Independent domestication events in the blue-cheese fungus Penicillium roqueforti

Domestication provides an excellent framework for studying adaptive
divergence. Using population genomics and phenotypic assays, we
reconstructed the domestication history of the blue cheese mold
Penicillium roqueforti. We showed that this fungus was domesticated twice
independently. The population used in Roquefort originated from an old
domestication event associated with weak bottlenecks and exhibited traits
beneficial for pre-industrial cheese production (slower growth in cheese
and greater spore production on bread, the traditional multiplication
medium). The other cheese population originated more recently from the
selection of a single clonal lineage, was associated to all types of blue
cheese worldwide but Roquefort, and displayed phenotypes more suited for
industrial cheese production (high lipolytic activity, efficient cheese
cavity colonization ability and salt tolerance). We detected genomic
regions affected by recent positive selection and putative horizontal gene
transfers. This study sheds light on the processes of rapid adaptation and
raises questions about genetic resource conservation.