title: Amplification of a Zygosaccharomyces bailii DNA segment in wine yeast genomes by extrachromosomal circular DNA formation.
abstract: We recently described the presence of large chromosomal segments resulting from independent horizontal gene transfer (HGT) events in the genome of Saccharomyces cerevisiae strains, mostly of wine origin. We report here evidence for the amplification of one of these segments, a 17 kb DNA segment from Zygosaccharomyces bailii, in the genome of S. cerevisiae strains. The copy number, organization and location of this region differ considerably between strains, indicating that the insertions are independent and that they are post-HGT events. We identified eight different forms in 28 S. cerevisiae strains, mostly of wine origin, with up to four different copies in a single strain. The organization of these forms and the identification of an autonomously replicating sequence functional in S. cerevisiae, strongly suggest that an extrachromosomal circular DNA (eccDNA) molecule serves as an intermediate in the amplification of the Z. bailii region in yeast genomes. We found little or no sequence similarity at the breakpoint regions, suggesting that the insertions may be mediated by nonhomologous recombination. The diversity between these regions in S. cerevisiae represents roughly one third the divergence among the genomes of wine strains, which confirms the recent origin of this event, posterior to the start of wine strain expansion. This is the first report of a circle-based mechanism for the expansion of a DNA segment, mediated by nonhomologous recombination, in natural yeast populations.
authors.affiliation: INRA, UMR1083 Sciences Pour l'Œnologie, Montpellier, France.
authors.forename: Virginie
authors.initials: V
authors.lastname: Galeote
authors.forename: Frédéric
authors.initials: F
authors.lastname: Bigey
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Beyne
authors.forename: Maite
authors.initials: M
authors.lastname: Novo
authors.forename: Jean-Luc
authors.initials: JL
authors.lastname: Legras
authors.forename: Serge
authors.initials: S
authors.lastname: Casaregola
authors.forename: Sylvie
authors.initials: S
authors.lastname: Dequin
mesh_terms: D001483:Base Sequence; D015139:Blotting, Southern; D056905:Chromosome Breakpoints; D015825:Chromosomes, Fungal / Q000235:genetics; D004270:DNA, Circular / Q000235:genetics*; D004271:DNA, Fungal / Q000235:genetics*; D004171:Diploidy; D016521:Electrophoresis, Gel, Pulsed-Field; D019143:Evolution, Molecular; D005111:Extrachromosomal Inheritance / Q000235:genetics; D005784:Gene Amplification / Q000235:genetics*; D018628:Gene Dosage / Q000235:genetics; D014644:Genetic Variation; D016681:Genome, Fungal / Q000235:genetics*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D014920:Wine / Q000382:microbiology*; D020068:Zygosaccharomyces / Q000235:genetics*
chemical_list: D004270:DNA, Circular; D004271:DNA, Fungal