Phylogenetic analysis of the Saccharomyces cerevisiae group based on polymorphisms of rDNA spacer sequences

This study examined phylogenetic relationships among closely related yeast species in the Saccharomyces sensu stricto group using molecular analysis of ribosomal DNA spacer sequences. Researchers analyzed 23 type strains representing different Saccharomyces species plus 26 wine yeast strains from French vineyards using two approaches: RFLP (restriction fragment length polymorphism) analysis of PCR-amplified internal transcribed spacer (ITS) and intergenic spacer (IGS) regions, and direct DNA sequencing of ITS regions. Both methods revealed two well-separated phylogenetic clusters termed 'cerevisiae' and 'bayanus.' The cerevisiae cluster contained S. cerevisiae and most related species (16 of 23 type strains), while the bayanus cluster contained S. bayanus and seven type strains. However, S. pastorianus and S. paradoxus could not be clearly separated from their respective clusters. Among wine yeasts, most (16 of 26) clustered with cerevisiae species, while 10 grouped within bayanus. The analysis confirmed rDNA spacer polymorphisms as a practical method for characterizing Saccharomyces strains used in food production, with IGS sequences showing greater variability than ITS sequences.

Key findings

• RFLP and sequence analysis of rDNA spacers divided Saccharomyces strains into two distinct phylogenetic clusters: 'cerevisiae' (containing 15 of 23 type strains) and 'bayanus' (containing 7 type strains), confirming S. cerevisiae and S. bayanus as well-defined taxa.
• S. pastorianus and S. paradoxus could not be clearly separated from their respective clusters, suggesting these species may represent subspecific variants rather than distinct taxa.
• PCR-RFLP analysis generated 18 different ITS types and 17 different IGS types among type strains, with IGS sequences showing higher polymorphism (92% of fragments were polymorphic) than ITS sequences (85% polymorphic).
• Wine yeast strains showed less genetic diversity than type strains, with multiple strains sharing identical RFLP patterns, and distribution predominantly in the cerevisiae cluster (16 of 26 strains).
• PCR-RFLP analysis of rDNA spacer sequences is a practical and suitable method for characterizing and identifying Saccharomyces strains in food processing applications.