Résumé
Apiculate yeasts are characterized by lemon-shaped cell structure and bipolar budding. They mainly belong to genus Hanseniaspora and Kloeckera, which have been reported in various habitats such as fruits, flowers, fermenting juices, soil or fruiting bodies of mushrooms. Hanseniaspora, is also a predominant yeast genus in grape musts at the beginning of spontaneous fermentation. Several studies report that they play an important role in wine making by producing flavours, modulating the growth and metabolism of Saccharomyces cerevisiae and affecting wine colour. The genus comprises sister species separated into two lineages, a fast-evolving lineage (FEL) and a slow-evolving lineage (SEL), which differ by their evolution rate and the extent of their gene loss. We investigated the genetic relationships between the four most closely related species of the FEL, at the population level. A multi-locus sequence typing strategy based on five markers applied on 107 strains, confirmed the clear delineation of species H. uvarum, H. opuntiae, H. guilliermondii and H. pseudoguilliermondii. Huge variations were observed in the level of intraspecific nucleotide diversity, and differences in heterozygosity between species indicate different life styles. Population genomics analysis provided a sharper view of population structure related to geography for H. uvarum. In addition, H. guilliermondii strains clustered into two distinct groups without geographical link. The absence of admixture between H. guilliermondii groups may reflect a recent step towards speciation. Interspecific hybrids were also detected, between H. opuntiae and H. pseudoguilliermondii. Their characterization using flow cytometry, karyotypes and genome sequencing showed different genome structures in different ploidy contexts: allodiploids, allotriploids, and allotetraploids. Subculturing of an allotriploid strain revealed chromosome loss equivalent to one chromosome set, followed by an auto-diploidization event, whereas another auto-diploidized tetraploid showed a segmental duplication. Altogether, these results suggest that Hanseniaspora genomes are not only fast evolving but also highly dynamic.