Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast

Abstract

BackgroundThe black yeast Hortaea werneckii (Dothideomycetes, Ascomycota) is one of the most extremely halotolerant fungi, capable of growth at NaCl concentrations close to saturation. Although dothideomycetous fungi are typically haploid, the reference H. werneckii strain has a diploid genome consisting of two subgenomes with a high level of heterozygosity.ResultsIn order to explain the origin of the H. werneckii diploid genome we here report the genome sequencing of eleven strains isolated from different habitats and geographic locations. Comparison of nine diploid and two haploid strains showed that the reference genome was likely formed by hybridization between two haploids and not by endoreduplication as suggested previously. Results also support additional hybridization events in the evolutionary history of investigated strains, however exchange of genetic material in the species otherwise appears to be rare. Possible links between such unusual reproduction and the extremotolerance of H. werneckii remain to be investigated.ConclusionsH. werneckii appears to be able to form persistent haploid as well as diploid strains, is capable of occasional hybridization between relatively heterozygous haploids, but is otherwise limited to clonal reproduction. The reported data and the first identification of haploid H. werneckii strains establish this species as a good model for studying the effects of ploidy and hybridization in an extremotolerant system unperturbed by frequent genetic recombination.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4751-5) contains supplementary material, which is available to authorized users.

Fifty Aureobasidium pullulans genomes reveal a recombining polyextremotolerant generalist

“…However, although the perception of many fungi as predominantly or strictly clonal has been changed through population genetics and genomics studies (Taylor et al, 2015), this is not necessarily true for all species. The extremely halotolerant Hortaea werneckii, which is another black yeast from extreme environments, was described to form unusually stable diploid strains through hybridization between relatively heterozygous ancestors, although apart from this, H. werneckii appears to be limited to clonal reproduction (Gostin car et al, 2018). Indeed, despite the apparent lack of recombination between strains of H. werneckii and the strong evidence for recombination between strains of A. pullulans, the inferred mating locus architecture of these two species is very similar: mating genes 1-1 and 1-2, flanked by genes that encode a pleckstrin homology domain protein and a transmembrane transporter on the one side, and an anaphase-promoting complex subunit and a DNA lyase on the other.…”

“…Culture, medium and growth conditions Fifty-four A. pullulans-like strains collected from various habitats around the world (Table 1) were obtained from the Ex Culture Collection of the Department of Biology, Biotechnical Faculty, University of Ljubljana (Slovenia) and were previously identified based on their internal transcribed spacer sequences. Their cultivation and DNA isolation were performed as described previously (Gostin car et al, 2018). In short, biomass was grown in the standard chemically defined Yeast Nitrogen Base medium (Qbiogene) with 0.5% (w/v) ammonium sulphate and 2% (w/v) glucose.…”

Fungal evolution: cellular, genomic and metabolic complexity

“…This event has contributed to the expansion of cationic transporters, important in surviving high salinity. The origin of this whole‐genome duplication has been ascribed to an inter‐species hybridization event (Gostinčar et al ., ). We are confident that many ancient whole‐genome duplication events resulting from either auto‐ or allopolyploidization events, are yet to be identified and will be discovered once sufficient genome sampling is available for enough fungal clades.…”

Hybridization Facilitates Adaptive Evolution in Two Major Fungal Pathogens

“…involved in beer brewing [115,116]. Finally, two examples of human pathogenic species appear to be largely of hybrid origin: the halophilic black yeast Hortaea warnecki is the cause of superficial skin infection, tinea nigra [117] and the recently described, but rare, Candida metapsilosis [118].…”