Kenneth H. Wolfe
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View article: Centromeres in budding yeasts are conserved in chromosomal location but not in structure
Centromeres in budding yeasts are conserved in chromosomal location but not in structure Open
The budding yeast Saccharomyces cerevisiae has ‘point’ centromeres, which are much smaller and simpler than centromeres of most other eukaryotes and have a defined DNA sequence. Other yeast taxa have different and highly diverse centromere…
View article: Enhanced Bioprocess Performance and β-Glucosidase Productivity of a Novel Komagataella phaffii Strain Generated by Intraspecific Crossing
Enhanced Bioprocess Performance and β-Glucosidase Productivity of a Novel Komagataella phaffii Strain Generated by Intraspecific Crossing Open
This research characterized a novel Komagataella phaffii strain generated through intraspecific crossing between a wild isolate and a laboratory strain. This segregant, called S467, expressed 2.2-fold more secreted recombinant β-glucosidas…
View article: Zymocin-like killer plasmids were present in the common ancestor of terrestrial fungi
Zymocin-like killer plasmids were present in the common ancestor of terrestrial fungi Open
Some budding yeasts secrete killer toxins made by linear dsDNA plasmids located in the cytosol. The best-known example is the Kluyveromyces lactis toxin zymocin, which is encoded by a 9-kb killer plasmid assisted by a 13-kb helper plasmid.…
View article: Cyberlindnera hibernica sp. nov. and Barnettozyma discipulorum sp. nov., isolated from forest soil in Ireland
Cyberlindnera hibernica sp. nov. and Barnettozyma discipulorum sp. nov., isolated from forest soil in Ireland Open
Two yeast strains, PYCC 10015 and PYCC 10016, were isolated from soil from an Irish forest. Sequence analysis of the internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2) of the rRNA gene repeat, and the D1/D2 domain of the LSU rRNA ge…
View article: Small pangenome of <i>Candida parapsilosis</i> reflects overall low intraspecific diversity
Small pangenome of <i>Candida parapsilosis</i> reflects overall low intraspecific diversity Open
Candida parapsilosis is an opportunistic yeast pathogen that can cause life-threatening infections in immunocompromised humans. Whole-genome sequencing studies of the species have demonstrated remarkably low diversity, with strains typical…
View article: Centromeres in budding yeasts are conserved in chromosomal location but not in structure
Centromeres in budding yeasts are conserved in chromosomal location but not in structure Open
The budding yeast Saccharomyces cerevisiae has ‘point’ centromeres, which are much smaller and simpler than centromeres of most other eukaryotes and have a defined DNA sequence. Other yeast taxa have different and highly diverse centromere…
View article: Small pangenome of <i>Candida parapsilosis</i> reflects overall low intraspecific diversity
Small pangenome of <i>Candida parapsilosis</i> reflects overall low intraspecific diversity Open
Candida parapsilosis is an opportunistic yeast pathogen that can cause life-threatening infections in immunocompromised humans. Whole genome sequencing (WGS) studies of the species have demonstrated remarkably low diversity, with strains t…
View article: Genome sequence of the yeast <i>Candida solani</i> UCD1087, isolated from soil in Ireland
Genome sequence of the yeast <i>Candida solani</i> UCD1087, isolated from soil in Ireland Open
Candida solani is a member of the Wickerhamomyces clade of budding yeasts. We present the genome sequence of C. solani strain UCD1087, which was isolated from soil on the University College Dublin (UCD) campus in Ireland. This genome is 12…
View article: Genome sequence of the yeast <i>Cyberlindnera sylvatica</i> UCD1060, isolated from soil in Ireland
Genome sequence of the yeast <i>Cyberlindnera sylvatica</i> UCD1060, isolated from soil in Ireland Open
Cyberlindnera sylvatica is a member of the Cyberlindnera clade in the order Phaffomycetales. We present the genome sequence of C. sylvatica . The sequenced strain, UCD1060, was isolated from soil in Wicklow, Ireland. This genome is 13.5 Mb…
View article: Cell engineering for bioprocess applications to enhance recombinant protein secretion in Komagataella phaffii
Cell engineering for bioprocess applications to enhance recombinant protein secretion in Komagataella phaffii Open
View article: Ancient origin and high diversity of zymocin-like killer toxins in the budding yeast subphylum
Ancient origin and high diversity of zymocin-like killer toxins in the budding yeast subphylum Open
Zymocin is a well-characterized killer toxin secreted by some strains of the yeast Kluyveromyces lactis . It acts by cleaving a specific tRNA in sensitive recipient cells. Zymocin is encoded by a killer plasmid or virus-like element (VLE),…
View article: Zymocin-like killer toxin gene clusters in the nuclear genomes of filamentous fungi
Zymocin-like killer toxin gene clusters in the nuclear genomes of filamentous fungi Open
Zymocin-like killer toxins are anticodon nucleases secreted by some budding yeast species, which kill competitor yeasts by cleaving tRNA molecules. They are encoded by virus-like elements (VLEs), cytosolic linear DNA molecules that are als…
View article: Evolution of the Genetic Code in the Ascoideales (CUG-Ser2) Yeast Clade: The Ancestral tRNA-Leu(CAG) Gene Is Retained in Most <i>Saccharomycopsis</i> Species but Is Nonessential and Not Used for Translation
Evolution of the Genetic Code in the Ascoideales (CUG-Ser2) Yeast Clade: The Ancestral tRNA-Leu(CAG) Gene Is Retained in Most <i>Saccharomycopsis</i> Species but Is Nonessential and Not Used for Translation Open
In the yeast genera Saccharomycopsis and Ascoidea, which comprise the taxonomic order Ascoideales, nuclear genes use a nonstandard genetic code in which CUG codons are translated as serine instead of leucine, due to a tRNA-Ser with the unu…
View article: Analysis of clinical <i>Candida parapsilosis</i> isolates reveals copy number variation in key fluconazole resistance genes
Analysis of clinical <i>Candida parapsilosis</i> isolates reveals copy number variation in key fluconazole resistance genes Open
We used whole-genome sequencing to analyze a collection of 35 fluconazole-resistant and 7 susceptible Candida parapsilosis isolates together with coverage analysis and GWAS techniques to identify new mechanisms of fluconazole resistance. P…
View article: WHO elements – A new category of selfish genetic elements at the borderline between homing elements and transposable elements
WHO elements – A new category of selfish genetic elements at the borderline between homing elements and transposable elements Open
Homing genetic elements are a form of selfish DNA that inserts into a specific target site in the genome and spreads through the population by a process of biased inheritance. Two well-known types of homing element, called inteins and homi…
View article: Genome Analysis of a Newly Discovered Yeast Species, Hanseniaspora menglaensis
Genome Analysis of a Newly Discovered Yeast Species, Hanseniaspora menglaensis Open
Annual surveys of Irish soil samples identified three isolates, CBS 16921 (UCD88), CBS 18246 (UCD443), and CBS 18247 (UCD483), of an apiculate yeast species within the Hanseniaspora genus. The internal transcribed spacer (ITS) and D1/D2 re…
View article: Genome sequences of two isolates of the yeast <i>Candida zeylanoides</i> : UCD849 from soil in Ireland, and AWD from an African wild dog
Genome sequences of two isolates of the yeast <i>Candida zeylanoides</i> : UCD849 from soil in Ireland, and AWD from an African wild dog Open
We report genome sequences of two new isolates of the budding yeast Candida zeylanoides . Strain UCD849 from soil in Ireland was assembled into eight complete chromosomes. Strain AWD from an African Wild Dog in a US zoo was sequenced to dr…
View article: Draft genome sequence of the yeast <i>Schwanniomyces capriottii</i> strain UCD805, isolated from soil in Ireland
Draft genome sequence of the yeast <i>Schwanniomyces capriottii</i> strain UCD805, isolated from soil in Ireland Open
Schwanniomyces capriottii is a member of the Debaryomycetaceae family in the order Saccharomycetales. Here, we present the genome sequence of S. capriottii UCD805, which was isolated from soil in Dublin, Ireland. This genome is 12.2 Mb and…
View article: Analysis of clinical<i>Candida parapsilosis</i>isolates reveals copy number variation in key fluconazole resistance genes
Analysis of clinical<i>Candida parapsilosis</i>isolates reveals copy number variation in key fluconazole resistance genes Open
We used whole-genome sequencing to analyse a collection of 35 fluconazole resistant and 7 susceptible Candida parapsilosis isolates together with coverage analysis and GWAS techniques to identify new mechanisms of fluconazole resistance. P…
View article: Cytosolic linear DNA plasmids in<i>Saccharomycopsis</i>species
Cytosolic linear DNA plasmids in<i>Saccharomycopsis</i>species Open
Some budding yeast species contain cytosolic linear DNA plasmids (also called virus-like elements, VLEs) that code for killer toxins that can kill other yeasts. The toxins are anticodon nucleases that cleave a specific tRNA in the cells be…
View article: Genome sequence data of the strongly antagonistic yeast Pichia kluyveri isolate APC 11.10 B as a foundation for analysing biocontrol mechanisms
Genome sequence data of the strongly antagonistic yeast Pichia kluyveri isolate APC 11.10 B as a foundation for analysing biocontrol mechanisms Open
Pichia kluyveri strain APC 11.10 B was isolated from apple bark in Switzerland and exhibited strong antagonistic activity against plant pathogenic fungi in vitro (e.g., Botrytis, Fusarium or Monilinia isolates).…
View article: A genetic code change in progress: tRNA-Leu(CAG) is conserved in most<i>Saccharomycopsis</i>yeast species but is non-essential and does not compete with tRNA-Ser(CAG) in translation
A genetic code change in progress: tRNA-Leu(CAG) is conserved in most<i>Saccharomycopsis</i>yeast species but is non-essential and does not compete with tRNA-Ser(CAG) in translation Open
In the yeast genera Saccharomycopsis and Ascoidea , nuclear genes use a non-standard genetic code in which CUG codons are translated as serine instead of leucine, due to a tRNA-Ser with the unusual anticodon CAG. However, some species in t…
View article: A genome-informed higher rank classification of the biotechnologically important fungal subphylum <i> Saccharomycotina</i>
A genome-informed higher rank classification of the biotechnologically important fungal subphylum <i> Saccharomycotina</i> Open
The subphylum Saccharomycotina is a lineage in the fungal phylum Ascomycota that exhibits levels of genomic diversity similar to those of plants and animals. The Saccharomycotina consist of more than 1 200 known species currently divided i…
View article: Genome Sequence Data of the Strongly Antagonistic Yeast Pichia Kluyveri Isolate APC 11.10 B as a Foundation for Analysing Biocontrol Mechanisms
Genome Sequence Data of the Strongly Antagonistic Yeast Pichia Kluyveri Isolate APC 11.10 B as a Foundation for Analysing Biocontrol Mechanisms Open
View article: Identification of genetic variants of the industrial yeast Komagataella phaffii (Pichia pastoris) that contribute to increased yields of secreted heterologous proteins
Identification of genetic variants of the industrial yeast Komagataella phaffii (Pichia pastoris) that contribute to increased yields of secreted heterologous proteins Open
The yeast Komagataella phaffii (formerly called Pichia pastoris ) is used widely as a host for secretion of heterologous proteins, but only a few isolates of this species exist and all the commonly used expression systems are derived from …
View article: A widespread inversion polymorphism conserved among Saccharomyces species is caused by recurrent homogenization of a sporulation gene family
A widespread inversion polymorphism conserved among Saccharomyces species is caused by recurrent homogenization of a sporulation gene family Open
Saccharomyces genomes are highly collinear and show relatively little structural variation, both within and between species of this yeast genus. We investigated the only common inversion polymorphism known in S . cerevisiae , which affects…
View article: Draft Genome Sequence of the Yeast Blastobotrys aristata Strain UCD613, Isolated from Soil in Ireland
Draft Genome Sequence of the Yeast Blastobotrys aristata Strain UCD613, Isolated from Soil in Ireland Open
Blastobotrys aristata is a member of the Trichomonascaceae family in the order Saccharomycetales. Here, we present the genome sequence of B. aristata UCD613, which was isolated from soil in Dublin, Ireland. This genome is 13.3 Mb and was a…
View article: Draft Genome Sequence of the Yeast Torulaspora quercuum Strain UCD657, Isolated from Soil in Ireland
Draft Genome Sequence of the Yeast Torulaspora quercuum Strain UCD657, Isolated from Soil in Ireland Open
Torulaspora quercuum is an ascomycete yeast first isolated in 2009. Here, we present the genome sequence of T. quercuum isolate UCD657, which was isolated from soil in Ireland. This genome is 10.4 Mb and was assembled into 8 chromosome-siz…
View article: Systematic Analysis of Copy Number Variations in the Pathogenic Yeast Candida parapsilosis Identifies a Gene Amplification in <i>RTA3</i> That is Associated with Drug Resistance
Systematic Analysis of Copy Number Variations in the Pathogenic Yeast Candida parapsilosis Identifies a Gene Amplification in <i>RTA3</i> That is Associated with Drug Resistance Open
Copy number variations (CNVs) are an important source of genomic diversity that have been associated with drug resistance. We identify two unusual CNVs in the human fungal pathogen Candida parapsilosis .
View article: Mating-Type Switching in Budding Yeasts, from Flip/Flop Inversion to Cassette Mechanisms
Mating-Type Switching in Budding Yeasts, from Flip/Flop Inversion to Cassette Mechanisms Open
Mating-type switching is a natural but unusual genetic control process that regulates cell identity in ascomycete yeasts. It involves physically replacing one small piece of genomic DNA by another, resulting in replacement of the master re…