Biology subjects

Wingfield, B. D.

Publications and source records attributed to Wingfield, B. D..

3 recordsLinked to original sources

bioRxiv2025

Mating-type locus structure affects gene expression in unidirectional mating-type switching fungi

Fungal species are typically either fully self-fertile or self-sterile, but some filamentous ascomycetes can commonly transition from self-fertility to self-sterility through unidirectional mating-type switching. In these fungi, the structure of the mating-type (MAT1) locus governs sexual behaviour: MAT-2 self-fertile individuals retain both MAT1-1 and MAT1-2 genes, while MAT-1 self-sterile isolates lose MAT1-2 genes during switching. A third type of isolate morphology also occurs under laboratory conditions: these are self-sterile isolates which retain both MAT1-1 and MAT1-2, but are unable to switch mating type. These are commonly referred to as MAT-2 self-sterile isolates. Two of the mating-type (MAT) genes, one of which is deleted during switching, encode transcription factors known to regulate not only the sexual cycle but also genes unrelated to mating. To test how MAT1 structural variations affects gene expression, we studied Ceratocystis albifundus, a species that switches mating type. To minimise variability caused by intraspecific genetic differences, two self-sterile isolates (MAT-1 and MAT-2 self-steriles) were derived from the same MAT-2 self-fertile parent, making all three isolates genetically identical except at the MAT1 locus. Comparative transcriptomic analyses revealed that the MAT-2 self-fertile, MAT-1 self-sterile and MAT-2 self-sterile isolates all exhibited distinct expression patterns, including differences in MAT genes, the pheromone-receptor pathway, and other genes not directly linked to mating. The results show that MAT1 locus structure influences gene expression more broadly than those only related to the sexual cycle.

molecular biology↗

bioRxiv2025

Chromosome-level genome assemblies for the latent pine pathogen, Diplodia sapinea, reveal two rapidly evolving accessory chromosomes

Diplodia sapinea (Dothideomycetes) is a latent fungal pathogen with a global distribution that predominantly infects Pinus species. The impact of the fungus is increasing due to climate-driven range expansion and thus wide-scale disease outbreaks. With the aim of developing high quality genome resources, we generated chromosome-level genome assemblies for three D. sapinea isolates and low-coverage Illumina genome data for six additional isolates. By comparing these genome assemblies, we identified 14 core chromosomes and two accessory chromosomes (ACs) in the pathogen. The ACs encode 80 and 155 proteins, respectively, while 11374 - 11609 genes were identified in the core chromosomes. Both ACs had lower gene density and higher proportions of transposable elements compared to the core chromosomes. Sequence analysis indicated that genes on the ACs are rapidly evolving, suggesting they serve as evolutionary hotspots in the species. Sequence homology analyses suggested that the ACs were likely acquired horizontally, probably from a species in the Dothideomycetes. We designed PCR-based assays to aid in the detection of the ACs and applied these on a set of 37 isolates from 14 countries. One of the ACs was detected in 33 isolates from 13 countries, while the other AC was absent in all isolates tested. Pathogenicity trials on Pinus patula seedlings showed no correlation between the presence of ACs and isolate aggressiveness. The high-quality genomes provided here offer important resources for future research on this globally important pathogen, including the biological roles of the ACs.

genomics↗

bioRxiv2025

Tracing the evolution and genomic dynamics of mating-type loci in Cryptococcus pathogens and closely related species

Sexual reproduction in basidiomycete fungi is governed by MAT loci (P/R and HD), which exhibit remarkable evolutionary plasticity, characterized by expansions, rearrangements, and gene losses often associated with mating system transitions. The sister genera Cryptococcus and Kwoniella provide a powerful framework for studying MAT loci evolution owing to their diverse reproductive strategies and distinct architectures, spanning bipolar and tetrapolar systems with either linked or unlinked MAT loci. Building on recent comparative genomic analyses, we generated additional chromosome-level assemblies, uncovering distinct trajectories shaping MAT loci organization. Contrasting with the small-scale expansions and gene acquisitions observed in Kwoniella, our analyses revealed independent expansions of the P/R locus in tetrapolar Cryptococcus, possibly driven by pheromone gene duplications. Notably, these expansions coincided with a pronounced GC-content reduction best explained by reduced GC-biased gene conversion following recombination suppression, rather than relaxed codon usage selection. Diverse modes of MAT locus linkage were also identified, including three previously unrecognized transitions: one resulting in a pseudobipolar arrangement and two leading to bipolarity. All three transitions involved translocations. In the pseudobipolar configuration, the P/R and HD loci remained on the same chromosome but genetically unlinked, whereas the bipolar transitions additionally featured rearrangements that fused the two loci into a nonrecombining region. Mating assays confirmed a sexual cycle in C. decagattii, demonstrating its ability to undergo mating and sporulation. Progeny analysis in K. mangrovensis revealed substantial ploidy variation and aneuploidy, likely stemming from haploid-diploid mating, yet evidence of recombination and loss of heterozygosity indicates that meiotic exchange occurs despite irregular chromosome segregation. Our findings underscore the importance of continued diversity sampling and provide further evidence for convergent evolution of fused MAT loci in basidiomycetes, offering new insights into the genetic and chromosomal changes driving reproductive transitions.

genetics↗