The molecular characterization of new types of Saccharomyces cerevisiae × S. kudriavzevii hybrid yeasts unveils a high genetic diversity

Abstract

New double-and triple-hybrid Saccharomyces yeasts were characterized using PCRrestriction fragment length polymorphism of 35 nuclear genes, located on different chromosome arms, and the sequencing of one nuclear and one mitochondrial gene. Most of these new hybrids were originally isolated from fermentations; however, two of them correspond to clinical and dietary supplement isolates. This is the first time that the presence of double-hybrid S. cerevisiae  S. kudriavzevii in non-fermentative substrates has been reported and investigated. Phylogenetic analysis of the MET6 nuclear gene confirmed the double or triple parental origin of the new hybrids. Restriction analysis of gene regions in these hybrids revealed a high diversity of genome types. From these molecular characterizations, a reduction of the S. kudriavzevii fraction of the hybrid genomes is observed in most hybrids. Mitochondrial inheritance in hybrids was deduced from the analysis of mitochondrial COX2 gene sequences, which showed that most hybrids received the mitochondrial genome from the S. kudriavzevii parent. However, two strains inherited a S. cerevisiae COX2, being the first report of S. cerevisiae  S. kudriavzevii hybrids with S. cerevisiae mitochondrial genomes. These two strains are those showing a higher S. kudriavzevii nuclear genome reduction, especially in the wine hybrid AMH. This may be due to the release of selective pressures acting on the other hybrids to maintain kudriavzevii mitochondriainteracting genes.

Evolutionary Role of Interspecies Hybridization and Genetic Exchanges in Yeasts

“…Molecular characterization of wine, beer, or cider yeasts revealed numerous independently formed hybrids between S. cerevisiae and S. kudriavzevii (8,9,22,57,63,64,120,121,164,198), between S. cerevisiae and S. bayanus (60,78,106,133,134,141,146,175,198), and even (triple hybrids) between S. cerevisiae, S. kudriavzevii, and S. bayanus (18,32,62). Such hybrids often exhibit more robust characteristics than the parental strains, such as tolerance to various stresses induced by artificial fermentations (11,174,175,216).…”

“…Hybrids have also been observed in natural environments (78,164,238). Indeed, it appears so universal between Saccharomyces yeasts that even some type strains, normally used to define the species, may eventually prove to be hybrids themselves after more extensive analysis.…”

“…Genome data are also particularly powerful for reconstructing phylogenies, one of the criteria used to define species in addition to the classical morphological and biological criteria (214). These data, although still limited relative to the large number of extant yeast isolates (101), were already sufficient to reveal the presence of introgressions between distantly related species (95,141,149,159), as well as the existence of natural hybrid genomes at various stages in their evolution (12,43,105,164).…”

Selection of Saccharomyces cerevisiae Strains Applied to the Production of Prieto Picudo Rosé Wines with a Different Aromatic Profile

“…1). A detailed analysis of clone P5/7 was also performed: restriction analyses of 35 nuclear genes and sequencing of the MET6 nuclear gene and the COX2 mitochondrial gene confirmed that this clone was a S. cerevisiae x S. kudriavzevii hybrid yeast (clone named PB7 in Peris et al 2012). The RFLP-mtDNA analysis led us to detect 119 different strains (Fig.…”

“…Lanes: M1, 25 bp ladder (Invitrogen); M2, 100 bp ladder (Invitrogen); 1, G6/25 clone corresponds to a typical S. cerevisiae strain (bands of 325, 230, 175 and 125 bp); 2, G6/2 clone exhibited an abnormal restriction pattern due to a point mutation generating a new HaeIII site that resulted in the splitting of the typical 175 bp HaeIII band into two new bands of 145 bp and 30 bp (indicated by a black arrow); 3, P5/7 clone also exhibited a non-typical restriction pattern that corresponded to a S. cerevisiae x S. kudriavzevii hybrid yeast (Peris et al, 2012).…”