Kevin P. Byrne

Candida sake is a member of the Debaryomycetaceae family of budding yeasts. We present the genome sequence of C. sake strain UCD2293, isolated from soil at Poolbeg, Co. Dublin, in Ireland. This genome is 14.26 Mb and was assembled into 8 chromosome-sized contigs plus a mitochondrial genome contig.

Candida solani is a member of the Wickerhamomyces clade of budding yeasts. We present the genome sequence of C. solani strain UCD2211 isolated from soil on the University College Dublin (UCD) campus in Ireland. This genome was 12.67 Mb and assembled into six chromosome-sized contigs plus a mitochondrial genome contig.

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 structures, but a clear picture of how yeast centromeres have evolved is lacking. Here, we investigated nine yeast species in two taxonomic orders that are close outgroups to S. cerevisiae . We find that they have a wide diversity of centromere structures, indicating that multiple transitions of structure have occurred within the last 200 Myr. Some species have centromeres with defined sequence motifs (17 – 200 bp), others consist of Inverted Repeats (IRs), and others have Ty5-like retroelement clusters. Strikingly, the chromosomal locations of centromeres have largely been conserved across taxonomic orders, even as their structures have changed, which suggests that structure replacement occurs in situ . In some Barnettozyma species we find that a single genome can contain chromosomes with different centromere structures – some with IRs and some without – which suggests that a structural transition is underway in this genus. We identified only one example of a centromere moving by a long distance: a new centromere formed recently at the MAT locus of Barnettozyma californica , 250 kb from the previous centromere on that chromosome.

In hematopoietic cell transplant patients, intestinal Candida parapsilosis expansion and translocation cause life-threatening candidemia, yet how commensal intestinal bacteria prevent Candida expansion remains incompletely defined. Here, we trained a machine learning model on supernatant metabolomic profiles of commensal bacteria to identify bacteria-derived inhibitors of fungal growth, with valeric and butyric acid as top hits. Experimental validation confirmed in silico predictions in three systems. First, in patient fecal samples, valeric and butyric acid levels inversely correlated with C. parapsilosis growth. Second, in vitro, valeric acid potently inhibited C. parapsilosis growth by causing intracellular acidification. Third, administration of glycerol valerate, and free or microencapsulated valeric acid blunted C. parapsilosis growth at murine intestinal sites where valeric acid could be detected. Thus, machine learning could identify a mechanistic driver of trans-kingdom ecology limiting C. parapsilosis intestinal expansion and may inform strategies to reduce patient risk of developing candidiasis during high-risk periods.

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 gene, showed that they belong to the Cyberlindnera and Barnettozyma genera of the order Phaffomycetales, but they did not exactly match any known species. The genomes of both isolates were sequenced using Oxford Nanopore Technologies and Illumina sequencing, generating chromosome-level genome assemblies. Phylogenomic analysis of 1,385 single-copy orthologues from 37 Phaffomycetales species and 2 outgroups showed that the closest relative of PYCC 10015 is Cyberlindnera galapagoensis and that PYCC 10016 is placed in a subclade containing 7 other species from the Barnettozyma genus. The average nucleotide identity between these strains and their closest relatives is Cyberlindnera hibernica sp. nov. and Barnettozyma discipulorum sp. nov. for PYCC 10015 and PYCC 10016, respectively.

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 structures, but a clear picture of how yeast centromeres have evolved is lacking. Here, we investigated nine yeast species in two taxonomic orders that are close outgroups to S. cerevisiae . We find that they have a wide diversity of centromere structures, indicating that multiple transitions of structure have occurred within the last 200 Myr. Some species have centromeres with defined sequence motifs (17 – 200 bp), others consist of Inverted Repeats (IRs), and others have Ty5-like retroelement clusters. Strikingly, the chromosomal locations of centromeres have largely been conserved across taxonomic orders, even as their structures have changed, which suggests that structure replacement occurs in situ . In some Barnettozyma species we find that a single genome can contain chromosomes with different centromere structures – some with IRs and some without – which suggests that a structural transition is underway in this genus. We identified only one example of a centromere moving by a long distance: a new centromere formed recently at the MAT locus of Barnettozyma californica , 250 kb from the previous centromere on that chromosome. Author summary: Centromeres are an evolutionary paradox. Their molecular function is highly conserved, but their structures vary tremendously among eukaryotes. The “point” centromeres of the yeast Saccharomyces cerevisiae are among the most unusual: they are tiny (< 200 bp) and non-repetitive, and unlike other centromeres they contain a single copy of a well-defined sequence motif. However, we have little knowledge about where these point centromeres came from, or more generally about how changes of centromere structure occur during evolution. Here, we characterized centromere structure and location in nine species of budding yeasts, spanning an evolutionary depth of approximately 200 million years. We find that the chromosomal locations of centromeres are extraordinarily well conserved, whereas their structures vary greatly. We show that sequence-defined centromeres are older and more widely distributed than previously realised. We identify some species in which the centromeres of different chromosomes have different structures, which suggests that they are in transition from one structure to another. The centromere variation observed makes it difficult to infer the ancestral structure.

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 12.85 Mb and was assembled into six chromosome-sized contigs plus a mitochondrial genome contig.

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 and was assembled into seven chromosome-sized contigs plus a mitochondrial genome contig.

Candida parapsilosis is an opportunistic fungal pathogen commonly isolated from the environment and associated with nosocomial infection outbreaks worldwide. We describe here the construction of a large collection of gene disruptions, greatly increasing the molecular tools available for probing gene function in C. parapsilosis. We use these to identify transcription factors associated with multiple metabolic pathways, and in particular to dissect the network regulating the assimilation of sulphur. We find that, unlike in other yeasts and filamentous fungi, the transcription factor Met4 is not the main regulator of methionine synthesis. In C. parapsilosis, assimilation of inorganic sulphur (sulphate) and synthesis of cysteine and methionine is regulated by Met28, a paralog of Met4, whereas Met4 regulates expression of a wide array of transporters and enzymes involved in the assimilation of organosulfur compounds. Analysis of transcription factor binding sites suggests that Met4 is recruited by the DNA-binding protein Met32, and Met28 is recruited by Cbf1. Despite having different target genes, Met4 and Met28 have partial functional overlap, possibly because Met4 can contribute to assimilation of inorganic sulphur in the absence of Met28.

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 draft level. The assemblies are 10.6 Mb and 99.57% identical.