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

Cene Gostinčar, Jason E. Stajich, Jerneja Zupančič, Polona Zalar, Nina Gunde-Cimerman

The 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. In 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. H. 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.