249W Poster - Population Genetics
Wednesday June 08, 9:15 PM - 10:00 PM

Authors:
Katherine Chacon-Vargas; Colin O. McCarthy; Victoria Donescu; John Gibbons

Affiliation: University of Massachusetts Amherst

Keywords:
Other (Artificial selection, domestication)

Human selection of desired traits to enhance their benefits has led to domestication in plants, animals and also microbes (bacteria, yeasts, and molds). Domesticated microbes play an important role in food preservation, nutrition and flavors. Aspergillus oryzae is a domesticated filamentous fungal species used during the fermentation of traditional Asian foods and beverages such as sake, soy sauce, and miso. The artisanal practice of continuous passage of A. oryzae on food substrates over thousands of years has resulted in adaptation to the food environment along with genetic differentiation from its wild relative A. flavus, a toxin producing agricultural pest. Here, we analyzed 300 isolates of A. oryzae and A. flavus to understand the history of domestication and how this process shaped patterns of genomic variation. Using population structure and phylogenetic analysis we identified 2 major A. oryzae populations and two major A. flavus lineages. Next, we used two population genomic metrics to identify regions of the A. oryzae genome displaying signatures of recent positive selection. We identified 30 candidate selective sweeps, several of which contain genes with functional annotations directly related to fermentation (e.g. an alcohol dehydrogenase, fructose transmembrane transporters, and genes involved in glutathione metabolism). Additionally, we examined differences in gene copy number variation between A. oryzae and A. flavus. We found major CN differences in chromosomes 3, 4 and 8 corresponding to to genes involved in primary and secondary metabolism. Most strikingly, we found significantly more copies of the α-amylase encoding genes in A. oryzae compared to A. flavus, suggesting selection for increased carbohydrate metabolism during domestication. Further, gene absences in A. oryzae compared to A. flavus were enriched for secondary metabolism function, suggesting selection for loss of toxicity in A. oryzae. Taken together, our results show the A. oryzae genome was significantly reshaped as a result of domestication to the food environment.