Phylogenomics of the Metschikowia pulcherrima species
Metschnikowia pulcherrima, an ascomycetous yeast, has been frequently isolated from various substrates associated with agriculture such as soils, nutrient-rich plant materials such as fruits, fruit flies and various insects that probably use these plant materials as feeding and breeding ground and especially from fruit juices and fermenting grape must. Due to the growing consumer demand for wines with reduced levels of additives such as sulphites, this yeast species has attracted great interest for its ability to compete with other fungi. However, many species close to M. pulcherrima have been described in the last 20 years, being grouped together as M. pulcherrima on the basis of barcodes (Sipiczki 2022) and the reality of this diversity has been contested. In this project we performed a genomic characterisation of 63 strains, including 10 synonyms type strains, and the combination of different genomic scale analyses shows beyond any doubt the existence of a main single cluster of strains representing the species M. pulcherrima, and a small basal cluster related to M. chrysoperlae that appeared as potential triploid hybrids. Metschnikowia pulcherrima strains showed high heterozygosity, significantly higher than S. cerevisiae, with the presence of large loss of heterozygosity (LOH) segments in some of them, and three strains were found to be homozygotes. A strong linkage disequilibrium decay, also suggests an active recombination in this species.
Metschnikowia pulcherrima, an ascomycetous yeast, has been frequently isolated from various substrates associated with agriculture such as soils, nutrient-rich plant materials such as fruits, fruit flies and various insects that probably use these plant materials as feeding and breeding ground and especially from fruit juices and fermenting grape must. Due to the growing consumer demand for wines with reduced levels of additives such as sulphites, this yeast species has attracted great interest for its ability to compete with other fungi. However, many species close to M. pulcherrima have been described in the last 20 years, being grouped together as M. pulcherrima on the basis of barcodes (Sipiczki 2022) and the reality of this diversity has been contested. In this project we performed a genomic characterisation of 63 strains, including 10 synonyms type strains, and the combination of different genomic scale analyses shows beyond any doubt the existence of a main single cluster of strains representing the species M. pulcherrima, and a small basal cluster related to M. chrysoperlae that appeared as potential triploid hybrids. Metschnikowia pulcherrima strains showed high heterozygosity, significantly higher than S. cerevisiae, with the presence of large loss of heterozygosity (LOH) segments in some of them, and three strains were found to be homozygotes. A strong linkage disequilibrium decay, also suggests an active recombination in this species.
INRAE