Marincowitz, S. | Search bioRxiv

bioRxiv2025

Phylogenetic and population genetic analyses reveal patterns of divergence among isolates in the Ceratocystis manginecans complex

The taxonomic boundaries within the Ceratocystis manginecans complex have remained contentious due to limited morphological variation, interfertility in laboratory mating studies, and the application of different species concepts. However, recent studies have highlighted significant differences among isolates, such as host associations and biological traits, all with important implications for disease management. We examined the phylogenetic relationships, genetic diversity, and population structure of isolates treated broadly in the Ceratocystis manginecans complex, specifically those treated as C. eucalypticola and C. manginecans in various studies. This study included a comprehensive dataset of isolates from multiple hosts and regions, including both historical and recent outbreaks of Ceratocystis canker and wilt disease. Detailed morphological comparisons for representative isolates residing in discrete clades were conducted. Phylogenetic analyses of sequence data for seven gene regions, supported by multilocus genotyping of 16 SSR loci, identified two genetically distinct groups that broadly separated isolates having distinct ecological characteristics, the most relevant of which are infections primarily of roots or above ground tree parts. Morphological comparisons also provided support for the two groupings. Although the results supported the existence of two groups in the C. manginecans complex, there was also evidence of hybridization between isolates in the respective groups suggesting incomplete reproductive isolation, leading to taxonomic ambiguity. Isolates in the two groups are, therefore, treated as distinct lineages within the C. manginecans complex, recognizing their divergence while maintaining a conservative taxonomic approach.

evolutionary biology↗

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↗