Contrasting evolutionary trajectories of nitrate assimilation across Brettanomyces bruxellensis lineages
Brettanomyces bruxellensis is a yeast species associated with diverse fermentation environments and characterized by extensive genetic diversity, including diploid, autotriploid, and allotriploid lineages resulting from independent hybridization events. These lineages are associated with distinct ecological niches and provide a framework for studying metabolic trait evolution in complex genomes.…
Nitrate assimilation is an uncommon trait among yeasts, yet it has been observed in Brettanomyces bruxellensis. This yeast species is genetically diverse, encompassing diploid, autotriploid, and allotriploid lineages that originated from separate hybridization events. These lineages occupy different ecological niches, offering an opportunity to study metabolic trait evolution in complex genomes.
To understand nitrate assimilation within B. bruxellensis, researchers analyzed 151 phenotypically characterized strains alongside 946 whole-genome sequences. The growth assays demonstrated that nitrate assimilation is prevalent but unevenly distributed across genetic lineages. Some populations maintained the trait, while others frequently lost it.
Further genomic analysis revealed extensive variation in the nitrate assimilation gene cluster comprising YNR1, YNI1, and YNT1. Nitrate assimilating strains typically had more functional copies of this cluster and a strong association with gene copy number and predicted functionality. By examining primary and acquired genomes in allotriploid lineages, researchers discovered contrasting evolutionary trajectories following hybridization.
Primary genomes generally maintained the nitrate assimilation genes, while acquired genomes exhibited a higher prevalence of gene loss and loss-of-function variants. This highlighted asymmetric dynamics between subgenomes. In conclusion, nitrate assimilation appears to be an ancestral trait that has been selectively maintained across B. bruxellensis lineages through a combination of copy number variation, gene degeneration, and genome-specific evolutionary dynamics.
These findings shed light on how genome architecture and polyploid evolution influence the maintenance and loss of metabolic traits in an industrially significant yeast species.
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