Evolution of a Yeast With Industrial Background Under Winemaking Conditions Leads to Diploidization and Chromosomal Copy Number Variation

Abstract

Industrial wine yeast strains show genome particularities, with strains showing polyploid genomes or chromosome copy number variations, being easier to identify. Although these genomic structures have classically been considered transitory steps in the genomic adaptation to new environmental conditions, they may be more stable than thought. These yeasts are highly specialized strains able to cope with the different stresses associated with the fermentation process, from the high osmolarity to the final ethanol content. In this work, we use adaptive laboratory evolution, focusing on the initial steps of the fermentation process, where growth rate is maximum, to provide new insights into the role of the different genomic and chromosomic rearrangements that occur during adaptation to wine conditions, and providing an understanding of the chronology of the different evolutionary steps.

Keywords: MAT locus switching; adaptive laboratory evolution; aneuploidies; evolution; wine fermentation.

FIGURE 1

Growth kinetics in synthetic grape must of the original industrial strain EC1118 (black), its segregant strain N2 (red), used in the evolution experiment, and the evolved strains NV3 (green), NV6 (orange), and NV15 (blue).

FIGURE 2

Coverage across the reference analysis of strain N2 (red), and the evolved strains NV3 (green), NV6 (orange), and NV15 (blue). Deviations from the average coverage of the genome are indicated by black triangles.

FIGURE 3

Mating type in the segregant and evolved strains. (A) The mating type by PCR amplification of the MAT locus for the different strains. First three lines are controls for MATa/α (BY4743), MATa (BY4741), and MATα (BY4742), then, the segregant strain N2 MATα ho, and the evolved strains NV3 MATa/α, NV6 MATα, and NV15 MATa/α. (B) The mating type by PCR amplification of the MAT locus for different time points during the evolution experiment. From line 1 to line 9, the evolving pool at generations 0, 50, 100, 150, 180, 200, 250, 263, and 273; line 10: positive control EC1118; line 11: positive control EC1118 (1/100 dilution); and line M: 100 bp marker.

FIGURE 4

Growth kinetics in synthetic grape must (A), SD media (B), and YPD media (C) of the original industrial strain EC1118 (black), its segregant strain N2 (red), the evolved strain NV3 (green), and four spore derivatives from the same ascus of NV3 (light green).

FIGURE 5

Growth kinetics in synthetic grape must of the original industrial strain EC1118 (black), its segregant strain N2 (red), the evolved strain NV15 (blue), and three spore derivatives from the same ascus of NV15 (light blue).

FIGURE 6

Growth kinetics in synthetic grape must (A), SD media (B), and YPD media (C) of the original industrial strain EC1118 (black), its segregant strain N2 (red), the evolved strains NV3 (green), NV6 (orange), NV15 (blue), and two strains isolated from the benomyl 40 μg/L treatment (light gray).

FIGURE 7

Schematic diagram showing the chronological order of the evolutionary events from the segregant strain N2 to the evolved strains NV3 (green), NV6 (orange), and NV15 (blue).