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.

Abstract Homing genetic elements are selfish elements that insert themselves into a specific site in a host gene without disrupting its function. They spread through the population because the element codes for an endonuclease that cleaves alleles of the host gene that do not contain the element, leading to DNA repair by gene conversion that increases the element’s frequency. Most homing genetic elements in eukaryotes are either self-splicing introns or inteins but we recently discovered a third category, called WHO elements, in the budding yeast genus Torulaspora . WHO elements code for endonuclease proteins with LAGLIDADG motifs and a zinc finger domain, and are related to the mating-type switching endonuclease HO. Their host gene is the aldolase gene FBA1 , which is essential. Clusters of up to 9 diverse WHO endonuclease genes are found downstream of FBA1 in different isolates of Torulaspora . Here, we show that there is a genetic conflict between WHO endonucleases and their target site in FBA1. Different alleles of FBA1 vary in their sensitivity or resistance to cleavage by individual WHO endonucleases. We show that a WHO endonuclease recognizes a 28-bp sequence in FBA1 and does not tolerate much sequence variation, but also that this region of FBA1 has experienced positive selection for sequence diversification to evade cleavage. WHO endonucleases and their target site in FBA1 are therefore engaged in an arms race in which each WHO element is under selection to home into other elements, while avoiding being homed into. Significance Statement WHO elements are a recently discovered type of homing genetic element in yeasts, targeting the aldolase gene FBA1 . Rather than disrupting FBA1 when they integrate, WHO elements instead replace the 3’ half of the gene with an alternative FBA1 3’ half. Each WHO element consists of an endonuclease gene and a version of the 3’ half of FBA1 , and there is high sequence diversity in both genes. We show that there is an evolutionary arms race between WHO endonucleases and their target site in FBA1 , which has resulted in rapid evolution of both genes and the formation of clusters of WHO elements at the FBA1 locus.

The first European isolates of Saccharomyces eubayanus were discovered in Ireland in 2022 and belong to the same clade as the S. eubayanus parent of the hybrid lager yeast Saccharomyces pastorianus. Here, we report the isolation of 10 additional Irish strains and we explore maltose metabolism. Maltose metabolism genes are clustered in subtelomeric MAL loci including maltase (MALS), maltose transporter (MALT), and regulator (MALR). Despite having intact MAL loci, the Irish strains do not grow on maltose. Two Irish S. eubayanus strains (UCD650 and UCD926) were passaged in medium containing maltose as the sole carbon source until they acquired the ability to metabolize maltose. The UCD650-derived lineage acquired an I243N substitution in MalR, and a 30-kb duplication of the MAL locus. The UCD926 parent has a similar MAL locus duplication and its evolved lineage acquired a W307L substitution in MalR. Expression of MALT and MALS was increased in the evolved isolates. Introducing the W307L mutation into UCD926 by CRISPR-Cas9 editing fully recapitulates the maltose utilization phenotype. The I243N variant alone has little effect on expression of maltose genes. We find that maltose utilization is influenced both by the copy number of MAL genes and by gain-of-function mutations in MalR.

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 <75%, supporting their designation as novel species. Here, we propose the names Cyberlindnera hibernica sp. nov. and Barnettozyma discipulorum sp. nov. for PYCC 10015 and PYCC 10016, respectively.

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.

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 homing introns, were discovered decades ago. In this review we describe WHO elements, a newly discovered type of homing element that constitutes a distinct third category but is rare, having been found only in a few yeast species so far. WHO elements are inferred to spread using the same molecular homing mechanism as inteins and introns: they encode a site-specific endonuclease that cleaves the genome at the target site, making a DNA break that is subsequently repaired by copying the element. For most WHO elements, the target site is in the glycolytic gene FBA1. WHO elements differ from inteins and homing introns in two fundamental ways: they do not interrupt their host gene (FBA1), and they occur in clusters. The clusters were formed by successive integrations of different WHO elements into the FBA1 locus, the result of an ‘arms race’ between the endonuclease and its target site. We also describe one family of WHO elements (WHO10) that is no longer specifically associated with the FBA1 locus and instead appears to have become transposable, inserting at random genomic sites in Torulaspora globosa with up to 26 copies per strain. The WHO family of elements is therefore at the borderline between homing genetic elements and transposable elements.

Identifying how various components of climate change will influence ecosystems and vegetation subsistence will be fundamental to mitigate negative effects. Climate change-induced waterlogging is understudied in comparison to temperature and CO2. Grasslands are especially vulnerable through the connection with global food security, with perennial ryegrass dominating many flood-prone pasturelands in North-western Europe. We investigated the effect of long-term waterlogging on phenotypic responses of perennial ryegrass using four common varieties (one diploid and three tetraploid) grown in atmospherically controlled growth chambers during two months of peak growth. The climate treatments compare ambient climatological conditions in North-western Europe to the RCP8.5 climate change scenario in 2050 (+2°C and 550 ppm CO2). At the end of each month multiple phenotypic plant measurements were made, the plants were harvested and then allowed to grow back. Using image analysis and principal component analysis (PCA) methodologies, we assessed how multiple predictors (phenotypic, environmental, genotypic, and temporal) influenced overall plant performance, productivity and phenotypic responses. Long-term waterlogging was found to reduce leaf-color intensity, with younger plants having purple hues indicative of anthocyanins. Plant performance and yield was lower in waterlogged plants, with tetraploid varieties coping better than the diploid one. The climate change treatment was found to reduce color intensities further. Flooding was found to reduce plant productivity via reductions in color pigments and root proliferation. These effects will have negative consequences for global food security brought on by increased frequency of extreme weather events and flooding. Our imaging analysis approach to estimate effects of waterlogging can be incorporated into plant health diagnostics tools via remote sensing and drone-technology.

Candida sanyaensis is a CUG-Ser1 clade yeast that is associated with soil. Assembly of short-read and long-read data shows that C. sanyaensis has a diploid and hybrid genome, with approximately 97% identity between the haplotypes. The haploid genome size is approximately 15.4 Mb.