Chimeric Genomes of Natural Hybrids of Saccharomyces cerevisiae and Saccharomyces kudriavzevii

Recently, a new type of hybrid resulting from the hybridization between Saccharomyces cerevisiae and Saccharomyces kudriavzevii was described. These strains exhibit physiological properties of potential biotechnological interest. A preliminary characterization of these hybrids showed a trend to reduce the S. kudriavzevii fraction of the hybrid genome. We characterized the genomic constitution of several wine S. cerevisiae × S. kudriavzevii strains by using a combined approach based on the restriction fragment length polymorphism analysis of gene regions, comparative genome hybridizations with S. cerevisiae DNA arrays, ploidy analysis, and gene dose determination by quantitative real-time PCR. The high similarity in the genome structures of the S. cerevisiae × S. kudriavzevii hybrids under study indicates that they originated from a single hybridization event. After hybridization, the hybrid genome underwent extensive chromosomal rearrangements, including chromosome losses and the generation of chimeric chromosomes by the nonreciprocal recombination between homeologous chromosomes. These nonreciprocal recombinations between homeologous chromosomes occurred in highly conserved regions, such as Ty long terminal repeats (LTRs), rRNA regions, and conserved protein-coding genes. This study supports the hypothesis that chimeric chromosomes may have been generated by a mechanism similar to the recombination-mediated chromosome loss acting during meiosis in Saccharomyces hybrids. As a result of the selective processes acting during fermentation, hybrid genomes maintained the S. cerevisiae genome but reduced the S. kudriavzevii fraction.The genus Saccharomyces consists of seven biological species: S. arboricolus, S. bayanus, S. cariocanus, S. cerevisiae, S. kudriavzevii, S. mikatae, and S. paradoxus (29, 59) and the partially allotetraploid species S. pastorianus (46, 58).The hybrid species S. pastorianus, restricted to lager brewing environments, arose from two or more natural hybridization events between S. cerevisiae and a S. bayanus-like yeast (7, 16, 28, 46). Recent studies of S. bayanus have also revealed the hybrid nature of certain strains of this species, which has subsequently been subdivided into two groups, S. bayanus var. bayanus, containing a variety of hybrid strains, and S. bayanus var. uvarum, also referred to as S. uvarum, that contains nonhybrid strains (45, 46).New hybrids of other species from the genus Saccharomyces have recently been described. Hybrid yeasts of S. cerevisiae and S. kudriavzevii have been characterized among wine (6, 20, 33) and brewing yeasts (21); even triple hybrids of S. cerevisiae, S. bayanus, and S. kudriavzevii have been identified (20, 41).The first natural Saccharomyces interspecific hybrid identified, the lager brewing yeast S. pastorianus (S. carlsbergensis) (42, 57), has become one of the most investigated types of yeast hybrids. The genome structure of these hybrids has been examined by competitive array comparative genome hybridization (aCGH) (5, 16, 28), complete genome sequencing (28), and PCR-restriction fragment length polymorphism (RFLP) analysis of 48 genes and partial sequences of 16 genes (46). The aCGH analyses of several S. pastorianus strains with S. cerevisiae-only DNA arrays (5, 28) revealed the presence of aneuploidies due to deletions of entire regions of the S. cerevisiae fraction of the hybrid genomes. A recent aCGH analysis of S. pastorianus strains with S. cerevisiae and S. bayanus DNA arrays (16) showed two groups of strains according to their genome structure and composition. These groups arose from two independent hybridization events, and each one is characterized by a reduction and an amplification of the S. cerevisiae genome fraction, respectively.The genetic characterization of the wine S. cerevisiae and S. kudriavzevii hybrids by restriction analysis of five nuclear genes located in different chromosomes, 5.8S-ITS rDNA region and the mitochondrial COX2 gene, revealed the presence of three types of hybrids in Swiss wines, thus indicating the presence of different hybrid genomes (20). In a recent study (21), we identified six new types of S. cerevisiae and S. kudriavzevii hybrids among brewing strains, which were compared to wine hybrids by a genetic characterization based on RFLP analysis of 35 protein-encoding genes. This analysis confirmed the presence of three different genome types among wine hybrids that contain putative chimeric chromosomes, probably generated by a recombination between homeologous chromosomes of different parental origins.The aim of the present study is to investigate the genome composition and structure of wine hybrids of S. cerevisiae and S. kudriavzevii. This has been achieved by a combined approach based on the RFLP analysis of 35 gene regions from our previous study, comparative genome hybridizations using S. cerevisiae DNA macroarrays, a ploidy analysis by flow cytometry, and gene dose determinations by quantitative real-time PCR. This multiple approach allowed us to confirm the presence of chimeric chromosomes and define the mechanisms involved in their origins.