Front. Fungal Biol. | doi: 10.3389/ffunb.2021.742894

Patterns of genomic instability in interspecific yeast hybrids with diverse ancestries

Provisionally accepted
The final, formatted version of the article will be published soon
  • 1Population Genetics Division, Department of Zoology, Stockholm University, Sweden
  • 2Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Norway
  • 3Department of Health, Valencian International University, Spain

The genomes of hybrids often show substantial deviations from the features of the parent genomes, including genomic instabilities characterized by chromosomal rearrangements, gains and losses. This plastic genomic architecture generates phenotypic diversity, potentially giving hybrids access to new ecological niches. It is however unclear if there are any generalizable patterns and predictability in the type and prevalence of genomic variation and instability across hybrids with different genetic and ecological backgrounds. Here, we analyzed the genomic architecture of 204 interspecific Saccharomyces yeast hybrids isolated from natural, industrial fermentation, clinical, and laboratory environments. Synchronous mapping to all eight putative parental species showed significant variation in read depth indicating frequent aneuploidy, affecting 44% of all hybrid genomes and particularly smaller chromosomes. Early generation hybrids with largely equal genomic content from both parent species were more likely to contain aneuploidies than introgressed genomes with an older hybridization history, which presumably stabilized the genome. Shared k-mer analysis showed that the degree of genomic diversity and variability varied among hybrids with different parent species. Interestingly, more genetically distant crosses produced more similar hybrid genomes, which may be a result of stronger negative epistasis at larger genomic divergence, putting constraints on hybridization outcomes. Mitochondrial genomes were typically inherited from the species also contributing the majority nuclear genome, but there were clear exceptions to this rule. Together, we find reliable genomic predictors of instability in hybrids, but also report interesting cross- and environment-specific idiosyncrasies. Our results are an important step in understanding the factors shaping divergent hybrid genomes and their role in adaptive evolution.

Keywords: yeast, hybridization, Aneuploidy, Introgression, genome instability, Loss of heterozygosity (LOH), Saccharomyces

Received: 16 Jul 2021; Accepted: 06 Sep 2021.

Copyright: © 2021 Bendixsen, Peris and Stelkens. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Devin P. Bendixsen, Stockholm University, Population Genetics Division, Department of Zoology, Stockholm, Sweden, devin.bendixsen@zoologi.su.se