Résumé
The molecular and evolutionary processes underlying fungal domestication
remain largely unknown despite the importance of fungi to bioindustry and
for comparative adaptation genomics in eukaryotes. Wine fermentation and
biological aging are performed by strains of S. cerevisiae with,
respectively, pelagic fermentative growth on glucose, and biofilm aerobic
growth utilizing ethanol. Here, we use environmental samples of wine and
flor yeasts to investigate the genomic basis of yeast adaptation to
contrasted anthropogenic environments. Phylogenetic inference and
population structure analysis based on single nucleotide polymorphisms
(SNPs) revealed a group of flor yeasts separated from wine yeasts. A
combination of methods revealed several highly differentiated regions
between wine and flor yeasts, and analyses using codon-substitution models
for detecting molecular adaptation identified sites under positive
selection in the high affinity transporter gene ZRT1. The Cross Population
Composite Likelihood Ratio (XP-CLR) revealed selective sweeps at three
regions, including in the hexose transporter gene HXT7, the yapsin gene
YPS6 and the membrane protein coding gene MTS27. Our analyses also
revealed that the biological aging environment has led to the accumulation
of numerous mutations in proteins from several networks, including Flo11
regulation and divalent metal transport. Together, our findings suggest
that the tuning of FLO11 expression and zinc transport networks are a
distinctive feature of the genetic changes underlying the domestication of
flor yeasts. Our study highlights the multiplicity of genomic changes
underlying yeast adaptation to man-made habitats, and reveals that
flor/wine yeast lineage can serve as a useful model for studying the
genomics of adaptive divergence.