Hanseniaspora yeasts from agave fermentations provide insight into intraspecific gene loss

Hanseniaspora species stand out among yeasts for having the smallest genomes, marked by extensive gene family contractions. Consequently, they have been proposed as model organisms for studying the evolution of free-living cells lacking genes otherwise considered essential. Here, we show that Hanseniaspora yeasts are prevalent in agave fermentations used to produce traditional spirits across Mexico. We sequenced the genomes of 15 strains, unambiguously identifying them as H. lachancei, H. pseudoguilliermondii, H. guilliermondii , and H. opuntiae . Comparative genomic analyses revealed dynamic shifts in gene family sizes and compositions, suggesting ongoing gene loss within the fast-evolving branch of this genus. Notably, gene losses varied across functional categories, even among isolates of the same species. Growth assays across diverse stress conditions and carbon sources indicated that these genomic disparities do not directly translate into phenotypic differences. Together, our findings suggest that differential gene loss within species is an active evolutionary process shaping Hanseniaspora genomes, highlighting agave-fermentation populations as valuable models for studying genome reduction in a natural context.