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Genomic Evidence for a-α Heterothallic and α-α Unisexual Mating and Recombination in an Environmental Cryptococcus deneoformans Population

M. Hitchcock,Veronica Thorn,H. Samarasinghe,Sheng Sun,J. Heitman,Jianping Xu

Published 2025 in bioRxiv

ABSTRACT

Cryptococcus deneoformans is a human fungal pathogen capable of both a-α and α-α mating and sexual reproduction in laboratory settings. However, the extent of a-α and α-α sexual reproductions in natural populations remain unexplored. Here we analyzed the whole-genome sequences of 24 environmental strains of C. deneoformans from western Saudi Arabia, including one MATa and 23 MATα isolates, with 15 MATα isolates belonging to multi-locus sequence type ST160 as defined by their combined DNA sequences at seven loci. To identify signatures for a-α and α-α reproduction, three samples were analyzed: total, MATα, and ST160. For each subpopulation, single nucleotide polymorphisms (SNPs) were identified for both the nuclear and mitochondrial genomes and subjected to four-gamete tests. In the total population and the MATα subpopulation, variable proportions of SNP pairs within as well as between the nuclear and the mitochondrial genomes showed evidence for recombination. Though no mitogenome SNPs were found among the 15 strains of ST160, the nuclear genome showed clear evidence for recombination, including among SNPs within the mating type region. In addition, the nuclear genome SNP pairs located further apart on the same chromosome showed a greater frequency of recombination in all three sample types. In contrast, mitogenome recombination breakpoints were mainly located in two genomic regions. Together, these results provide robust evidence for both a-α and α-α sexual reproduction within this environmental population of C. deneoformans. Article Summary This study compares conclusions drawn from multilocus sequence data and whole-genome SNP data regarding genetic diversity and reproduction in an environmental population of Cryptococcus deneoformans. By analyzing bi-allelic SNPs across 24 strains isolated from western Saudi Arabian soils, evidence of both a-α and α-α recombination was found, suggesting the occurrence of both a-α and α-α sexual reproduction in nature. This provides strong support for these reproductive modes and indicates diverse mechanisms of genetic exchange in fungal pathogens in nature. Additionally, our results suggest that multi-locus sequence typing underestimates genetic diversity, potentially confounding interpretations of population structure and evolutionary history.

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