Saccharomyces jurei sp. nov., isolation and genetic identification of a novel yeast species from Quercus robur.

Two strains, D5088T and D5095, representing a novel yeast species belonging to the genus Saccharomyces were isolated from oak tree bark and surrounding soil located at an altitude of 1000 m above sea level in Saint Auban, France. Sequence analyses of the internal transcribed spacer (ITS) region and 26S rRNA D1/D2 domains indicated that the two strains were most closely related to Saccharomyces mikatae and Saccharomyces paradoxus. Genetic hybridization analyses showed that both strains are reproductively isolated from all other Saccharomyces species and, therefore, represent a distinct biological species. The species name Saccharomyces jurei sp. nov. is proposed to accommodate these two strains, with D5088T (=CBS 14759T=NCYC 3947T) designated as the type strain.

Reconstructing (super)trees from data sets with missing distances: not all is lost.

The wealth of phylogenetic information accumulated over many decades of biological research, coupled with recent technological advances in molecular sequence generation, presents significant opportunities for researchers to investigate relationships across and within the kingdoms of life. However, to make best use of this data wealth, several problems must first be overcome. One key problem is finding effective strategies to deal with missing data. Here, we introduce Lasso, a novel heuristic approach for reconstructing rooted phylogenetic trees from distance matrices with missing values, for data sets where a molecular clock may be assumed. Contrary to other phylogenetic methods on partial data sets, Lasso possesses desirable properties such as its reconstructed trees being both unique and edge-weighted. These properties are achieved by Lasso restricting its leaf set to a large subset of all possible taxa, which in many practical situations is the entire taxa set. Furthermore, the Lasso approach is distance-based, rendering it very fast to run and suitable for data sets of all sizes, including large data sets such as those generated by modern Next Generation Sequencing technologies. To better understand the performance of Lasso, we assessed it by means of artificial and real biological data sets, showing its effectiveness in the presence of missing data. Furthermore, by formulating the supermatrix problem as a particular case of the missing data problem, we assessed Lasso's ability to reconstruct supertrees. We demonstrate that, although not specifically designed for such a purpose, Lasso performs better than or comparably with five leading supertree algorithms on a challenging biological data set. Finally, we make freely available a software implementation of Lasso so that researchers may, for the first time, perform both rooted tree and supertree reconstruction with branch lengths on their own partial data sets.

Yeast culture collections in the twenty-first century: new opportunities and challenges.

The twenty-first century has brought new opportunities and challenges to yeast culture collections, whether they are long-standing or recently established. Basic functions such as archiving, characterizing and distributing yeasts continue, but with expanded responsibilities and emerging opportunities. In addition to a number of well-known, large public repositories, there are dozens of smaller public collections that differ in the range of species and strains preserved, field of emphasis and services offered. Several collections have converted their catalogues to comprehensive databases and synchronize them continuously through public services, making it easier for users worldwide to locate a suitable source for specific yeast strains and the data associated with these yeasts. In-house research such as yeast taxonomy continues to be important at culture collections. Because yeast culture collections preserve a broad diversity of species and strains within a species, they are able to make discoveries in many other areas as well, such as biotechnology, functional, comparative and evolution genomics, bioprocesses and novel products. Due to the implementation of the Convention of Biological Diversity (CBD) and the Nagoya Protocol (NP), there are new requirements for both depositors and users to ensure that yeasts were collected following proper procedures and to guarantee that the country of origin will be considered if benefits arise from a yeast's utilization. Intellectual property rights (IPRs) are extremely relevant to the current access and benefit-sharing (ABS) mechanisms; most research and development involving genetic resources and associated traditional knowledge will be subject to this topic. Copyright © 2016 John Wiley & Sons, Ltd.

Apiotrichum terrigenum sp. nov., a soil-associated yeast found in both the UK and mainland Europe.

Five arthroconidium-producing yeast strains representing a novel Trichosporon-like species were independently isolated from the UK, Hungary and Norway. Two strains (Bio4T and Bio21) were isolated from biogas reactors used for processing grass silage, with a third strain (S8) was isolated from soil collected at the same UK site. Two additional strains were isolated in mainland Europe, one from soil in Norway (NCAIM Y.02175) and the other from sewage in Hungary (NCAIM Y.02176). Sequence analyses of the D1/D2 domains of the LSU rRNA gene and internal transcribed spacer (ITS) region indicated that the novel species belongs to the recently reinstated genus Apiotrichum and is most closely related to Apiotrichum scarabaeorum, a beetle-associated species first found in South Africa. Despite having similar physiological characteristics, the two species can be readily distinguished from one another by ITS sequencing. The species name Apiotrichum terrigenum sp. nov. is proposed to accommodate these strains, with Bio4T (=CBS 11373T=NCYC 3540T) designated as the type strain. The Mycobank deposit number is MB817431.

Investigating flavour characteristics of British ale yeasts: techniques, resources and opportunities for innovation.

Five British ale yeast strains were subjected to flavour profiling under brewery fermentation conditions in which all other brewing parameters were kept constant. Significant variation was observed in the timing and quantity of flavour-related chemicals produced. Genetic tests showed no evidence of hybrid origins in any of the strains, including one strain previously reported as a possible hybrid of Saccharomyces cerevisiae and S. bayanus. Variation maintained in historical S. cerevisiae ale yeast collections is highlighted as a potential source of novelty in innovative strain improvement for bioflavour production.

Ribosomal DNA sequence heterogeneity reflects intraspecies phylogenies and predicts genome structure in two contrasting yeast species.

The ribosomal RNA encapsulates a wealth of evolutionary information, including genetic variation that can be used to discriminate between organisms at a wide range of taxonomic levels. For example, the prokaryotic 16S rDNA sequence is very widely used both in phylogenetic studies and as a marker in metagenomic surveys and the internal transcribed spacer region, frequently used in plant phylogenetics, is now recognized as a fungal DNA barcode. However, this widespread use does not escape criticism, principally due to issues such as difficulties in classification of paralogous versus orthologous rDNA units and intragenomic variation, both of which may be significant barriers to accurate phylogenetic inference. We recently analyzed data sets from the Saccharomyces Genome Resequencing Project, characterizing rDNA sequence variation within multiple strains of the baker's yeast Saccharomyces cerevisiae and its nearest wild relative Saccharomyces paradoxus in unprecedented detail. Notably, both species possess single locus rDNA systems. Here, we use these new variation datasets to assess whether a more detailed characterization of the rDNA locus can alleviate the second of these phylogenetic issues, sequence heterogeneity, while controlling for the first. We demonstrate that a strong phylogenetic signal exists within both datasets and illustrate how they can be used, with existing methodology, to estimate intraspecies phylogenies of yeast strains consistent with those derived from whole-genome approaches. We also describe the use of partial Single Nucleotide Polymorphisms, a type of sequence variation found only in repetitive genomic regions, in identifying key evolutionary features such as genome hybridization events and show their consistency with whole-genome Structure analyses. We conclude that our approach can transform rDNA sequence heterogeneity from a problem to a useful source of evolutionary information, enabling the estimation of highly accurate phylogenies of closely related organisms, and discuss how it could be extended to future studies of multilocus rDNA systems. [concerted evolution; genome hydridisation; phylogenetic analysis; ribosomal DNA; whole genome sequencing; yeast].

Kazachstania yasuniensis sp. nov., an ascomycetous yeast species found in mainland Ecuador and on the Galápagos.

Seven strains representing a novel yeast species belonging to the genus Kazachstania were found at several collection sites on both mainland Ecuador (Yasuní National Park) and the Galápagos (Santa Cruz Island). Two strains (CLQCA 20-132(T) and CLQCA 24SC-045) were isolated from rotten wood samples, two further strains (CLQCA 20-280 and CLQCA 20-348) were isolated from soil samples, and three strains (CLQCA 20-198, CLQCA 20-374 and CLQCA 20-431) were isolated from decaying fruits. Sequence analyses of the D1/D2 domains of the LSU rRNA gene and ribosomal internal transcribed spacer (ITS) region indicated that the novel species is most closely related to Kazachstania servazzii and Kazachstania unispora. Although the strains could not be distinguished from one another based upon their differing geographical origins, they could be differentiated according to their isolation source (fruit, soil or wood) by ITS sequencing. The species name Kazachstania yasuniensis sp. nov. is proposed to accommodate these strains, with CLQCA 20-132(T) ( = CBS 13946(T) = NCYC 4008(T)) designated the type strain.

Population genomics of domestic and wild yeasts.

Since the completion of the genome sequence of Saccharomyces cerevisiae in 1996 (refs 1, 2), there has been a large increase in complete genome sequences, accompanied by great advances in our understanding of genome evolution. Although little is known about the natural and life histories of yeasts in the wild, there are an increasing number of studies looking at ecological and geographic distributions, population structure and sexual versus asexual reproduction. Less well understood at the whole genome level are the evolutionary processes acting within populations and species that lead to adaptation to different environments, phenotypic differences and reproductive isolation. Here we present one- to fourfold or more coverage of the genome sequences of over seventy isolates of the baker's yeast S. cerevisiae and its closest relative, Saccharomyces paradoxus. We examine variation in gene content, single nucleotide polymorphisms, nucleotide insertions and deletions, copy numbers and transposable elements. We find that phenotypic variation broadly correlates with global genome-wide phylogenetic relationships. S. paradoxus populations are well delineated along geographic boundaries, whereas the variation among worldwide S. cerevisiae isolates shows less differentiation and is comparable to a single S. paradoxus population. Rather than one or two domestication events leading to the extant baker's yeasts, the population structure of S. cerevisiae consists of a few well-defined, geographically isolated lineages and many different mosaics of these lineages, supporting the idea that human influence provided the opportunity for cross-breeding and production of new combinations of pre-existing variations.

Wickerhamomyces arborarius f.a., sp. nov., an ascomycetous yeast species found in arboreal habitats on three different continents.

Five strains representing a novel yeast species belonging to the genus Wickerhamomyces were independently isolated from Ecuador, Taiwan and the USA. One strain (CLQCA 10-161(T)) was isolated from the white flower of an unidentified plant species collected in the Maquipucuna cloud forest reserve, near Quito, in Ecuador. A second strain (GY7L12) was isolated from the leaf of a Chinese sumac or nutgall tree (Rhus chinensis 'roxburghiana') collected in the Taoyuan mountain area, Kachsiung, in Taiwan. Three additional strains (A543, A546 and A563) were isolated from two species of wood-boring beetle (Xyleborus glabratus and Xyleborinus saxeseni) collected near Clyo, Georgia, USA. Analysis of the D1/D2 domains of the LSU rRNA gene indicated that the novel species belongs to the genus Wickerhamomyces, and is most closely related to Wickerhamomyces sydowiorum, an insect-associated species predominantly found in South Africa. The North American and Taiwanese strains have identical internal transcribed spacer (ITS) sequences and can be distinguished from the Ecuadorian strain based on a single nucleotide substitution in the ITS1 region. The species name of Wickerhamomyces arborarius f.a., sp. nov. is proposed to accommodate these strains, with CLQCA 10-161(T) ( = CBS 12941(T) = NCYC 3743(T)) designated the type strain.

Candida ecuadorensis sp. nov., an ascomycetous yeast species found in two separate regions of Ecuador.

In the course of an on-going study aimed at cataloguing the natural yeast biodiversity found in Ecuador, two strains (CLQCA 13-025 and CLQCA 20-004(T)) were isolated from samples of cow manure and rotten wood collected in two separate provinces of the country (Orellana and Bolívar). These strains were found to represent a novel yeast species based on the sequences of their D1/D2 domain of the large-subunit (LSU) rRNA gene and their physiological characteristics. Phylogenetic analysis based on LSU D1/D2 sequences revealed this novel species to belong to the Metschnikowia clade and to be most closely related to Candida suratensis, a species recently discovered in a mangrove forest in Thailand. The species name of Candida ecuadorensis sp. nov. is proposed to accommodate these strains, with strain CLQCA 20-004(T) (=CBS 12653(T) = NCYC 3782(T)) designated as the type strain.

TURNIP: tracking unresolved nucleotide polymorphisms in large hard-to-assemble regions of repetitive DNA sequence.

UNLABELLED: TURNIP comprises a suite of Perl scripts and modules that facilitates the resolution of microheterogeneity within hard-to-assemble repetitive DNA sequences. TURNIP was originally developed for the Saccharomyces Genome Resequencing Project (SGRP) within which the ribosomal DNA (rDNA) of 36 strains of S.cerevisiae were analysed to investigate the occurrence of potential polymorphisms. Here, 'partially resolved SNPs', or pSNPs, as well as indels, were found to be far more prevalent than previously suspected. More generally, the TURNIP software ascertains degrees of variation between large tandem repeats within a single locus, offering insights into mechanisms of genome stability and gene conversion in any organism for which genome sequence data are available. AVAILABILITY: The TURNIP source code, results files and online help are available at http://www.ncyc.co.uk/software/turnip.html.

Saturnispora quitensis sp. nov., a yeast species isolated from the Maquipucuna cloud forest reserve in Ecuador.

A single strain, CLQCA-10-114(T), representing a novel yeast species belonging to the genus Saturnispora was isolated from the fruit of an unidentified species of bramble (Rubus sp.), collected from the Maquipucuna cloud forest reserve, near Quito, in Ecuador. Sequence analyses of the D1/D2 domains of the large-subunit rRNA gene and ribosomal internal transcribed spacer region indicated that the novel species is most closely related to the recently described species Saturnispora gosingensis, isolated from the fruiting body of a mushroom collected in Taiwan, and Saturnispora hagleri, a Drosophila-associated yeast found in Brazil. The name Saturnispora quitensis sp. nov. is proposed to accommodate this strain; the type strain is CLQCA-10-114(T) (=CBS 12184(T)=NCYC 3744(T)).

Candida northwykensis sp. nov., a novel yeast isolated from the gut of the click beetle Melanotus villosus.

Two yeast morphotypes, BET 4(T) and BET 7, were isolated from the gut of click beetle Melanotus villosus. Click beetles were collected from the decaying timber within the woodlands of North Wyke Research, South West England, UK (latitude, 50°46'29″N; longitude, 3°55'23″W). Morphotype BET 7 was identified as Debaryomyces hansenii, and the other morphotype, BET 4(T), was found to differ from Priceomyces castillae and Priceomyces haplophilus, its closest phylogenetic neighbours, by 5.0% with respect to the nucleotide sequence of the D1/D2 domain of the large-subunit (LSU) rRNA gene, and by 8.0% with respect to the ribosomal internal-transcribed spacer (ITS) region. BET 4(T) also differ from P. castillae and P. haplophilus in a number of different phenotypic characteristics. Thus, based on the unique nucleotide sequences of its D1/D2 domain and ITS region, its physiological characteristics and an inability to sporulate, strain BET 4(T) is assigned the status of a new species of Candida, for which the name Candida northwykensis sp. nov., is proposed. The type strain is BET 4(T) (NCYC 3525(T) = CBS 11370(T)).

The yin and yang of yeast: biodiversity research and systems biology as complementary forces driving innovation in biotechnology.

The aim of this article is to review how yeast has contributed to contemporary biotechnology and to seek underlying principles relevant to its future exploitation for human benefit. Recent advances in systems biology combined with new knowledge of genome diversity promise to make yeast the eukaryotic workhorse of choice for production of everything from probiotics and pharmaceuticals to fuels and chemicals. The ability to engineer new capabilities through introduction of controlled diversity based on a complete understanding of genome complexity and metabolic flux is key. Here, we briefly summarise the history that has led to these apparently simple organisms being employed in such a broad range of commercial applications. Subsequently, we discuss the likely consequences of current yeast research for the future of biotechnological innovation.

Cryptococcus shivajii sp. nov.: a novel basidiomycetous yeast isolated from biogas reactor.

Five yeast morphotypes were isolated from biogas reactors at North Wyke Research, Okehampton, UK. Out of the five morphotypes, four were identified as known species. In contrast, the fifth morphotype strain, Bio10(T), was found to differ from Bullera dendrophila and Kwoniella mangroviensis, its closest phylogenetic neighbours, by 2.6-2.9% with respect to the nucleotide sequence of the D1/D2 domain of the 26S rRNA gene and by 5.6-6.2% with respect to the internal transcribed spacer 1 (ITS1)-5.8S rRNA gene-ITS2 region. Bio10(T) also differs from these two species by a number of phenotypic characteristics. Thus, based on the phenotypic differences and phylogenetic analysis, strain Bio10(T) is assigned the status of a new species of Cryptococcus, for which the name Cryptococcus shivajii sp. nov. is proposed. The type strain is Bio10(T) (NCYC 3541(T) = CBS 11374(T)).

Candida carvajalis sp. nov., an ascomycetous yeast species from the Ecuadorian Amazon jungle.

In the course of a yeast biodiversity survey of different ecological habitats found in Ecuador, two yeast strains (CLQCA 20-011(T) and CLQCA20-014) were isolated from samples of rotten wood and fallen leaf debris collected at separate sites in the central region of the Ecuadorian Amazonia. These strains were found to represent a novel yeast species based on the sequences of their D1/D2 domain of the large-subunit (LSU) rRNA gene and their physiological characteristics. Phylogenetic analysis based on LSU D1/D2 sequences revealed this novel species to be most closely related to Candida asparagi, Candida fructus, Candida musae and two as yet undescribed Candida species, with the six yeast taxa collectively forming a distinct species group within the Clavispora clade. The species name of Candida carvajalis sp. nov. is proposed to accommodate these strains, with CLQCA 20-011(T) (NCYC 3509(T), CBS 11361(T)) designated as the type strain.

Diverse Lineages of Candida albicans Live on Old Oaks.

The human pathogen Candida albicans is considered an obligate commensal of animals, yet it is occasionally isolated from trees, shrubs, and grass. We generated genome sequence data for three strains of C. albicans that we isolated from oak trees in an ancient wood pasture, and compared these to the genomes of over 200 clinical strains. C. albicans strains from oak are similar to clinical C. albicans in that they are predominantly diploid and can become homozygous at the mating locus through whole-chromosome loss of heterozygosity. Oak strains differed from clinical strains in showing slightly higher levels of heterozygosity genome-wide. Using phylogenomic analyses and in silico chromosome painting, we show that each oak strain is more closely related to strains from humans and other animals than to strains from other oaks. The high genetic diversity of C. albicans from old oaks shows that they can live in this environment for extended periods of time.

MPP: a microarray-to-phylogeny pipeline for analysis of gene and marker content datasets.

UNLABELLED: MPP is a Java application, encompassing both new and established algorithms, for the analysis of gene and marker content datasets arising from high-throughput microarray techniques. MPP analyses flat file output from microarray experiments to determine the probability of the presence or absence of genes or markers within a genome. MPP can construct gene or marker content datasets for a number of genomes and can use the data to estimate an evolutionary tree or network. Results from gene content analyses may be validated by comparing them to known gene contents. MPP was initially developed to analyse data derived from comparative genome hybridization (CGH) microarray experiments in fungi and bacteria. It has recently been adapted to analyse retrotransposon-based insertion polymorphism (RBIP) marker scores derived from tagged microarray marker (TAM) experiments in pea. New analytical procedures may be added easily to MPP as plugins in order to increase the scope of the software. AVAILABILITY: MPP source code, executables and online help are available at http://cbr.jic.ac.uk/dicks/software/

Relatedness of medically important strains of Saccharomyces cerevisiae as revealed by phylogenetics and metabolomics.

Ten medically important Saccharomyces strains, comprising six clinical isolates of Saccharomyces cerevisiae and four probiotic strains of Saccharomyces boulardii, were characterized at the genetic and metabolic level and compared with non-medical, commercial yeast strains used in baking and wine-making. Strains were compared by genetic fingerprinting using amplified fragment length polymorphism (AFLP) analysis, by ribosomal DNA ITS1 sequencing and by metabolic footprinting using both direct injection mass spectrometry (DIMS) and gas chromatography-time of flight-mass spectrometry (GC-ToF-MS). Overall, the clinical isolates fell into different groupings when compared with the non-medical strains, with good but not perfect correlation amongst strains at both the genetic and metabolic levels. Probiotic strains of S. boulardii that are used therapeutically to treat human gastro-intestinal tract disorders showed tight clustering both genetically and metabolically. Metabolomics was found to be of value both as a taxonomic tool and as a means to investigate anomalous links between genotype and phenotype. Key discriminatory metabolites were identified when comparing the three main groups of clinical, probiotic and non-medical strains and included molecules such as trehalose, myo-inositol, lactic acid, fumaric acid and glycerol 3-phosphate. This study confirmed the link between a subset of clinical isolates and baking or probiotic strains but also highlighted that in general the clinical strains were more diverse at both the genomic and metabolic levels.

Species-specific variation in efficacy of yeast genomic DNA isolation techniques assessed using amplified fragment length polymorphism.

Methods for isolating genomic DNA from yeasts are optimized for strains of Saccharomyces cerevisiae. The DNeasy tissue kit proved to be effective with 65 additional yeast species, providing 0.1 to 4.7 microg DNA/ml culture with sufficient purity to give reproducible amplified fragment length polymorphism (AFLP) profiles, but was unsuccessful with 13 other species. Two alternative yeast DNA purification kits, MasterPure and Y-DER, were effective with 6 of these and 2 additional species, leaving only 9 species that remained recalcitrant to yielding sufficient amounts of DNA with the required purity.