Using Whole Genome Sequencing to Decipher the Metschnikowia pulcherrima Complex

Metschnikowia pulcherrima, an ascomycetous yeast, has been frequently isolated from various substrates associated with agriculture such as nutrient-rich plant materials (fruit, fruit juices and fermenting grape must), soil and with various insects including fruit flies. Due to the growing consumer demand for wines with reduced levels of additives such as sulphites, there has been great interest in this yeast species for its ability to compete with other fungi. Despite having similar phenotypes, many species related to M. pulcherrima have been described in the last 20 years based on the sequences of the LSU D1/D2 domain. These species were grouped together as M. pulcherrima based on primary and secondary barcode sequences, physiological tests and hybridization experiments (Sipiczki 2022a). However, this new classification is supported by limited genetic information. In this project we performed a genomic characterization of 63 strains, including 10 type strains of current synonyms. The combination of different genomic-scale analyses (ANI, k-mer, Busco genes, whole-genome genotyping) conclusively demonstrated the existence of a main cluster of strains representing the M. pulcherrima species and a small sister cluster related to M. chrysoperlae that appeared as potential triploid hybrids. We also observed a high heterozygosity in M. pulcherrima which was significantly higher than S. cerevisiae and the presence of some homozygous strains. Strong linkage disequilibrium decay also suggests active outcrossing leading to recombination in this species. This demonstrates the power of phylogenomic in resolving taxonomic issues and the ability of such approaches to provide information on the life cycle of this species.