalmia; the proportions and diagnoses of associated FCAs; impairment of ocular appendages; extracranial or facial anomalies; genetic alterations; and surgical approach. RESULTS: A total of 56 patients had anophthalmia (52.3%), 35 had microphthalmia (32.7%), and 16 patients had both (15%). Individuals with FCAs associated with microphthalmia, anophthalmia, or both totaled 74, corresponding to 69.2%. Anophthalmia was more likely than microphthalmia to be accompanied by FCAs, at 76.4% of patients ( P < 0.05). Cleft lip and palate were the main malformations associated with anophthalmia (23.64%), with microphthalmia (45%), and with both (44.44%). Reconstructive surgery was done in 63.6% of cases. The ocular attachments were compromised in 71% of cases. Extracraniofacial malformations were found in 9.3% of patients. Only 7 records contained karyotypes, and no changes directly related to anophthalmia or microphthalmia were found. CONCLUSION: Anophthalmia is more frequent than microphthalmia and is more often accompanied by FCA. Cleft lip and cleft palate are the most frequent concomitant malformations.

White wine grape pomace as a suitable carbon source for lipid and carotenoid production by fructophilic Rhodorotula babjevae.

AIM: We aim to explore the non-structural sugars from white wine grape pomace (WWGP) as the input carbon source for the co-production of multiple high-value products by the non-fastidious yeast Rhodotorula babjevae to create a sustainable and economically appealing process. METHODS AND RESULTS: Water extraction of unfermented, soluble sugars from WWGP yielded extracts with similar amounts of glucose and fructose, which were used to prepare a growth medium. Rhodorotula babjevae multiplied as fast on WWGP-based medium as on a reference medium but achieved higher cell dry weight (CDW) and lower intracellular triacylglycerol accumulation (22.5% vs. 28.6%) in WWGP-based medium. In addition, R. babjevae produced mannitol and arabitol and carotenoids and secreted polyol esters of fatty acids, a rare type of glycolipid as confirmed by Fourier transform-infrared, nuclear magnetic resonance and high-performance liquid chromatography analyses. Remarkably, R. babjevae consumed simultaneously both fructose and glucose when on WWGP-based medium and left glucose practically untouched in the reference medium, evidencing a fructophilic character. CONCLUSIONS: Rhodorotula babjevae, a metabolic versatile yeast, proliferated on a minimally processed extract and successfully converted glucose and fructose into high-value products. SIGNIFICANCE AND IMPACT OF STUDY: Different chemicals with market potential can be produced through the valorization of abundant waste feedstocks generated by the wine industry to which R. babjevae can contribute.

Multilayered horizontal operon transfers from bacteria reconstruct a thiamine salvage pathway in yeasts.

Horizontal acquisition of bacterial genes is presently recognized as an important contribution to the adaptation and evolution of eukaryotic genomes. However, the mechanisms underlying expression and consequent selection and fixation of the prokaryotic genes in the new eukaryotic setting are largely unknown. Here we show that genes composing the pathway for the synthesis of the essential vitamin B1 (thiamine) were lost in an ancestor of a yeast lineage, the Wickerhamiella/Starmerella (W/S) clade, known to harbor an unusually large number of genes of alien origin. The thiamine pathway was subsequently reassembled, at least twice, by multiple HGT events from different bacterial donors involving both single genes and entire operons. In the W/S-clade species Starmerella bombicola we obtained direct genetic evidence that all bacterial genes of the thiamine pathway are functional. The reconstructed pathway is composed by yeast and bacterial genes operating coordinately to scavenge thiamine derivatives from the environment. The adaptation of the newly acquired operons to the eukaryotic setting involved a repertoire of mechanisms until now only sparsely documented, namely longer intergenic regions, post-horizontal gene transfer (HGT) gene fusions fostering coordinated expression, gene relocation, and possibly recombination generating mosaic genes. The results provide additional evidence that HGT occurred recurrently in this yeast lineage and was crucial for the reestablishment of lost functions and that similar mechanisms are used across a broad range of eukaryotic microbes to promote adaptation of prokaryotic genes to their new environment.

Improving the quality of organic compost of sewage sludge using grass cultivation followed by composting.

Composting is one of the main processes of stabilization of sewage sludge and its association with cultivation in this residue has a great potential to produce stabilized organic fertilizer and, or substrate for plant development. The aim of this work was to evaluate the physical, chemical, and microbial attributes of sewage sludge (SS) aerated and cultivated with Pennisetum purpureum or Urochloa brizantha and, later, composted. The study was installed in a 2x2+2 factorial scheme, with four replications. The factors consisted of cultivation of P. purpureum or U. brizantha in SS for 90 days, with or without intermittent aeration for 60 days. The control treatments were SS without cultivation, with the presence or absence of aeration. After 90 days of cultivation, the grass was cut, crushed, and incorporated into the SS for composting for 60 days. The composted sewage sludge showed an increase of 26, 24, 17, 123, 19, 32, and 7.7% in the levels of P, Ca, Cu, Fe, Mn, Zn, and Pb; and a reduction of 22, 5.2, 26, 30, 8.8, and 70% in the levels of C, N, K, Mg, Ni, and Na, respectively. The levels of Cu, Ni, Zn, and Pb remained below the maximum limit allowed by environmental resolution. The degradation of SS decreased the particle diameter, increasing the bulk density and total porosity, improving the physical properties of the compost. The SS cultivation and composting, regardless of the grass, led to a reduction in pH, basal and accumulated respiration, nitrification index, and C/N ratio and an increase in the CEC/C ratio, showing adequate maturation of the compost produced. Thus, the SS cultivation and composting with grasses were effective for producing matured and quality organic compost with low risk of environmental contamination.

Impact of Hemorrhagic Stroke on Molar Bite Force: A Prospective Study.

Stroke is a neurological deficit of cerebrovascular origin that promotes physical impairments of adult individuals. The present study is aimed to demonstrate whether hemorrhagic stroke affects the maximum molar bite force. The prospective study carried in Centro Universitario Claretiano de Batatais, Brazil, determined the distribution of the sample into two groups: hemorrhagic stroke group (n=18, median age, 62.5 years) and disease-free group (n=18, median age, 62.0 years), with 10 men and 8 women in each group. Subjects were paired one-to-one (age and body mass index). The dynamometer was used to measure the maximum molar bite force (right and left). All analyses were performed with a significance level of 5% (Student's t-test). Differences were found on the right (p=0.048) and left (p=0.042) molar bite force, with lower bite force (both sides) in hemorrhagic stroke group. The study suggests that hemorrhagic stroke negatively affects the maximum molar bite force and necessitates changes in food intake to nutritious and softer consistency foods.

Evaluation of overtime phenotypic variation of yeasts in chronic vulvovaginal candidosis cases.

Chronic vulvovaginal candidosis results either from reinfection or from the ability of Candida spp. to persist in the vulva and/or vagina. Persistence is usually associated with increased antifungal (mainly azoles) resistance rates, which can explain treatment failure, and/or increased expression of virulence factors by Candida spp. The aim of this study was to assess the mechanisms leading to Candida spp persistence, by studying sequential isolates from women with chronic vulvovaginal candidosis, focusing on strains genotypes, azole resistance, and ability to form biofilms along the period of clinical evaluation. The strains were identified at species level by automated analysis of biochemical profiles and molecular typing evaluated by polymorphic DNA analysis. The capacity to form biofilm was assessed with a microtiter plate assay. Fluconazole susceptibility was determined by the microdilution broth assay at both pH 7 (following the recommended guideline) and pH 4.5 (as representative of vaginal pH). We studied samples from 17 clinically recurrent cases. In 53% of the chronic cases there were two or more isolates that had a phylogenetic relationship while the remaining (47%) were caused by different species. In those cases where related strains were involved in recurrence, we verified an increase in MIC at pH 7 and also an increased capacity to form biofilms over time. Significant correlation between these two parameters was observed only in cases caused by C. glabrata, evidencing the importance of these two factors to enhance persistence in the vaginal mucosa for this particular species.

Chronic vulvovaginal candidosis (VVC) affects millions of women worldwide. We found that persistence of the same Candida strain on the vaginal mucosa does not account for the great majority of VVC cases. Moreover, modulation of biofilm formation and azole resistance overtime was investigated.

Virulence Factors as Promoters of Chronic Vulvovaginal Candidosis: A Review.

INTRODUCTION: The vast majority of the species of the genus Candida spp. is commensal in humans; however, some are opportunistic pathogens that can cause infection, called candidosis. Among the different types of candidosis, we highlight the vulvovaginal (VVC) which can occur in two main clinical variants: chronic (cVVC) and episodic or sporadic. The incidence of cVVC has been worrying the scientific community, promoting the research on genotypic and phenotypic causes of its occurrence. We summarize important findings on factors that favor chronic vulvovaginal candidosis with respect to molecular epidemiology and the expression of various virulence factors, while clarifying the terminology involving these infections. AIM AND METHODOLOGY: The aim of this review was to gather research that linked virulence factors to VVC and its persistence and recurrence, using two databases (Pubmed and Google Scholar). Predisposing factors in women for the occurrence of cVVC and some studies that refer new preventive and alternative therapies were also included, where appropriate. RESULTS AND DISCUSSION: Several studies have been shedding light on the increasing number of persistence and recurrences of VVC. The expression of virulence factors has been related to both chronic forms of VVC and antifungal resistance. Other studies report mutations occurring in the genome of Candida spp. during the infection phase which may be important indications for new therapies. The introduction of preventive therapies and new therapies has revealed great importance and is also highlighted here.

In Vitro and In Vivo Effects of SerpinA1 on the Modulation of Transthyretin Proteolysis.

Transthyretin (TTR) proteolysis has been recognized as a complementary mechanism contributing to transthyretin-related amyloidosis (ATTR amyloidosis). Accordingly, amyloid deposits can be composed mainly of full-length TTR or contain a mixture of both cleaved and full-length TTR, particularly in the heart. The fragmentation pattern at Lys48 suggests the involvement of a serine protease, such as plasmin. The most common TTR variant, TTR V30M, is susceptible to plasmin-mediated proteolysis, and the presence of TTR fragments facilitates TTR amyloidogenesis. Recent studies revealed that the serine protease inhibitor, SerpinA1, was differentially expressed in hepatocyte-like cells (HLCs) from ATTR patients. In this work, we evaluated the effects of SerpinA1 on in vitro and in vivo modulation of TTR V30M proteolysis, aggregation, and deposition. We found that plasmin-mediated TTR proteolysis and aggregation are partially inhibited by SerpinA1. Furthermore, in vivo downregulation of SerpinA1 increased TTR levels in mice plasma and deposition in the cardiac tissue of older animals. The presence of TTR fragments was observed in the heart of young and old mice but not in other tissues following SerpinA1 knockdown. Increased proteolytic activity, particularly plasmin activity, was detected in mice plasmas. Overall, our results indicate that SerpinA1 modulates TTR proteolysis and aggregation in vitro and in vivo.

The Wickerhamiella/Starmerella clade-A treasure trove for the study of the evolution of yeast metabolism.

The Wickerhamiella and Starmerella genera form a clade (W/S clade) that branches close to Yarrowia lipolytica in the Saccharomycotina species tree. It comprises approximately 90 recognized species and 50 putative new species not formally described yet. The large majority of the members of the W/S clade are ecologically associated with flowers and floricolous insects. Many species exhibit unusual metabolic traits, like fructophily and the production of sophorolipids, which are glycolipids that can be used as environmentally friendly biosurfactants. Genomic data have not only firmly established the W/S clade but have also revealed a tumultuous evolution of metabolism marked by losses and gains of important metabolic pathways, among which alcoholic fermentation. Possibly the most surprising finding brought to light by comparative genomics concerned the large number of genes acquired by some species of the W/S clade from bacteria through horizontal gene transfer, many of which were shown to be functional in their new setting. This was facilitated by the genetic tractability of one species in the clade, Starmerella bombicola, which is used for the industrial production of sophorolipids. We suggest that high-density coverage of genome sequencing in this clade, combined with the possibility to conduct molecular genetics experiments in at least one species, has the potential to set the stage for yet more exciting discoveries concerning the evolution of yeast metabolism.

Recurrent vulvovaginal Candida spp isolates phenotypically express less virulence traits.

OBJECTIVE: Vulvovaginal candidosis (VVC) is a condition that impacts the quality of life of women worldwide. At least 5-8% of all VVC cases re-occur. Recurrent vulvovaginal candidosis (RVVC) can be defined as the occurrence of a VVC episode at least four times per year. The reasons for recurrence to occur are poorly understood. This work aims to identify key phenotypic traits associated with RVVC Candida spp. isolates that might be used to plan strategies to control RVVC. METHODS: The capacity to form biofilms (with the microtitration plate assay), to develop germinative tube in the presence of fetal bovine serum and to produce phospholipase (in the egg-yolk plate assay) was assessed for a collection of Candida spp. isolates obtained from 17 women diagnosed with RVVC and 16 women with non-recurrent VVC (VVC). The differences obtained regarding the proportion of isolates expressing each virulence factor was assessed by statistical analysis (χ2). RESULTS: We found that C. albicans isolates had a higher ability to form germinative tubes than RVVC isolates (29% vs 4%, p < 0.05). In addition, the ability of Candida spp. isolates to form biofilm (63% vs 51%) and to produce phospholipase (13% vs 11%) was also higher, though not statistically different (p > 0.05). CONCLUSIONS: We conclude that biofilm formation and phenotypic-switching associated with germinative tube production are particularly important C. albicans virulence factors for acute, sporadic VVC cases.

Genetic Dissection of Sexual Reproduction in a Primary Homothallic Basidiomycete.

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.

Stepwise Functional Evolution in a Fungal Sugar Transporter Family.

Sugar transport is of the utmost importance for most cells and is central to a wide range of applied fields. However, despite the straightforward in silico assignment of many novel transporters, including sugar porters, to existing families, their exact biological role and evolutionary trajectory often remain unclear, mainly because biochemical characterization of membrane proteins is inherently challenging, but also owing to their uncommonly turbulent evolutionary histories. In addition, many important shifts in membrane carrier function are apparently ancient, which further limits our ability to reconstruct evolutionary trajectories in a reliable manner. Here, we circumvented some of these obstacles by examining the relatively recent emergence of a unique family of fungal sugar facilitators, related to drug antiporters. The former transporters, named Ffz, were previously shown to be required for fructophilic metabolism in yeasts. We first exploited the wealth of fungal genomic data available to define a comprehensive but well-delimited family of Ffz-like transporters, showing that they are only present in Dikarya. Subsequently, a combination of phylogenetic analyses and in vivo functional characterization was used to retrace important changes in function, while highlighting the evolutionary events that are most likely to have determined extant distribution of the gene, such as horizontal gene transfers (HGTs). One such HGT event is proposed to have set the stage for the onset of fructophilic metabolism in yeasts, a trait that according to our results may be the metabolic hallmark of close to 100 yeast species that thrive in sugar rich environments.

Adaptive divergence in wine yeasts and their wild relatives suggests a prominent role for introgressions and rapid evolution at noncoding sites.

In Saccharomyces cerevisiae, the main yeast in wine fermentation, the opportunity to examine divergence at the molecular level between a domesticated lineage and its wild counterpart arose recently due to the identification of the closest relatives of wine strains, a wild population associated with Mediterranean oaks. As genomic data are available for a considerable number of representatives belonging to both groups, we used population genomics to estimate the degree and distribution of nucleotide variation between wine yeasts and their closest wild relatives. We found widespread genomewide divergence, particularly at noncoding sites, which, together with above average divergence in trans-acting DNA binding proteins, may suggest an important role for divergence at the level of transcriptional regulation. Nine outlier regions putatively under strong divergent selection were highlighted by a genomewide scan under stringent conditions. Several cases of introgressions, originating in the sibling species Saccharomyces paradoxus, were also identified in the Mediterranean oak population. FZF1 and SSU1, mostly known for conferring sulphite resistance in wine yeasts, were among the introgressed genes, although not fixed. Because the introgressions detected in our study are not found in wine strains, we hypothesize that ongoing divergent ecological selection segregates the two forms between the different niches. Together, our results provide a first insight into the extent and kind of divergence between wine yeasts and their closest wild relatives.

Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma.

BACKGROUND: The class Tremellomycete (Agaricomycotina) encompasses more than 380 fungi. Although there are a few edible Tremella spp., the only species with current biotechnological use is the astaxanthin-producing yeast Phaffia rhodozyma (Cystofilobasidiales). Besides astaxanthin, a carotenoid pigment with potent antioxidant activity and great value for aquaculture and pharmaceutical industries, P. rhodozyma possesses multiple exceptional traits of fundamental and applied interest. The aim of this study was to obtain, and analyze two new genome sequences of representative strains from the northern (CBS 7918T, the type strain) and southern hemispheres (CRUB 1149) and compre them to a previously published genome sequence (strain CBS 6938). Photoprotection and antioxidant related genes, as well as genes involved in sexual reproduction were analyzed. RESULTS: Both genomes had ca. 19 Mb and 6000 protein coding genes, similar to CBS 6938. Compared to other fungal genomes P. rhodozyma strains and other Cystofilobasidiales have the highest number of intron-containing genes and highest number of introns per gene. The Patagonian strain showed 4.4 % of nucleotide sequence divergence compared to the European strains which differed from each other by only 0.073 %. All known genes related to the synthesis of astaxanthin were annotated. A hitherto unknown gene cluster potentially responsible for photoprotection (mycosporines) was found in the newly sequenced P. rhodozyma strains but was absent in the non-mycosporinogenic strain CBS 6938. A broad battery of enzymes that act as scavengers of free radical oxygen species were detected, including catalases and superoxide dismutases (SODs). Additionally, genes involved in sexual reproduction were found and annotated. CONCLUSIONS: A draft genome sequence of the type strain of P. rhodozyma is now available, and comparison with that of the Patagonian population suggests the latter deserves to be assigned to a distinct variety. An unexpected genetic trait regarding high occurrence of introns in P. rhodozyma and other Cystofilobasidiales was revealed. New genomic insights into fungal homothallism were also provided. The genetic basis of several additional photoprotective and antioxidant strategies were described, indicating that P. rhodozyma is one of the fungi most well-equipped to cope with environmental oxidative stress, a factor that has probably contributed to shaping its genome.