The curious case of the black yeast Hortaea werneckii and its genome duplication


Cene Gostinčar 1 Polona Zalar 1 Jerneja Zupančič 1 Janja Zajc 1 Jason E. Stajich 2 Nina Gunde-Cimerman 1
1Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
2Department of Plant Pathology and Microbiology, Institute for Integrative Genome Biology, University of California, Riverside, California, USA

The black yeast Hortaea werneckii (Pezizomycotina, Dothideomycetes, Capnodiales) is notable for its extreme halotolerance, being able to thrive at near-saturating concentrations of sodium chloride, but also growing in normal media without added salt. Cellular mechanisms behind its physiology are of considerable scientific interest, also due to their possible applications. However, nearly two decades of research on H. werneckii extremotolerance and taxonomy have been hampered by its diploid genome since the very beginning. The genome of the species has been published in 2013, but it was of poor quality due to suboptimal assembly of conserved duplicated regions. Four years later this led to a publication of a second genomic sequence, improved by the use of long-read, single-molecule sequencing. Analysis of duplicated genes showed that their coding sequences differed in almost 10% of nucleotides, while in 400 bp long upstream regions of these genes the level of mismatches was around 15%. The level of divergence and the structure of the predicted mating locus led to the conclusion that the diploid H. werneckii genome is most likely a consequence of a relatively recent endoreduplication rather than intra- or interspecific hybridisation. However, the conclusions that can be drawn from a single genome sequence are necessarily limited. In order to further investigate the phylogeny of H. werneckii and address the origin of its diploidisation, we re-sequenced 11 strains of the species isolated from different habitats around the world, as well as a strain of the related Hortaea thailandica. Results of the comparative genomic analyses of these data will be presented with a special focus on the whole genome duplication of H. werneckii and the challenges such a genome represents to wet laboratory and bioinformatic work.