Genetic Changes in Experimental Populations of a Hybrid in the Cryptococcus neoformans Species Complex

Abstract

Hybrids between Cryptococcus neoformans and Cryptococcus deneoformans are commonly found in patients and the environment. However, the genetic stability of these hybrids remains largely unknown. Here, we established mutation accumulation lines of a diploid C. neoformans × C. deneoformans laboratory hybrid and analyzed the genotypes at 33 markers distributed across all 14 chromosomes. Our analyses found that under standard culture conditions, heterozygosity at most loci was maintained over 800 mitotic generations, with an estimated 6.44 × 10−5 loss-of-heterozygosity (LoH) event per mitotic division. However, under fluconazole stress, the observed LoH frequency increased by > 50 folds for the two markers on Chromosome 1, all due to the loss of the fluconazole susceptible allele on this chromosome. Flow cytometry analyses showed that after the 40th transfer (120 days), 19 of the 20 lines maintained the original ploidy level (2N), while one line was between 2N and 3N. The combined flow cytometry, genotyping at 33 markers, and quantitative PCR analyses showed the allelic loss was compensated for by amplification of the resistant ERG11 allele in eight of the ten fluconazole-stress lines. Our results suggest that hybrids in C. neoformans species complex are generally stable but that they can undergo rapid adaptation to environmental stresses through LoH and gene duplication.

Fungal species concepts in the genomics era

“…On the other hand, divergent populations with significant genome sequence and chromosome structure differences can mate and generate viable sexual progeny (e.g., Samarasinghe and Xu 2018;Steenkamp et al 2018;You and Xu 2018). Furthermore, sterile fungal hybrids can reproduce asexually by mitosis and generate abundant genetic diversity through mitotic recombination, contributing to their rapid adaptations to novel environmental conditions (Mixao and Gabaldon 2018; Dong et al 2020;Samarasinghe et al 2020). Indeed, the uniqueness of fungal reproduction has made the application of bio-logical species concepts to define fungal species often not practical (Singer 1986;Kurtzman et al 2011).…”

Mitochondrial Genome Polymorphisms in the Human Pathogenic Fungus Cryptococcus neoformans

“…During asexual reproduction, both the nuclear and mitochondrial genomes are faithfully transmitted from the parental cells to offspring. However, new mutations could emerge during asexual reproduction, including nucleotide substitutions and changes in chromosome structure and chromosome number, especially under certain selection pressure such as exposure to antifungal drugs (e.g., Hua et al, 2019;Dong et al, 2020). If asexual reproduction were the only mode of reproduction for C. neoformans in nature, we should observe strain relationships inferred based on their nuclear genome sequences to be similar to those based on their mitochondrial genome sequences.…”

Hybridization Facilitates Adaptive Evolution in Two Major Fungal Pathogens

“…A very recent study conducted by Dong et al estimated the rate of LOH during mutation accumulation in a laboratory-constructed diploid AD hybrid (CDC15 × JEC20) during mitotic divisions. They used 33 genetic markers located on 14 chromosomes to determine genome-wide allele distributions in the AD hybrid [76]. The parental haploid strain CDC15 (serotype A, MATα) is more resistant to fluconazole (minimum inhibitory concentration [MIC] = 64 µg/mL) than the other parent JEC20 (serotype D, MATa, MIC = 4 µg/mL).…”

“…Hybrids face significant challenges to survival and functionality due to two divergent genomes residing in the same cell. In a process referred to as genome stabilization, hybrids eliminate unfavorable combinations of the two parental genomes via a variety of mechanisms including recombination, gene conversion and chromosome loss [76]. The rate at which genome stabilization is achieved in a hybrid may be related to the extent of divergence between the two parental genomes, since incompatibilities between more differentiated genomes will be resolved faster within the hybrids.…”