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Serge Casaregola - One of the best experts on this subject based on the ideXlab platform.
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Large biodiversity of yeasts in French Guiana and the description of Suhomyces coccinellae f.a. sp. nov. and Suhomyces faveliae f.a. sp. nov.
International Journal of Systematic and Evolutionary Microbiology, 2019Co-Authors: Noemie Jacques, Serge CasaregolaAbstract:The extent of the diversity of yeasts in tropical rain forest and different environments from French Guiana was investigated. A total of 365 samples were collected from various substrates, such as plants, fruits and insects, at 13 locations, yielding 276 pure yeast isolates. Sequence analysis of the D1/D2 domains of the large subunit rRNA gene indicated that 210 isolates out of 276 belonged to 82 described species (67 Saccharomycotina, 14 Basidiomycota and 1 Pezizomycotina). In addition to these, a total of 54 Saccharomycotina isolates could not be assigned to a known species. These belonged to 14 genera and should be studied further from a taxonomic point of view. In addition, among the 43 Basidiomycotina isolates found, 12 could not be assigned to a known species. This report shows an unexpected biodiversity and indicates that oversea territories, such as French Guiana, constitute a largely unexplored reservoir for yeast diversity. Two Saccharomycotina strains, CLIB 1706 and CLIB 1725, isolated from an insect and from a fern respectively, were characterized further and were shown to belong to the Suhomyces clade on the basis of the rDNA sequence comparison. CLIB 1706TrDNA sequences showed nine substitutions and three indels out of 556 bp (D1/D2 domains) and 32 substitutions and 12 indels out of 380 bp [internal transcribed spacer (ITS)] with that of the most closely related species Suhomyces guaymorum CBS 9823T. CLIB 1725T rDNA sequences presented 18 substitutions and one indel out of 549 bp (D1/D2 domains) and 48 substitutions and 11 indels out of 398 bp (ITS) with that of its closest relative Suhomyces vadensis CBS 9454T. Two novel species of the genus Suhomyces were described to accommodate these two strains: Suhomyces coccinellae f.a. sp. nov. (CLIB 1706T=CBS 14298T) and Suhomyces faveliae f.a. sp. nov. (CLIB 1725T=CBS 14299T).
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Lipids containing medium-chain fatty acids are specific to post-whole genome duplication Saccharomycotina yeasts
BMC Evolutionary Biology, 2015Co-Authors: Marine Froissard, Michel Canonge, Marie Pouteaux, Bernard Cintrat, Sabrina Mohand-Oumoussa, Noemie Jacques, Stéphane E. Guillouet, Thierry Chardot, Serge CasaregolaAbstract:Background Yeasts belonging to the subphylum Saccharomycotina have been used for centuries in food processing and, more recently, biotechnology. Over the past few decades, these yeasts have also been studied in the interest of their potential to produce oil to replace fossil resources. Developing yeasts for massive oil production requires increasing yield and modifying the profiles of the fatty acids contained in the oil to satisfy specific technical requirements. For example, derivatives of medium-chain fatty acids (MCFAs, containing 6–14 carbons) are used for the production of biodiesels, cleaning products, lubricants and cosmetics. Few studies are available in the literature on the production of MCFAs in yeasts.
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Lipids containing medium-chain fatty acids are specific to post-whole genome duplication Saccharomycotina yeasts
BMC Evolutionary Biology, 2015Co-Authors: Marine Froissard, Michel Canonge, Marie Pouteaux, Bernard Cintrat, Sabrina Mohand-Oumoussa, Noemie Jacques, Stéphane E. Guillouet, Thierry Chardot, Serge CasaregolaAbstract:Background: Yeasts belonging to the subphylum Saccharomycotina have been used for centuries in food processing and, more recently, biotechnology. Over the past few decades, these yeasts have also been studied in the interest of their potential to produce oil to replace fossil resources. Developing yeasts for massive oil production requires increasing yield and modifying the profiles of the fatty acids contained in the oil to satisfy specific technical requirements. For example, derivatives of medium-chain fatty acids (MCFAs, containing 6-14 carbons) are used for the production of biodiesels, cleaning products, lubricants and cosmetics. Few studies are available in the literature on the production of MCFAs in yeasts. Results: We analyzed the MCFA content in Saccharomyces cerevisiae grown in various conditions. The results revealed that MCFAs preferentially accumulated when cells were grown on synthetic media with a high C/N ratio at low temperature (23 degrees C). Upon screening deletion mutant strains for genes encoding lipid droplet-associated proteins, we found two genes, LOA1 and TGL3, involved in MCFA homeostasis. A phylogenetic analysis on 16 Saccharomycotina species showed that fatty acid profiles differed drastically among yeasts. Interestingly, MCFAs are only present in post-whole genome duplication yeast species. Conclusions: In this study, we produced original data on fatty acid diversity in yeasts. We demonstrated that yeasts are amenable to genetic and metabolic engineering to increase their MCFA production. Furthermore, we revealed that yeast lipid biodiversity has not been fully explored, but that yeasts likely harbor as-yet-undiscovered strains or enzymes that can contribute to the production of high-value fatty acids for green chemistry.
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Transposable Elements and Their Activities in Y. lipolytica
Yarrowia lipolytica, 2013Co-Authors: Serge Casaregola, Gerold BarthAbstract:Y. lipolytica harbors an unusually diverse set of transposable elements among Saccharomycotina yeasts. Among them, members of both the families of transposons, retrotransposons as well as DNA transposons, are represented. Two of the LTR retrotransposons, Ylt1 and Tyl6, are members of the Ty3/gypsy group but have some uncommon features. Ylt1 is the largest hitherto detected fungal retrotransposon and is, in contrast to the other transposons, present in a high copy number of about 35 copies/haploid genome. Its proteins are encoded by a single ORF expressed under certain conditions resulting in transposition. Tyl6 is the only one retrotransposon among Saccharomycotina yeasts which displays a program −1 ribosomal frameshifting. The LINE-like element Ylli is also unique among Saccharomycotina yeasts and forms with the C. albicans counterparts Zorro 1,2,3 a new family. It belongs to the L1 clade, which also contains the human LINEs. Like these element, the large majority of the Ylli copies are 5′ truncated, the characteristics of Ylli being that its copies are very short. The detected DNA transposon Mutator of Y. lipolytica (Mutyl) shares some similarities with several MULE elements found mainly in plants and in fungi. It is the first described DNA transposon in Saccharomycotina yeasts and like many of its counterparts, it may have invaded its host through horizontal transfer.
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YeastIP: a database for identification and phylogeny of Saccharomycotina yeasts
FEMS Yeast Research, 2013Co-Authors: Stéphanie Weiss, Franck Samson, David Navarro, Serge CasaregolaAbstract:With the advances in sequencing techniques, identification of ascomycetous yeasts to the species level and phylogeny reconstruction increasingly require curated and updated taxonomic information. A specific database with nucleotide sequences of the most common markers used for yeast taxonomy and phylogeny and a user-friendly interface allowing identification, taxonomy and phylogeny of yeasts species was developed. By 1 September 2012, the YeastIP database contained all the described Saccharomycotina species for which sequences used for taxonomy and phylogeny, such as D1/D2 rDNA and ITS, are available. The database interface was developed to provide a maximum of relevant information and data mining tools, including the following features: (1) the blast n program for the sequences of the YeastIP database; (2) easy retrieval of selected sequences; (3) display of the available markers for each selected group of species; and (4) a tool to concatenate marker sequences, including those provided by the user. The concatenation tool allows phylogeny reconstruction through a direct link to the Phylogeny.fr platform. YeastIP is thus a unique database in that it provides taxonomic information and guides users in their taxonomic analyses. YeastIP facilitates multigenic analysis to encourage good practice in ascomycetous yeast phylogeny (URL: http://genome.jouy.inra.fr/yeastip.)
Geraldine Butler - One of the best experts on this subject based on the ideXlab platform.
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TPP riboswitch-dependent regulation of an ancient thiamin transporter in Candida.
PLOS Genetics, 2018Co-Authors: Paul D. Donovan, Linda M. Holland, Lisa Lombardi, Aisling Y. Coughlan, Desmond G Higgins, Kenneth H. Wolfe, Geraldine ButlerAbstract:Riboswitches are non-coding RNA molecules that regulate gene expression by binding to specific ligands. They are primarily found in bacteria. However, one riboswitch type, the thiamin pyrophosphate (TPP) riboswitch, has also been described in some plants, marine protists and fungi. We find that riboswitches are widespread in the budding yeasts (Saccharomycotina), and they are most common in homologs of DUR31, originally described as a spermidine transporter. We show that DUR31 (an ortholog of N. crassa gene NCU01977) encodes a thiamin transporter in Candida species. Using an RFP/riboswitch expression system, we show that the functional elements of the riboswitch are contained within the native intron of DUR31 from Candida parapsilosis, and that the riboswitch regulates splicing in a thiamin-dependent manner when RFP is constitutively expressed. The DUR31 gene has been lost from Saccharomyces, and may have been displaced by an alternative thiamin transporter. TPP riboswitches are also present in other putative transporters in yeasts and filamentous fungi. However, they are rare in thiamin biosynthesis genes THI4 and THI5 in the Saccharomycotina, and have been lost from all genes in the sequenced species in the family Saccharomycetaceae, including S. cerevisiae.
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Diutina catenulata is a member of the Debaryomycetaceae/Metschnikowiaceae clade.
2018Co-Authors: Caoimhe E. O’brien, Charley G. P. Mccarthy, Annie E. Walshe, Dennis R. Shaw, Deirdre A. Sumski, Tadeusz Krassowski, David A. Fitzpatrick, Geraldine ButlerAbstract:The phylogenetic tree was inferred from a superalignment of 204 ubiquitous gene families from 42 species. A consensus Bayesian supermatrix phylogeny was generated using PhyloBayes [38]. Clades within the Saccharomycotina (Debaryomycetaceae/Metschnikowiaceae, Pichiaceae, Phaffomycetaceae, Saccharomycodaceae and Saccharomycetaceae) are highlighted in color. Species within the Lodderomyces clade in the Debaryomycetaceae/Metschnikowiaceae are surrounded with a gray box. The exact definition of the Lodderomyces clade is not clear, and it may include Spathaspora species [48]. The branch supports show Bayesian Posterior Probabilities.
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Identification of riboswitches and thiamin metabolism and transport genes in the Saccharomycotina.
2018Co-Authors: Paul D. Donovan, Linda M. Holland, Lisa Lombardi, Aisling Y. Coughlan, Desmond G Higgins, Kenneth H. Wolfe, Geraldine ButlerAbstract:The presence of a riboswitch is indicated with a pink dot, and the number of orthologs of thiamin biosynthesis (THI4 and THI5) and transport (DUR31 and THI7) genes in each species is shown. The number of THI5 orthologs in Wickerhamomyces anomalus is not clear, because this species is a diploid hybrid. In nine species there are riboswitches in genes that are not orthologs of DUR31, THI4, THI5, or THI7. These are indicated under “other”, and are labeled as THI9, AN4526.2, MCP or unknown. The presence of orthologs of these genes without riboswitches is not recorded for other species. Absence of DUR31, THI4, THI5, or THI7 orthologs is shown with a dash. The most likely timings of gene or riboswitch loss are shown in the branches of the tree. The phylogeny and clade names of 86 Saccharomycotina and 10 outgroup species is taken from Shen et al [34]. WGD = the whole genome duplication.
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Evolution of Mating in the Saccharomycotina
Annual Review of Microbiology, 2017Co-Authors: Kenneth H. Wolfe, Geraldine ButlerAbstract:The fungal phylum Ascomycota comprises three subphyla: Saccharomycotina, Pezizomycotina, and Taphrinomycotina. In many Saccharomycotina species, cell identity is determined by genes at the MAT (mating-type) locus; mating occurs between MATa and MATα cells. Some species can switch between MATa and MATα mating types. Switching in the Saccharomycotina originated in the common ancestor of the Saccharomycetaceae, Pichiaceae, and Metschnikowiaceae families, as a flip/flop mechanism that inverted a section of chromosome. Switching was subsequently lost in the Metschnikowiaceae, including Candida albicans, but became more complex in the Saccharomycetaceae when the mechanism changed from inversion to copy-and-paste between HML/HMR and MAT. Based on their phylogenetic closeness and the similarity of their MTL (mating-type like) loci, some Metschnikowia species may provide useful models for the sexual cycles of Candida species. Conservation of synteny demonstrates that, despite changes in its gene content, a single ...
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Zinc Finger Transcription Factors Displaced SREBP Proteins as the Major Sterol Regulators during Saccharomycotina Evolution
PLoS Genetics, 2014Co-Authors: Sarah L. Maguire, Linda M. Holland, Kenneth H. Wolfe, François Brunel, Cécile Neuvéglise, Can Wang, Jean-marc Nicaud, Martin Zavrel, Theodore C. White, Geraldine ButlerAbstract:In most eukaryotes, including the majority of fungi, expression of sterol biosynthesis genes is regulated by Sterol-Regulatory Element Binding Proteins (SREBPs), which are basic helix-loop-helix transcription activators. However, in yeasts such as Saccharomyces cerevisiae and Candida albicans sterol synthesis is instead regulated by Upc2, an unrelated transcription factor with a Gal4-type zinc finger. The SREBPs in S. cerevisiae (Hms1) and C. albicans (Cph2) have lost a domain, are not major regulators of sterol synthesis, and instead regulate filamentous growth. We report here that rewiring of the sterol regulon, with Upc2 taking over from SREBP, likely occurred in the common ancestor of all Saccharomycotina. Yarrowia lipolytica, a deep-branching species, is the only genome known to contain intact and full-length orthologs of both SREBP (Sre1) and Upc2. Deleting YlUPC2, but not YlSRE1, confers susceptibility to azole drugs. Sterol levels are significantly reduced in the YlUPC2 deletion. RNA-seq analysis shows that hypoxic regulation of sterol synthesis genes in Y. lipolytica is predominantly mediated by Upc2. However, YlSre1 still retains a role in hypoxic regulation; growth of Y. lipolytica in hypoxic conditions is reduced in a Ylupc2 deletion and is abolished in a Ylsre1/Ylupc2 double deletion, and YlSre1 regulates sterol gene expression during hypoxia adaptation. We show that YlSRE1, and to a lesser extent YlUPC2, are required for switching from yeast to filamentous growth in hypoxia. Sre1 appears to have an ancestral role in the regulation of filamentation, which became decoupled from its role in sterol gene regulation by the arrival of Upc2 in the Saccharomycotina.
Noemie Jacques - One of the best experts on this subject based on the ideXlab platform.
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Large biodiversity of yeasts in French Guiana and the description of Suhomyces coccinellae f.a. sp. nov. and Suhomyces faveliae f.a. sp. nov.
International Journal of Systematic and Evolutionary Microbiology, 2019Co-Authors: Noemie Jacques, Serge CasaregolaAbstract:The extent of the diversity of yeasts in tropical rain forest and different environments from French Guiana was investigated. A total of 365 samples were collected from various substrates, such as plants, fruits and insects, at 13 locations, yielding 276 pure yeast isolates. Sequence analysis of the D1/D2 domains of the large subunit rRNA gene indicated that 210 isolates out of 276 belonged to 82 described species (67 Saccharomycotina, 14 Basidiomycota and 1 Pezizomycotina). In addition to these, a total of 54 Saccharomycotina isolates could not be assigned to a known species. These belonged to 14 genera and should be studied further from a taxonomic point of view. In addition, among the 43 Basidiomycotina isolates found, 12 could not be assigned to a known species. This report shows an unexpected biodiversity and indicates that oversea territories, such as French Guiana, constitute a largely unexplored reservoir for yeast diversity. Two Saccharomycotina strains, CLIB 1706 and CLIB 1725, isolated from an insect and from a fern respectively, were characterized further and were shown to belong to the Suhomyces clade on the basis of the rDNA sequence comparison. CLIB 1706TrDNA sequences showed nine substitutions and three indels out of 556 bp (D1/D2 domains) and 32 substitutions and 12 indels out of 380 bp [internal transcribed spacer (ITS)] with that of the most closely related species Suhomyces guaymorum CBS 9823T. CLIB 1725T rDNA sequences presented 18 substitutions and one indel out of 549 bp (D1/D2 domains) and 48 substitutions and 11 indels out of 398 bp (ITS) with that of its closest relative Suhomyces vadensis CBS 9454T. Two novel species of the genus Suhomyces were described to accommodate these two strains: Suhomyces coccinellae f.a. sp. nov. (CLIB 1706T=CBS 14298T) and Suhomyces faveliae f.a. sp. nov. (CLIB 1725T=CBS 14299T).
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Corrigendum: Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts.
Scientific Reports, 2015Co-Authors: Guillaume Morel, Noemie Jacques, Lieven Sterck, Dominique Swennen, Marina Marcet-houben, Djamila Onesime, Anthony Levasseur, Sandrine Mallet, Arnaux Couloux, Karine LabadieAbstract:The evolutionary history of the characters underlying the adaptation of microorganisms to food and biotechnological uses is poorly understood. We undertook comparative genomics to investigate evolutionary relationships of the dairy yeast Geotrichum candidum within Saccharomycotina. Surprisingly, a remarkable proportion of genes showed discordant phylogenies, clustering with the filamentous fungus subphylum (Pezizomycotina), rather than the yeast subphylum (Saccharomycotina), of the Ascomycota. These genes appear not to be the result of Horizontal Gene Transfer (HGT), but to have been specifically retained by G. candidum after the filamentous fungi–yeasts split concomitant with the yeasts’ genome contraction. We refer to these genes as SRAGs (Specifically Retained Ancestral Genes), having been lost by all or nearly all other yeasts, and thus contributing to the phenotypic specificity of lineages. SRAG functions include lipases consistent with a role in cheese making and novel endoglucanases associated with degradation of plant material. Similar gene retention was observed in three other distantly related yeasts representative of this ecologically diverse subphylum. The phenomenon thus appears to be widespread in the Saccharomycotina and argues that, alongside neo-functionalization following gene duplication and HGT, specific gene retention must be recognized as an important mechanism for generation of biodiversity and adaptation in yeasts.
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Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts
Scientific Reports, 2015Co-Authors: Guillaume Morel, Noemie Jacques, Lieven Sterck, Dominique Swennen, Marina Marcet-houben, Djamila Onesime, Anthony Levasseur, Sandrine Mallet, Arnaux Couloux, Karine LabadieAbstract:The evolutionary history of the characters underlying the adaptation of microorganisms to food and biotechnological uses is poorly understood. We undertook comparative genomics to investigate evolutionary relationships of the dairy yeast Geotrichum candidum within Saccharomycotina. Surprisingly, a remarkable proportion of genes showed discordant phylogenies, clustering with the filamentous fungus subphylum (Pezizomycotina), rather than the yeast subphylum (Saccharomycotina), of the Ascomycota. These genes appear not to be the result of Horizontal Gene Transfer (HGT), but to have been specifically retained by G. candidum after the filamentous fungi–yeasts split concomitant with the yeasts’ genome contraction. We refer to these genes as SRAGs (Specifically Retained Ancestral Genes), having been lost by all or nearly all other yeasts and thus contributing to the phenotypic specificity of lineages. SRAG functions include lipases consistent with a role in cheese making and novel endoglucanases associated with degradation of plant material. Similar gene retention was observed in three other distantly related yeasts representative of this ecologically diverse subphylum. The phenomenon thus appears to be widespread in the Saccharomycotina and argues that, alongside neo-functionalization following gene duplication and HGT, specific gene retention must be recognized as an important mechanism for generation of biodiversity and adaptation in yeasts.
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Lipids containing medium-chain fatty acids are specific to post-whole genome duplication Saccharomycotina yeasts
BMC Evolutionary Biology, 2015Co-Authors: Marine Froissard, Michel Canonge, Marie Pouteaux, Bernard Cintrat, Sabrina Mohand-Oumoussa, Stéphane E. Guillouet, Thierry Chardot, Noemie JacquesAbstract:BackgroundYeasts belonging to the subphylum Saccharomycotina have been used for centuries in food processing and, more recently, biotechnology. Over the past few decades, these yeasts have also been studied in the interest of their potential to produce oil to replace fossil resources. Developing yeasts for massive oil production requires increasing yield and modifying the profiles of the fatty acids contained in the oil to satisfy specific technical requirements. For example, derivatives of medium-chain fatty acids (MCFAs, containing 6–14 carbons) are used for the production of biodiesels, cleaning products, lubricants and cosmetics. Few studies are available in the literature on the production of MCFAs in yeasts.ResultsWe analyzed the MCFA content in Saccharomyces cerevisiae grown in various conditions. The results revealed that MCFAs preferentially accumulated when cells were grown on synthetic media with a high C/N ratio at low temperature (23 °C). Upon screening deletion mutant strains for genes encoding lipid droplet-associated proteins, we found two genes, LOA1 and TGL3, involved in MCFA homeostasis. A phylogenetic analysis on 16 Saccharomycotina species showed that fatty acid profiles differed drastically among yeasts. Interestingly, MCFAs are only present in post-whole genome duplication yeast species.ConclusionsIn this study, we produced original data on fatty acid diversity in yeasts. We demonstrated that yeasts are amenable to genetic and metabolic engineering to increase their MCFA production. Furthermore, we revealed that yeast lipid biodiversity has not been fully explored, but that yeasts likely harbor as-yet-undiscovered strains or enzymes that can contribute to the production of high-value fatty acids for green chemistry.
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Lipids containing medium-chain fatty acids are specific to post-whole genome duplication Saccharomycotina yeasts
BMC Evolutionary Biology, 2015Co-Authors: Marine Froissard, Michel Canonge, Marie Pouteaux, Bernard Cintrat, Sabrina Mohand-Oumoussa, Noemie Jacques, Stéphane E. Guillouet, Thierry Chardot, Serge CasaregolaAbstract:Background Yeasts belonging to the subphylum Saccharomycotina have been used for centuries in food processing and, more recently, biotechnology. Over the past few decades, these yeasts have also been studied in the interest of their potential to produce oil to replace fossil resources. Developing yeasts for massive oil production requires increasing yield and modifying the profiles of the fatty acids contained in the oil to satisfy specific technical requirements. For example, derivatives of medium-chain fatty acids (MCFAs, containing 6–14 carbons) are used for the production of biodiesels, cleaning products, lubricants and cosmetics. Few studies are available in the literature on the production of MCFAs in yeasts.
Cletus P. Kurtzman - One of the best experts on this subject based on the ideXlab platform.
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Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data.
G3: Genes|Genomes|Genetics, 2016Co-Authors: Xing-xing Shen, Cletus P. Kurtzman, Xiaofan Zhou, Jacek Kominek, Chris Todd Hittinger, Antonis RokasAbstract:Understanding the phylogenetic relationships among the yeasts of the subphylum Saccharomycotina is a prerequisite for understanding the evolution of their metabolisms and ecological lifestyles. In the last two decades, the use of rDNA and multilocus data sets has greatly advanced our understanding of the yeast phylogeny, but many deep relationships remain unsupported. In contrast, phylogenomic analyses have involved relatively few taxa and lineages that were often selected with limited considerations for covering the breadth of yeast biodiversity. Here we used genome sequence data from 86 publicly available yeast genomes representing nine of the 11 known major lineages and 10 nonyeast fungal outgroups to generate a 1233-gene, 96-taxon data matrix. Species phylogenies reconstructed using two different methods (concatenation and coalescence) and two data matrices (amino acids or the first two codon positions) yielded identical and highly supported relationships between the nine major lineages. Aside from the lineage comprised by the family Pichiaceae, all other lineages were monophyletic. Most interrelationships among yeast species were robust across the two methods and data matrices. However, eight of the 93 internodes conflicted between analyses or data sets, including the placements of: the clade defined by species that have reassigned the CUG codon to encode serine, instead of leucine; the clade defined by a whole genome duplication; and the species Ascoidea rubescens . These phylogenomic analyses provide a robust roadmap for future comparative work across the yeast subphylum in the disciplines of taxonomy, molecular genetics, evolutionary biology, ecology, and biotechnology. To further this end, we have also provided a BLAST server to query the 86 Saccharomycotina genomes, which can be found at http://y1000plus.org/blast.
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Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data
2016Co-Authors: Xing-xing Shen, Cletus P. Kurtzman, Xiaofan Zhou, Jacek Kominek, Chris Todd Hittinger, Antonis RokasAbstract:Understanding the phylogenetic relationships among the yeasts of the subphylum Saccharomycotina is a prerequisite for understanding the evolution of their metabolisms and ecological lifestyles. In the last two decades, the use of rDNA and multi-locus data sets has greatly advanced our understanding of the yeast phylogeny, but many deep relationships remain unsupported. In contrast, phylogenomic analyses have involved relatively few taxa and lineages that were often selected with limited considerations for covering the breadth of yeast biodiversity. Here we used genome sequence data from 86 publicly available yeast genomes representing 9 of the 11 major lineages and 10 non-yeast fungal outgroups to generate a 1,233-gene, 96-taxon data matrix. Species phylogenies reconstructed using two different methods (concatenation and coalescence) and two data matrices (amino acids or the first two codon positions) yielded identical and highly supported relationships between the 9 major lineages. Aside from the lineage comprised by the family Pichiaceae, all other lineages were monophyletic. Most interrelationships among yeast species were robust across the two methods and data matrices. However, 8 of the 93 internodes conflicted between analyses or data sets, including the placements of: the clade defined by species that have reassigned the CUG codon to encode serine, instead of leucine; the clade defined by a whole genome duplication; and of Ascoidea rubescens. These phylogenomic analyses provide a robust roadmap for future comparative work across the yeast subphylum in the disciplines of taxonomy, molecular genetics, evolutionary biology, ecology, and biotechnology. To further this end, we have also provided a BLAST server to query the 86 Saccharomycotina genomes, which can be found at http://y1000plus.org/blast.
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Cyberlindnera xylosilytica sp. nov., a xylitol-producing yeast species isolated from lignocellulosic materials.
International journal of systematic and evolutionary microbiology, 2015Co-Authors: Raquel M. Cadete, Cletus P. Kurtzman, Monaliza A. M. Cheab, Renata O. Santos, Silvana V. B. Safar, Jerri Édson Zilli, Marcos José Salgado Vital, Luiz Carlos Basso, Ching-fu Lee, Marc-andré LachanceAbstract:Independent surveys of yeasts associated with lignocellulosic-related materials led to the discovery of a novel yeast species belonging to the Cyberlindnera clade (Saccharomycotina, Ascomycota). Analysis of the sequences of the internal transcribed spacer (ITS) region and the D1/D2 domains of the large subunit rRNA gene showed that this species is related to C. japonica, C. maesa and C. easanensis. Six isolates were obtained from different sources, including rotting wood, tree bark and sugar cane filter cake in Brazil, frass from white oak in the USA and decayed leaf in Taiwan. A novel species is suggested to accommodate these isolates, for which the name C. xylosilytica sp. nov. is proposed. The type strain of C. xylosilytica sp. nov. is NRRL YB-2097T ( = CBS 13984T = UFMG-CM-Y347T) and the allotype is UFMG-CM-Y409 ( = CBS 14083). The novel species is heterothallic and complementary mating types are represented by the type and allotype strains. The MycoBank number is MB 811428.
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1 Saccharomycotina0Saccharomycotina and Taphrinomycotina:0Taphrinomycotina The Yeasts and Yeastlike Fungi of the Ascomycota
Systematics and Evolution, 2015Co-Authors: Cletus P. Kurtzman, Junta SugiyamaAbstract:The phylum Ascomycota has been resolved into three major phylogenetic lineages: the subphyla Saccharomycotina (e.g., Saccharomyces, Pichia, Candida), Taphrinomycotina (e.g., Protomyces, Taphrina, Pneumocystis), and Pezizomycotina (e.g., Aspergillus, Neurospora, Peziza). We discuss the ecology, physiology, molecular biology, biotechnology, phylogeny, and systematics of Saccharomycotina and Taphrinomycotina, which represent the yeasts and yeastlike fungi of Ascomycota. Major changes in all aspects of our knowledge of these two subphyla have resulted from molecular studies, and the focus of the chapter is on these changes and their impact on present and future applications of the yeasts.
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1 Saccharomycotina and taphrinomycotina the yeasts and yeastlike fungi of the ascomycota
2015Co-Authors: Cletus P. Kurtzman, Junta SugiyamaAbstract:The phylum Ascomycota has been resolved into three major phylogenetic lineages: the subphyla Saccharomycotina (e.g., Saccharomyces, Pichia, Candida), Taphrinomycotina (e.g., Protomyces, Taphrina, Pneumocystis), and Pezizomycotina (e.g., Aspergillus, Neurospora, Peziza). We discuss the ecology, physiology, molecular biology, biotechnology, phylogeny, and systematics of Saccharomycotina and Taphrinomycotina, which represent the yeasts and yeastlike fungi of Ascomycota. Major changes in all aspects of our knowledge of these two subphyla have resulted from molecular studies, and the focus of the chapter is on these changes and their impact on present and future applications of the yeasts.
Kenneth H. Wolfe - One of the best experts on this subject based on the ideXlab platform.
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TPP riboswitch-dependent regulation of an ancient thiamin transporter in Candida.
PLOS Genetics, 2018Co-Authors: Paul D. Donovan, Linda M. Holland, Lisa Lombardi, Aisling Y. Coughlan, Desmond G Higgins, Kenneth H. Wolfe, Geraldine ButlerAbstract:Riboswitches are non-coding RNA molecules that regulate gene expression by binding to specific ligands. They are primarily found in bacteria. However, one riboswitch type, the thiamin pyrophosphate (TPP) riboswitch, has also been described in some plants, marine protists and fungi. We find that riboswitches are widespread in the budding yeasts (Saccharomycotina), and they are most common in homologs of DUR31, originally described as a spermidine transporter. We show that DUR31 (an ortholog of N. crassa gene NCU01977) encodes a thiamin transporter in Candida species. Using an RFP/riboswitch expression system, we show that the functional elements of the riboswitch are contained within the native intron of DUR31 from Candida parapsilosis, and that the riboswitch regulates splicing in a thiamin-dependent manner when RFP is constitutively expressed. The DUR31 gene has been lost from Saccharomyces, and may have been displaced by an alternative thiamin transporter. TPP riboswitches are also present in other putative transporters in yeasts and filamentous fungi. However, they are rare in thiamin biosynthesis genes THI4 and THI5 in the Saccharomycotina, and have been lost from all genes in the sequenced species in the family Saccharomycetaceae, including S. cerevisiae.
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Identification of riboswitches and thiamin metabolism and transport genes in the Saccharomycotina.
2018Co-Authors: Paul D. Donovan, Linda M. Holland, Lisa Lombardi, Aisling Y. Coughlan, Desmond G Higgins, Kenneth H. Wolfe, Geraldine ButlerAbstract:The presence of a riboswitch is indicated with a pink dot, and the number of orthologs of thiamin biosynthesis (THI4 and THI5) and transport (DUR31 and THI7) genes in each species is shown. The number of THI5 orthologs in Wickerhamomyces anomalus is not clear, because this species is a diploid hybrid. In nine species there are riboswitches in genes that are not orthologs of DUR31, THI4, THI5, or THI7. These are indicated under “other”, and are labeled as THI9, AN4526.2, MCP or unknown. The presence of orthologs of these genes without riboswitches is not recorded for other species. Absence of DUR31, THI4, THI5, or THI7 orthologs is shown with a dash. The most likely timings of gene or riboswitch loss are shown in the branches of the tree. The phylogeny and clade names of 86 Saccharomycotina and 10 outgroup species is taken from Shen et al [34]. WGD = the whole genome duplication.
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Evolution of Mating in the Saccharomycotina
Annual Review of Microbiology, 2017Co-Authors: Kenneth H. Wolfe, Geraldine ButlerAbstract:The fungal phylum Ascomycota comprises three subphyla: Saccharomycotina, Pezizomycotina, and Taphrinomycotina. In many Saccharomycotina species, cell identity is determined by genes at the MAT (mating-type) locus; mating occurs between MATa and MATα cells. Some species can switch between MATa and MATα mating types. Switching in the Saccharomycotina originated in the common ancestor of the Saccharomycetaceae, Pichiaceae, and Metschnikowiaceae families, as a flip/flop mechanism that inverted a section of chromosome. Switching was subsequently lost in the Metschnikowiaceae, including Candida albicans, but became more complex in the Saccharomycetaceae when the mechanism changed from inversion to copy-and-paste between HML/HMR and MAT. Based on their phylogenetic closeness and the similarity of their MTL (mating-type like) loci, some Metschnikowia species may provide useful models for the sexual cycles of Candida species. Conservation of synteny demonstrates that, despite changes in its gene content, a single ...
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Zinc Finger Transcription Factors Displaced SREBP Proteins as the Major Sterol Regulators during Saccharomycotina Evolution
PLoS Genetics, 2014Co-Authors: Sarah L. Maguire, Linda M. Holland, Kenneth H. Wolfe, François Brunel, Cécile Neuvéglise, Can Wang, Jean-marc Nicaud, Martin Zavrel, Theodore C. White, Geraldine ButlerAbstract:In most eukaryotes, including the majority of fungi, expression of sterol biosynthesis genes is regulated by Sterol-Regulatory Element Binding Proteins (SREBPs), which are basic helix-loop-helix transcription activators. However, in yeasts such as Saccharomyces cerevisiae and Candida albicans sterol synthesis is instead regulated by Upc2, an unrelated transcription factor with a Gal4-type zinc finger. The SREBPs in S. cerevisiae (Hms1) and C. albicans (Cph2) have lost a domain, are not major regulators of sterol synthesis, and instead regulate filamentous growth. We report here that rewiring of the sterol regulon, with Upc2 taking over from SREBP, likely occurred in the common ancestor of all Saccharomycotina. Yarrowia lipolytica, a deep-branching species, is the only genome known to contain intact and full-length orthologs of both SREBP (Sre1) and Upc2. Deleting YlUPC2, but not YlSRE1, confers susceptibility to azole drugs. Sterol levels are significantly reduced in the YlUPC2 deletion. RNA-seq analysis shows that hypoxic regulation of sterol synthesis genes in Y. lipolytica is predominantly mediated by Upc2. However, YlSre1 still retains a role in hypoxic regulation; growth of Y. lipolytica in hypoxic conditions is reduced in a Ylupc2 deletion and is abolished in a Ylsre1/Ylupc2 double deletion, and YlSre1 regulates sterol gene expression during hypoxia adaptation. We show that YlSRE1, and to a lesser extent YlUPC2, are required for switching from yeast to filamentous growth in hypoxia. Sre1 appears to have an ancestral role in the regulation of filamentation, which became decoupled from its role in sterol gene regulation by the arrival of Upc2 in the Saccharomycotina.
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Genome Sequences of Saccharomycotina: Resources and Applications in Phylogenomics
The Yeasts, 2011Co-Authors: Elżbieta Rozpędowska, Jure Piškur, Kenneth H. WolfeAbstract:Publisher Summary This chapter reviews the data that are currently available in yeast comparative genomics, and discusses how taxonomists can access and make use of these data. Genomes can be sequenced to various levels of completion. The “gold standard” is a sequence that spans every chromosome from telomere to telomere, with no gaps or ambiguities. The genome sequence of Saccharomyces cerevisiae comes close to meeting this standard, but even for this species it has proved impossible (with current technology) to determine the complete sequence of the rDNA locus. An alternative strategy in genomics is whole-genome shotgun (WGS) sequencing without further finishing. This strategy saves much time and expense, but loses out in terms of the completeness of the information obtained. The shotgun sequencing process involves “assembling” the raw data, by finding overlaps between individual sequence reads of random fragments of genomic DNA to form larger “contigs” of contiguous genomic sequence data.
