Genomic Evidence for a-α Heterothallic and α-α Unisexual Mating and Recombination in an Environmental <i>Cryptococcus deneoformans</i> Population
Bibliographic record
Abstract
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 MAT a and 23 MAT α isolates, with 15 MAT α 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, MAT α, 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 MAT α 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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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".