Chimeric genomes of natural hybrids of Saccharomyces cerevisiae and Saccharomyces kudriavzevii

Abstract

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 x 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 x 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.

FIG. 1.

Chromosome structures in the S. cerevisiae × S. kudriavzevii hybrid strain W27 as deduced from the DNA array analysis. These putative structures were deduced from the plots of the log₂ hybridization ratios (W27 hybrid gene signals divided by those of the homoploid S. cerevisiae FY1679 genes) with respect to the S. cerevisiae gene order of each chromosome. Abrupt changes in the hybridization ratios of some chromosome regions are due to the presence of chimeric recombinant chromosomes generated by the nonreciprocal recombination between homeologous chromosomes. Chromosomes and chromosome regions coming from the S. cerevisiae parent are represented as black bars and those coming from the S. kudriavzevii parent as white bars; vertical gray bars correspond to centromeres. These chromosome structures are congruent with the results of a previous study on the presence/absence of parental genes based on the RFLP analysis of 35 gene regions (21). The locations of these gene regions are indicated above each chromosome, and the results of presence/absence of the parental alleles are summarized as follows: when both parental genes are present, the gene name is in black, but when only the S. cerevisiae gene is present, the gene name is in red. The presence of a S. kudriavzevii gene was not observed.

FIG. 2.

Variable chromosome structures in S. cerevisiae × S. kudriavzevii hybrids. Putative structures, as deduced from the results of the macroarray analysis, of those chromosomes of S. cerevisiae × S. kudriavzevii hybrids differing from the structures of strain W27 chromosomes. (a) Structure differences in chromosome XII of hybrid SPG16-91 with respect to that of hybrid W27; (b) structure differences in chromosome I of hybrid 441 with respect to that of hybrid W27. The representation of the chromosomes, plots, and presence/absence of parental genes is the same as described in the legend to Fig. 1.

FIG. 3.

Flow cytometry analysis of the DNA content per cell in the S. cerevisiae × S. kudriavzevii hybrid strains. The DNA content per cell was measured by flow cytometry for the following S. cerevisiae × S. kudriavzevii hybrid strains: W27 (a), SPG16-91 (b), and 441 (c). The signal of the haploid reference strain S288c is depicted in light green, that of the reference diploid strain FY1679 in black, and those of the hybrids under study in purple.

FIG. 4.

Chromosome copy numbers in the S. cerevisiae × S. kudriavzevii hybrids. Copy numbers of chromosomes from hybrid W27 were deduced from the gene dose analysis by the qRT-PCR of 19 gene regions. The gene copy estimations were performed, as indicated, with general primers designed and tested for S. cerevisiae and S. kudriavzevii and/or with species-specific primers, either for S. cerevisiae or for S. kudriavzevii. The genes under analysis are located, as depicted, in the different chromosome regions defined by the aCGH analysis. Chromosomes and chromosome regions from the S. cerevisiae parent are represented as black bars and those from the S. kudriavzevii parent as white bars; the positions of the centromeres are shown as vertical gray bars.

FIG. 5.

Location of the putative recombination sites in the chimeric chromosomes of S. cerevisiae × S. kudriavzevii hybrids. The location of these recombinant regions was deduced from the abrupt changes in the hybridization ratios depicted in Fig. 1 and 2. In the case of chromosome XII, the recombinant form is present only in hybrid SPG16-91 but not in the other, as depicted. The hybrid genes from the S. cerevisiae parent are indicated as black arrows and those from the S. kudriavzevii parent as white arrows, and those genes where the putative recombination site is located are indicated as gray arrows. A gray box represents the large cluster of 100 to 200 tandem repeats containing the highly conserved rRNA genes (RDN genes), where the putative recombination site in the chimeric chromosome XII of strain SPG16-91 is located. A vertical black bar denotes the position of the centromere in chromosome XIV. Dotted and striped arrows represent tRNA and LTRs (delta, sigma, or tau) from Ty retrotransposons, respectively, which could be involved in the recombination events. The recombination site located within PMT1 was confirmed by sequencing (see Fig. 6).

FIG. 6.

Alignment of the partial sequences of the nonrecombinant (cer; S. cerevisiae origin) and recombinant (rec) PMT1 alleles found in S. cerevisiae × S. kudriavzevii hybrid strains and those of the reference strains of the parent species, S. cerevisiae (Sce) S288c and S. kudriavzevii (Sku) type strain IFO1802. A dot indicates nucleotides identical to that from the reference PMT1 sequence of S. cerevisiae S288c. Regions in the hybrid alleles that exhibit a higher similarity to S. cerevisiae sequences are indicated by a lack of shading, and those with a higher similarity to S. kudriavzevii sequences are indicated by gray shading. A continuous rectangle highlights the 5′ end of the PMT1 coding region. The black box indicates the crossing-over site involved in the nonreciprocal recombination between homeologous chromosomes V of the common ancestor of the hybrids.