Biology subjects

Helmstetter, N.

Publications and source records attributed to Helmstetter, N..

5 recordsLinked to original sources

bioRxiv2026

Genomic hallmarks of parasexual reproduction in three hybrid groups of the human pathogen Cryptococcus neoformans

Hybridization is a major driver of fungal evolution, yet knowledge of the molecular mechanisms underpinning hybridization and its genomic impact remain limited. Here, we analyse 197 Cryptococcus neoformans genomic sequences, including 13 newly sequenced strains, identifying three genetically clustered and distinct hybrid groups (H1, H2 and H3) each with unique parental origins and ecological associations. Using phylogenomics, population structure analyses, and long-read genome assemblies, we identified hybrid genomes with chromosome-wide loss of heterozygosity (LOH), inheritance of large intact parental haplotype blocks and widespread aneuploidy within and across genomes. These patterns are also observed when progeny were generated with spo11{Delta} parents, indicating these features are a result of a meiotic-independent process such as parasex. This is further underscored by discovery of haploid and near-haploid recombinants in both spo11{Delta} mutant progeny and reanalysed wild-type hybrid progeny. We hypothesise these haploid and near-haploid recombinants are generated through ploidy reduction via independent chromosome assortment because of concerted chromosomal loss, which is a key feature of the parasexual cycle. Phenotypic assays demonstrated that several hybrid isolates have diverse growth and virulence patterns, underscoring functional consequences of genome plasticity. Together, our work suggests a non-meiotic reproductive process contributes to shape the genotypic and phenotypic diversity of Cryptococcus neoformans.

genomics↗

bioRxiv2026

Global genomic epidemiology of Candida auris: analysis of 12,644 whole genome sequences from 1997-2024

Candida auris is a critical priority fungal pathogen (World Health Organization) that has emerged into human populations pre-1996 from an unknown environmental reservoir. Genomic sequencing data has been used extensively in the last decade, leading to a largely unharnessed dataset with potential to unlock understanding of emerging fungal pathogen evolution. Here, we compiled publicly available Illumina paired-end whole genome sequences (WGS) for variant calling, supplemented by isolates from the worlds first four-clade single-facility outbreak in Algeria (n = 7), totaling 12,644 WGS. We describe the geographic, clinical, and temporal epidemiology of the outbreak across the globe between 1997 and 2024, indicating a conserved six-clade structure. Despite the evidence of earlier species diversity in low- and lower-middle income countries (LLMIC), the majority of WGS derived from high-income (12,035, 93.2%) and upper-middle-income countries (719, 5.57%), where cases are believed to be imported from endemic regions, with few from lower-middle-income countries (165, 1.28%) and none from lower-income countries. Copy number variation was present, including azole drug target ERG11, with seven isolates displaying ten to fifteen copies. Alarmingly, the standing variation of C. auris reveals emerging variation in hot-spots of the echinocandin drug target FKS1, which encodes a {beta}-1,3-glucan synthase. Eighteen emerging FKS1 hot-spot variants have not been detected or described in databases, and mostly occured in Northern America (57/61, 93.4%), where echinocandin monotherapy is standard treatment. Well-studied FKS1 variants known to cause resistance are significantly more common in clade I isolates derived from urine compared to blood, consistent with a role for the urinary niche as a low echinocandin concentration safe-haven for the development of resistance. The insights from this global genomic epidemiology survey of C. auris highlight sequencing inequality and detect ongoing genomic innovation in clinical settings, raising predictable and urgent concerns around the ongoing use of echinocandin monotherapy and potential emerging antifungal drug resistance-related genotypes in high-income settings.

microbiology↗

bioRxiv2024

A near-complete telomere-to-telomere genome assembly for Batrachochytrium dendrobatidis GPL JEL423 reveals a CBM18 gene family expansion and a M36 metalloprotease gene family contraction.

Batrachochytrium dendrobatidis (Bd) is responsible for mass extinctions and extirpations of amphibians, mainly driven by the Global Panzootic Lineage (BdGPL). BdGPL isolate JEL423 is a commonly used reference strain in studies exploring the evolution, epidemiology and pathogenicity of chytrid pathogens. These studies have been hampered by the fragmented, erroneous and incomplete B. dendrobatidis JEL423 genome assembly, which includes long stretches of ambiguous positions, and poorly resolved telomeric regions. Here we present and describe a substantially improved, near telomere-to-telomere genome assembly and gene annotation for B. dendrobatidis JEL423. Our new assembly is 24.5 Mb in length, [~]800 kb longer than the previously published assembly for this organism, comprising 18 nuclear scaffolds and 2 mitochondrial scaffolds and including an extra 839 kb of repetitive sequence. We discovered that the patterns of aneuploidy in B. dendrobatidis JEL423 have remained stable over approximately 5 years. We found that our updated assembly encodes fewer than half the number of M36 metalloprotease genes predicted in the previous assembly. In contrast, members of the crinkling and necrosis gene family were found in similar numbers to the previous assembly. We also identified a more extensive carbohydrate binding module 18 gene family than previously observed. We anticipate our findings, and the updated genome assembly will be a useful tool for further investigation of the genome evolution of the pathogenic chytrids. Author SummaryB. dendrobatidis is a fungus that has been implicated in the extinctions and declines of dozens of amphibians globally. Here we describe a new genome assembly for the commonly used B. dendrobatidis isolate JEL423, which is a substantial improvement from the previously used assembly. Compared with the previous assembly, we reveal that some gene families (such as carbohydrate binding module 18 genes) are more expanded than previously recognised, while others (such as the M36 metalloproteases) are more contracted than previously recognised. Our new genome assembly will be useful for future work exploring the pathogenicity, epidemiology and evolution of chytrid fungi.

genomics↗

bioRxiv2024

Xenosiderophore transporter gene expression and clade-specific filamentation in Candida auris killifish infection

Candida auris is a critical priority fungal pathogen (World Health Organization). Clinical management is challenging due to a high mortality rate, rapidly increasing antifungal resistance, and frequent nosocomial outbreaks. A critical bottleneck in understanding virulence is the lack of gene expression profiling models during infection. We developed a fish embryo yolk-sac microinjection model using Aphanius dispar (Arabian killifish; AK) at human body temperature. This enabled interrogation of infection dynamics via dual host-pathogen RNA-seq across five major clades of C. auris (I-V). Host responses included heat shock, complement activation, and nutritional immunity, notably haem oxygenase (HMOX) expression during clade IV infection. We identified a pathogen transcriptional signature across all five clades of C. auris strongly enriched for putative xenosiderophore transmembrane transporters. We describe this novel family and a sub-clade of five putative haem transport-related (HTR) genes. Only the basal clade V isolate formed filaments, associated with canonical and atypical regulators of morphogenesis. Clades I and IV demonstrated increased virulence, accompanied by up-regulation of three HTR genes in clade IV, and the non-mating mating-type locus (MTL) gene PIKA in both clades. Our study provides new insight into C. auris pathogenesis, highlighting species-wide in vivo up-regulation of XTC genes during host tissue infection. Significance statementCandida auris is an emerging human fungal pathogen and global public health threat, yet in vivo transcriptomic analysis of tissue infection has remained elusive. Using yolk-sac infection in Arabian killifish, we profiled gene expression across five major C. auris clades. We found that the basal clade V uniquely undergoes filamentation during infection, while all clades upregulate members of a large, expanded family of xenosiderophore transporter candidate genes. These findings highlight the important roles for iron acquisition and morphological switching in pathogenesis, revealing potential mechanisms of immune evasion and fungal persistence, and identifying candidate targets for antifungal therapy.

microbiology↗

bioRxiv2021

Two-speed genome expansion drives the evolution of pathogenicity in animal fungal pathogens

The origins of virulence in amphibian-infecting chytrids Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal) are largely unknown. Here, we use deep nanopore sequencing of Bsal and comparative genomics against 21 high-quality genome assemblies that span the fungal Chytridiomycota. Bsal has the most repeat-rich genome, comprising 40.9% repetitive elements, which has expanded to more than 3X the length of its conspecific Bd. M36 metalloprotease virulence factors are highly expanded in Bsal and 53% of the 177 unique genes are flanked by transposable elements, suggesting repeat-driven expansion. The largest M36 sub-family are mostly (84%) flanked upstream by a novel LINE element, a repeat superfamily implicated with gene copy number variations. We find that Bsal has a highly compartmentalized genome architecture, with virulence factors enriched in gene-sparse/repeat-rich compartments, while core conserved genes occur in gene-rich/repeat-poor compartments. This is a hallmark of two-speed genome evolution. Furthermore, genes with signatures of positive selection in Bd are enriched in repeat-rich regions, suggesting they are a cradle for chytrid pathogenicity evolution, and Bd also has a two-speed genome. This is the first evidence of two-speed genomes in any animal pathogen, and sheds new light on the evolution of fungal pathogens of vertebrates driving global declines and extinctions.

genomics↗