0000000000484844
AUTHOR
Miguel Morard
Genome structure reveals the diversity of mating mechanisms in Saccharomyces cerevisiae x Saccharomyces kudriavzevii hybrids, and the genomic instability that promotes phenotypic diversity
Interspecific hybridization has played an important role in the evolution of eukaryotic organisms by favouring genetic interchange between divergent lineages to generate new phenotypic diversity involved in the adaptation to new environments. This way, hybridization between Saccharomyces species, involving the fusion between their metabolic capabilities, is a recurrent adaptive strategy in industrial environments. In the present study, whole-genome sequences of natural hybrids between Saccharomyces cerevisiae and Saccharomyces kudriavzevii were obtained to unveil the mechanisms involved in the origin and evolution of hybrids, as well as the ecological and geographic contexts in which sponta…
Additional file 7: Figure S5. of The genetic architecture of low-temperature adaptation in the wine yeast Saccharomyces cerevisiae
Outline of the construction of advanced intercross lines. We carried out a strategy that forces yeast cells through multiple rounds of random mating and sporulation to create advanced intercross lines (AILs). This step can improve genetic mapping in two ways: increasing resolution by reducing linkage and unlinking nearby QTLs. (PDF 168 kb)
Additional file 3: Figure S2. of The genetic architecture of low-temperature adaptation in the wine yeast Saccharomyces cerevisiae
Workflow of populations’ selection and sequencing. Cells were grown in complete media (YPD) and synthetic must (SM), and were incubated at either optimum temperature (28 °C) or low temperature (15 °C) until the stationary phase was reached. At this time, the volume required to inoculate at an OD of 0.2 was re-inoculated into 60 mL of fresh medium. The experiment was carried out 8 times after which the selected populations were analyzed and sequenced. (PDF 43 kb)
The genetic architecture of low-temperature adaptation in the wine yeast Saccharomyces cerevisiae
[Background] Low-temperature growth and fermentation of wine yeast can enhance wine aroma and make them highly desirable traits for the industry. Elucidating response to cold in Saccharomyces cerevisiae is, therefore, of paramount importance to select or genetically improve new wine strains. As most enological traits of industrial importance in yeasts, adaptation to low temperature is a polygenic trait regulated by many interacting loci.
RNAseq-based transcriptome comparison of Saccharomyces cerevisiae strains isolated from diverse fermentative environments.
Transcriptome analyses play a central role in unraveling the complexity of gene expression regulation in Saccharomyces cerevisiae. This species, one of the most important microorganisms for humans given its industrial applications, shows an astonishing degree of genetic and phenotypic variability among different strains adapted to specific environments. In order to gain novel insights into the Saccharomyces cerevisiae biology of strains adapted to different fermentative environments, we analyzed the whole transcriptome of three strains isolated from wine, flor wine or mezcal fermentations. An RNA-seq transcriptome comparison of the different yeasts in the samples obtained during synthetic m…
Additional file 5: Figure S4. of The genetic architecture of low-temperature adaptation in the wine yeast Saccharomyces cerevisiae
QTL analysis for low-temperature adaptation. The figure shows the allele frequency change of the selected pools at YPD 15 °C (purple), SM 15 °C (pink) and SM 28 °C (blue) compared with the unselected population. QTLs are indicated at the corresponding positions with red (YPD 15 °C), green (SM 15 °C) and orange triangles (SM 28 °C). (PDF 70 kb)
Interspecific hybridization and aneuploidy as adaptive mechanisms in saccharomyces yeasts
Doctorado en Biomedicina y Biotecnología.
Additional file 2: Figure S1. of The genetic architecture of low-temperature adaptation in the wine yeast Saccharomyces cerevisiae
Distribution of private nonsynonymous SNPs in P5 and P24 compared to S288c. An external circle indicates P24 and an internal circle indicates P5. Homozygous changes are colored in green, while heterozygous changes are marked in red. (PDF 243 kb)
Additional file 4: Figure S3. of The genetic architecture of low-temperature adaptation in the wine yeast Saccharomyces cerevisiae
Hybrid population phenotyping after the selection experiment compared with the unselected F13 population using the opposite temperature to that used during the selection process (nonspecific improvement). The selected population (SP) in the YPD medium (A) and synthetic must (SM) (C) at 15 °C. The selected population (SP) in YPD (B) and SM (D) at 28 °C. Box plot represents μmax distribution in each population and the black bar inside the box represents the mean value. *Significant differences in the SP compared with the F13. (PDF 66 kb)
Comparative Genomics Between Saccharomyces kudriavzevii and S. cerevisiae Applied to Identify Mechanisms Involved in Adaptation
Yeasts belonging to the Saccharomyces genus play an important role in human-driven fermentations. The species S. cerevisiae has been widely studied because it is the dominant yeast in most fermentations and it has been widely used as a model eukaryotic organism. Recently, other species of the Saccharomyces genus are gaining interest to solve the new challenges that the fermentation industry are facing. One of these species is S. kudriavzevii, which exhibits interesting physiological properties compared to S. cerevisiae, such as a better adaptation to grow at low temperatures, a higher glycerol synthesis and lower ethanol production. The aim of this study is to understand the molecular basis…
Genomic instability in an interspecific hybrid of the genus Saccharomyces: a matter of adaptability
Ancient events of polyploidy have been linked to huge evolutionary leaps in the tree of life, while increasing evidence shows that newly established polyploids have adaptive advantages in certain stress conditions compared to their relatives with a lower ploidy. The genus Saccharomyces is a good model for studying such events, as it contains an ancient whole-genome duplication event and many sequenced Saccharomyces cerevisiae are, evolutionary speaking, newly formed polyploids. Many polyploids have unstable genomes and go through large genome erosions; however, it is still unknown what mechanisms govern this reduction. Here, we sequenced and studied the natural S. cerevisiae × Saccharomyces…
Aneuploidy and Ethanol Tolerance in Saccharomyces cerevisiae
Response to environmental stresses is a key factor for microbial organism growth. One of the major stresses for yeasts in fermentative environments is ethanol. Saccharomyces cerevisiae is the most tolerant species in its genus, but intraspecific ethanol-tolerance variation exists. Although, much effort has been done in the last years to discover evolutionary paths to improve ethanol tolerance, this phenotype is still hardly understood. Here, we selected five strains with different ethanol tolerances, and used comparative genomics to determine the main factors that can explain these phenotypic differences. Surprisingly, the main genomic feature, shared only by the highest ethanol-tolerant st…
Additional file 6: Table S2. of The genetic architecture of low-temperature adaptation in the wine yeast Saccharomyces cerevisiae
List of genes used in the RH analysis with the BY4741 strain that are present in the subtelomeric regions and are not essential. (XLSX 13 kb)
Additional file 1: Table S1. of The genetic architecture of low-temperature adaptation in the wine yeast Saccharomyces cerevisiae
Genomic comparison among strains. Single nucleotide polymorphism (SNPs) population distribution. SNPs were classified according to genome localization and change in protein sequence (nonsynonymous variant). (XLSX 5469 kb)