CE20 - Biologie des animaux, des organismes photosynthétiques et des microorganismes

Adaptation mechanisms in food-fermenting Penicillium fungi – FUNGADAPT

FUNGADAPT

Adaptation mechanisms in food-fermenting Penicillium fungi

Divergent adaptation as a biodiversity source

Studying adaptive divergence, a key process in evolutionary biology, is essential for understanding the adaptation of organisms to their environment and how biodiversity arises. Domestication is a good model for studying adaptive divergence, as it involves strong and recent selection for known traits. Domesticated fungi used for fermented food have been rarely studied while they constitute highly tractable eukaryotic models, with repeated and recent adaptation events to the same environment. The Fungadapt project aims at elucidating the domestication history and the genomic mechanisms of adaptation, and their repeatability, in emblematic Penicillium fungi used for cheese and dry-cured meat production.

Genetic and phenotypic diversity as well as differentiation are assessed by identifying footprints of selection in genomes and by deciphering the genomic determinants of adaptive traits. Methodological approaches include high-throughput phenotyping, comparative and population genomics, QTL mapping and functional validation.

For the cheese-associated Penicillia, the obtained results showed i) divergent adaptation and recent domestications in P. roqueforti which led to the existence of distinct cheese-related populations and ii) domestication of P. camemberti, with two clonal varieties within the species, one being white and cottony used for “Camembert” and “Brie” cheeses, and the other being grey used for “Rigotte de Condrieu” cheese.
For the Penicillia associated with dry-cured meats, the obtained results highlighted the selection of certain phenotypic traits for the fungal strains associated with these food products.

The next steps of the project will focus only on P. roqueforti. Phenotypic approaches will be used to potentially highlight further differences between the identified populations. A QTL approach will also be used on the offsprings of inter-population crosses in order to elucidate the genomic determinants of traits important for foodmaking. Finally, gene edition approaches will be used to functionnaly validate the genes of interest role.

1. Dumas E, Feurtey A, Rodríguez de la Vega RC, Le Prieur S, Snirc A, Coton M, Thierry A, Coton E, Le Piver M, Roueyre D, Ropars J, Branca A, Giraud T. Independent domestication events in the blue-cheese fungus Penicillium roqueforti.Mol Ecol. 2020;29(14):2639-2660. doi: 10.1111/mec.15359.
2. Ropars J, Didiot E, Rodríguez de la Vega RC, Bennetot B, Coton M, Poirier E, Coton E, Snirc A, Le Prieur S, Giraud T. Domestication of the emblematic white cheese-making fungus Penicillium camemberti and its diversification into two varieties. Curr Biol. 2020;30(22):4441-4453.e4. doi: 10.1016/j.cub.2020.08.082
3. Coton E, Coton M, Hymery N, Mounier J, Jany J-L. Penicillium roqueforti: an overview of its genetics, physiology, metabolism and biotechnological applications. Fung. Biol. Rev. 2020; 34, 59-73 doi.org/10.1016/j.fbr.2020.03.001
4. Caron T, Piver ML, Péron AC, Lieben P, Lavigne R, Brunel S, Roueyre D, Place M, Bonnarme P, Giraud T, Branca A, Landaud S, Chassard C. Strong effect of Penicillium roqueforti populations on volatile and metabolic compounds responsible for aromas, flavor and texture in blue cheeses. Int J Food Microbiol. 2021;354:109174. doi:10.1016/j.ijfoodmicro.2021.109174
5. Ropars J, Caron T, Lo YC, Bennetot B, Giraud T. Domestication of cheese fungi CR Biol. 2020 Oct 9;343(2):155-176. doi: 10.5802/crbiol.15.

Studying adaptive divergence, a key process in evolutionary biology, is essential for understanding the adaptation of organisms to their environment and how biodiversity arises. Domestication is a good model for studying adaptive divergence, as it involves strong and recent selection for known traits. Domesticated fungi used for fermented food have been rarely studied while they constitute highly tractable eukaryotic models, with repeated and recent adaptation events to the same environment. The Fungadapt project aims at elucidating the domestication history and the genomic mechanisms of adaptation, and their repeatability, in emblematic Penicillium fungi used for cheese and dry-cured meat production by assessing their genetic and phenotypic diversity as well as differentiation, by identifying footprints of selection in genomes and by deciphering the genomic determinants of adaptive traits. Methodological approaches include high-throughput phenotyping, comparative and population genomics, QTL mapping and functional validation.

Project coordinator

Monsieur Emmanuel Coton (LABORATOIRE UNIVERSITAIRE DE BIODIVERSITE ET ECOLOGIE MICROBIENNE)

The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.

Partner

EA3882 LABORATOIRE UNIVERSITAIRE DE BIODIVERSITE ET ECOLOGIE MICROBIENNE
ESE Écologie, systématique et évolution

Help of the ANR 425,712 euros
Beginning and duration of the scientific project: January 2020 - 48 Months

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