title: Genomic signatures of adaptation to wine biological ageing conditions in biofilm-forming flor yeasts.
abstract: 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 ageing 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 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 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 ageing 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.
authors.affiliation: Dipartimento di Agraria, Università di Sassari, 07100, Sassari, Italy.
authors.forename: A L
authors.initials: AL
authors.lastname: Coi
authors.affiliation: SPO, INRA, SupAgro, Université de Montpellier, 34060, Montpellier, France.
authors.forename: F
authors.initials: F
authors.lastname: Bigey
authors.affiliation: SPO, INRA, SupAgro, Université de Montpellier, 34060, Montpellier, France.
authors.forename: S
authors.initials: S
authors.lastname: Mallet
authors.affiliation: SPO, INRA, SupAgro, Université de Montpellier, 34060, Montpellier, France.
authors.forename: S
authors.initials: S
authors.lastname: Marsit
authors.affiliation: Dipartimento di Agraria, Università di Sassari, 07100, Sassari, Italy.
authors.forename: G
authors.initials: G
authors.lastname: Zara
authors.affiliation: INRA, UMR BGPI, 34398, Montpellier, France.
authors.forename: P
authors.initials: P
authors.lastname: Gladieux
authors.affiliation: SPO, INRA, SupAgro, Université de Montpellier, 34060, Montpellier, France.
authors.forename: V
authors.initials: V
authors.lastname: Galeote
authors.affiliation: Dipartimento di Agraria, Università di Sassari, 07100, Sassari, Italy.
authors.forename: M
authors.initials: M
authors.lastname: Budroni
authors.affiliation: SPO, INRA, SupAgro, Université de Montpellier, 34060, Montpellier, France.
authors.forename: S
authors.initials: S
authors.lastname: Dequin
authors.affiliation: SPO, INRA, SupAgro, Université de Montpellier, 34060, Montpellier, France.
authors.forename: J L
authors.initials: JL
authors.lastname: Legras
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D018441:Biofilms; D005285:Fermentation; D005828:Genetics, Population; D016681:Genome, Fungal; D010641:Phenotype; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D012641:Selection, Genetic; D014920:Wine / Q000382:microbiology*
keywords: 
  Saccharomyces cerevisiae
  ; 
  ZRT1
  ; FLO11; adaptation; biofilm; biological ageing; domestication; flor yeast; genome