Evolutionary Biology

Domestication of different varieties in the cheese-making fungus Geotrichum candidum

10.24072/pcjournal.266 - Peer Community Journal, Volume 3 (2023), article no. e45.

Get full text PDF Peer reviewed and recommended by PCI

Domestication is an excellent model for studying adaptation processes, involving recent adaptation and diversification, convergence following adaptation to similar conditions, as well as degeneration of unused functions. Geotrichum candidum is a fungus used for cheese making and is also found in other environments such as soil and plants. By analyzing whole-genome data from 98 strains, we found that all strains isolated from cheese formed a monophyletic clade. Within the cheese clade, we identified three genetically differentiated populations and we detected footprints of recombination and admixture. The genetic diversity in the cheese clade was similar as that in the wild clade, suggesting the lack of strong bottlenecks. Commercial starter strains were scattered across the cheese clade, thus not constituting a single clonal lineage. The cheese populations were phenotypically differentiated from other populations, with a slower growth on all media, even cheese, a prominent production of typical cheese volatiles and a lower proteolytic activity. One of the cheese clusters encompassed all soft goat cheese strains, suggesting an effect of cheese-making practices on differentiation. Another of the cheese populations seemed to represent a more advanced stage of domestication, with stronger phenotypic differentiation from the wild clade, harboring much lower genetic diversity, and phenotypes more typical of cheese fungi, with denser and fluffier colonies and a greater ability of excluding cheese spoiler fungi. Cheese populations lacked two beta lactamase-like genes present in the wild clade, involved in xenobiotic clearance, and displayed higher contents of transposable elements, likely due to relaxed selection. Our findings suggest the existence of genuine domestication in G. candidum, which led to diversification into different varieties with contrasted phenotypes. Some of the traits acquired by cheese strains indicate convergence with other, distantly related fungi used for cheese maturation.

Published online:
DOI: 10.24072/pcjournal.266
Bennetot, Bastien 1; Vernadet, Jean-Philippe 1; Perkins, Vincent 2; Hautefeuille, Sophie 1; Rodríguez de la Vega, Ricardo C. 1; O’Donnell, Samuel 1; Snirc, Alodie 1; Grondin, Cécile 3; Lessard, Marie-Hélène 2; Peron, Anne-Claire 4; Labrie, Steve 2; Landaud, Sophie 4; Giraud, Tatiana 1; Ropars, Jeanne 1

1 Laboratoire Ecologie Systématique et Evolution, Université Paris-Saclay, CNRS, AgroParisTech, site IDEEV, Gif-sur-Yvette, France
2 Département des sciences des aliments, Centre de recherche STELA, INAF, Université Laval, Québec, Canada
3 SPO, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
4 UMR SayFood, Université Paris-Saclay, INRAe, AgroParisTech, Thiverval Grignon, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights
     author = {Bennetot, Bastien and Vernadet, Jean-Philippe and Perkins, Vincent and Hautefeuille, Sophie and Rodr{\'\i}guez de la Vega, Ricardo C. and O{\textquoteright}Donnell, Samuel and Snirc, Alodie and Grondin, C\'ecile and Lessard, Marie-H\'el\`ene and Peron, Anne-Claire and Labrie, Steve and Landaud, Sophie and Giraud, Tatiana and Ropars, Jeanne},
     title = {Domestication of different varieties in the cheese-making fungus {\protect\emph{Geotrichum} candidum}
     journal = {Peer Community Journal},
     eid = {e45},
     publisher = {Peer Community In},
     volume = {3},
     year = {2023},
     doi = {10.24072/pcjournal.266},
     url = {https://peercommunityjournal.org/articles/10.24072/pcjournal.266/}
AU  - Bennetot, Bastien
AU  - Vernadet, Jean-Philippe
AU  - Perkins, Vincent
AU  - Hautefeuille, Sophie
AU  - Rodríguez de la Vega, Ricardo C.
AU  - O’Donnell, Samuel
AU  - Snirc, Alodie
AU  - Grondin, Cécile
AU  - Lessard, Marie-Hélène
AU  - Peron, Anne-Claire
AU  - Labrie, Steve
AU  - Landaud, Sophie
AU  - Giraud, Tatiana
AU  - Ropars, Jeanne
TI  - Domestication of different varieties in the cheese-making fungus Geotrichum candidum

JO  - Peer Community Journal
PY  - 2023
VL  - 3
PB  - Peer Community In
UR  - https://peercommunityjournal.org/articles/10.24072/pcjournal.266/
DO  - 10.24072/pcjournal.266
ID  - 10_24072_pcjournal_266
ER  - 
%0 Journal Article
%A Bennetot, Bastien
%A Vernadet, Jean-Philippe
%A Perkins, Vincent
%A Hautefeuille, Sophie
%A Rodríguez de la Vega, Ricardo C.
%A O’Donnell, Samuel
%A Snirc, Alodie
%A Grondin, Cécile
%A Lessard, Marie-Hélène
%A Peron, Anne-Claire
%A Labrie, Steve
%A Landaud, Sophie
%A Giraud, Tatiana
%A Ropars, Jeanne
%T Domestication of different varieties in the cheese-making fungus Geotrichum candidum

%J Peer Community Journal
%D 2023
%V 3
%I Peer Community In
%U https://peercommunityjournal.org/articles/10.24072/pcjournal.266/
%R 10.24072/pcjournal.266
%F 10_24072_pcjournal_266
Bennetot, Bastien; Vernadet, Jean-Philippe; Perkins, Vincent; Hautefeuille, Sophie; Rodríguez de la Vega, Ricardo C.; O’Donnell, Samuel; Snirc, Alodie; Grondin, Cécile; Lessard, Marie-Hélène; Peron, Anne-Claire; Labrie, Steve; Landaud, Sophie; Giraud, Tatiana; Ropars, Jeanne. Domestication of different varieties in the cheese-making fungus Geotrichum candidum
. Peer Community Journal, Volume 3 (2023), article  no. e45. doi : 10.24072/pcjournal.266. https://peercommunityjournal.org/articles/10.24072/pcjournal.266/

Peer reviewed and recommended by PCI : 10.24072/pci.evolbiol.100592

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

[1] Diamond, J. Evolution, consequences and future of plant and animal domestication, Nature, Volume 418 (2002) no. 6898, pp. 700-707 | DOI

[2] Frantz, L. A. F.; Schraiber, J. G.; Madsen, O.; Megens, H.-J.; Cagan, A.; Bosse, M.; Paudel, Y.; Crooijmans, R. P. M. A.; Larson, G.; Groenen, M. A. M. Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes, Nature Genetics, Volume 47 (2015) no. 10, pp. 1141-1148 | DOI

[3] Petersen, J. L.; Mickelson, J. R.; Rendahl, A. K.; Valberg, S. J.; Andersson, L. S.; Axelsson, J.; Bailey, E.; Bannasch, D.; Binns, M. M.; Borges, A. S.; Brama, P.; da Câmara Machado, A.; Capomaccio, S.; Cappelli, K.; Cothran, E. G.; Distl, O.; Fox-Clipsham, L.; Graves, K. T.; Guérin, G.; Haase, B.; Hasegawa, T.; Hemmann, K.; Hill, E. W.; Leeb, T.; Lindgren, G.; Lohi, H.; Lopes, M. S.; McGivney, B. A.; Mikko, S.; Orr, N.; Penedo, M. C. T.; Piercy, R. J.; Raekallio, M.; Rieder, S.; Røed, K. H.; Swinburne, J.; Tozaki, T.; Vaudin, M.; Wade, C. M.; McCue, M. E. Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds, PLoS Genetics, Volume 9 (2013) no. 1 | DOI

[4] Warmuth, V.; Eriksson, A.; Bower, M. A.; Cañon, J.; Cothran, G.; Distl, O.; Glowatzki-Mullis, M.-L.; Hunt, H.; Luís, C.; do Mar Oom, M.; Yupanqui, I. T.; Ząbek, T.; Manica, A. European Domestic Horses Originated in Two Holocene Refugia, PLoS ONE, Volume 6 (2011) no. 3 | DOI

[5] Hufford, M. B.; Xu, X.; van Heerwaarden, J.; Pyhäjärvi, T.; Chia, J.-M.; Cartwright, R. A.; Elshire, R. J.; Glaubitz, J. C.; Guill, K. E.; Kaeppler, S. M.; Lai, J.; Morrell, P. L.; Shannon, L. M.; Song, C.; Springer, N. M.; Swanson-Wagner, R. A.; Tiffin, P.; Wang, J.; Zhang, G.; Doebley, J.; McMullen, M. D.; Ware, D.; Buckler, E. S.; Yang, S.; Ross-Ibarra, J. Comparative population genomics of maize domestication and improvement, Nature Genetics, Volume 44 (2012) no. 7, pp. 808-811 | DOI

[6] Mabry, M. E.; Turner-Hissong, S. D.; Gallagher, E. Y.; McAlvay, A. C.; An, H.; Edger, P. P.; Moore, J. D.; Pink, D. A. C.; Teakle, G. R.; Stevens, C. J.; Barker, G.; Labate, J.; Fuller, D. Q.; Allaby, R. G.; Beissinger, T.; Decker, J. E.; Gore, M. A.; Pires, J. C. The Evolutionary History of Wild, Domesticated, and Feral Brassica oleracea (Brassicaceae), Molecular Biology and Evolution, Volume 38 (2021) no. 10, pp. 4419-4434 | DOI

[7] Peng, J. H.; Sun, D.; Nevo, E. Domestication evolution, genetics and genomics in wheat, Molecular Breeding, Volume 28 (2011) no. 3, pp. 281-301 | DOI

[8] Liu, X.; Zhang, Y.; Liu, W.; Li, Y.; Pan, J.; Pu, Y.; Han, J.; Orlando, L.; Ma, Y.; Jiang, L. A single-nucleotide mutation within the TBX3 enhancer increased body size in Chinese horses, Current Biology, Volume 32 (2022) no. 2 | DOI

[9] Plassais, J.; vonHoldt, B. M.; Parker, H. G.; Carmagnini, A.; Dubos, N.; Papa, I.; Bevant, K.; Derrien, T.; Hennelly, L. M.; Whitaker, D. T.; Harris, A. C.; Hogan, A. N.; Huson, H. J.; Zaibert, V. F.; Linderholm, A.; Haile, J.; Fest, T.; Habib, B.; Sacks, B. N.; Benecke, N.; Outram, A. K.; Sablin, M. V.; Germonpré, M.; Larson, G.; Frantz, L.; Ostrander, E. A. Natural and human-driven selection of a single non-coding body size variant in ancient and modern canids, Current Biology, Volume 32 (2022) no. 4 | DOI

[10] Qanbari, S.; Pausch, H.; Jansen, S.; Somel, M.; Strom, T. M.; Fries, R.; Nielsen, R.; Simianer, H. Classic Selective Sweeps Revealed by Massive Sequencing in Cattle, PLoS Genetics, Volume 10 (2014) no. 2 | DOI

[11] Cornille, A.; Giraud, T.; Smulders, M. J.; Roldán-Ruiz, I.; Gladieux, P. The domestication and evolutionary ecology of apples, Trends in Genetics, Volume 30 (2014) no. 2, pp. 57-65 | DOI

[12] Purugganan, M. D. Evolutionary Insights into the Nature of Plant Domestication, Current Biology, Volume 29 (2019) no. 14 | DOI

[13] Marsden, C. D.; Ortega-Del Vecchyo, D.; O’Brien, D. P.; Taylor, J. F.; Ramirez, O.; Vilà, C.; Marques-Bonet, T.; Schnabel, R. D.; Wayne, R. K.; Lohmueller, K. E. Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs, Proceedings of the National Academy of Sciences, Volume 113 (2015) no. 1, pp. 152-157 | DOI

[14] Zhu, Q.; Zheng, X.; Luo, J.; Gaut, B. S.; Ge, S. Multilocus Analysis of Nucleotide Variation of Oryza sativa and Its Wild Relatives: Severe Bottleneck during Domestication of Rice, Molecular Biology and Evolution, Volume 24 (2007) no. 3, pp. 875-888 | DOI

[15] Steensels, J.; Gallone, B.; Verstrepen, K. J. Interspecific hybridization as a driver of fungal evolution and adaptation, Nature Reviews Microbiology, Volume 19 (2021) no. 8, pp. 485-500 | DOI

[16] Gladieux, P.; Ropars, J.; Badouin, H.; Branca, A.; Aguileta, G.; Vienne, D. M.; Rodríguez de la Vega, R. C.; Branco, S.; Giraud, T. Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes, Molecular Ecology, Volume 23 (2014) no. 4, pp. 753-773 | DOI

[17] Bai, F.-Y.; Han, D.-Y.; Duan, S.-F.; Wang, Q.-M. The Ecology and Evolution of the Baker’s Yeast Saccharomyces cerevisiae, Genes, Volume 13 (2022) no. 2 | DOI

[18] Barbosa, R.; Pontes, A.; Santos, R. O.; Montandon, G. G.; de Ponzzes-Gomes, C. M.; Morais, P. B.; Gonçalves, P.; Rosa, C. A.; Sampaio, J. P. Multiple Rounds of Artificial Selection Promote Microbe Secondary Domestication—The Case of Cachaça Yeasts, Genome Biology and Evolution, Volume 10 (2018) no. 8, pp. 1939-1955 | DOI

[19] Bigey, F.; Segond, D.; Friedrich, A.; Guezenec, S.; Bourgais, A.; Huyghe, L.; Agier, N.; Nidelet, T.; Sicard, D. Evidence for Two Main Domestication Trajectories in Saccharomyces cerevisiae Linked to Distinct Bread-Making Processes, Current Biology, Volume 31 (2021) no. 4 | DOI

[20] Duan, S.-F.; Han, P.-J.; Wang, Q.-M.; Liu, W.-Q.; Shi, J.-Y.; Li, K.; Zhang, X.-L.; Bai, F.-Y. The origin and adaptive evolution of domesticated populations of yeast from Far East Asia, Nature Communications, Volume 9 (2018) no. 1 | DOI

[21] Fay, J. C.; Benavides, J. A. Evidence for Domesticated and Wild Populations of Saccharomyces cerevisiae, PLoS Genetics, Volume 1 (2005) no. 1 | DOI

[22] Gallone, B.; Steensels, J.; Prahl, T.; Soriaga, L.; Saels, V.; Herrera-Malaver, B.; Merlevede, A.; Roncoroni, M.; Voordeckers, K.; Miraglia, L.; Teiling, C.; Steffy, B.; Taylor, M.; Schwartz, A.; Richardson, T.; White, C.; Baele, G.; Maere, S.; Verstrepen, K. J. Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts, Cell, Volume 166 (2016) no. 6 | DOI

[23] Gonçalves, M.; Pontes, A.; Almeida, P.; Barbosa, R.; Serra, M.; Libkind, D.; Hutzler, M.; Gonçalves, P.; Sampaio, J. P. Distinct Domestication Trajectories in Top-Fermenting Beer Yeasts and Wine Yeasts, Current Biology, Volume 26 (2016) no. 20, pp. 2750-2761 | DOI

[24] Lahue, C.; Madden, A. A.; Dunn, R. R.; Smukowski Heil, C. History and Domestication of Saccharomyces cerevisiae in Bread Baking, Frontiers in Genetics, Volume 11 (2020) | DOI

[25] Legras, J.-L.; Galeote, V.; Bigey, F.; Camarasa, C.; Marsit, S.; Nidelet, T.; Sanchez, I.; Couloux, A.; Guy, J.; Franco-Duarte, R.; Marcet-Houben, M.; Gabaldon, T.; Schuller, D.; Sampaio, J. P.; Dequin, S. Adaptation of S. cerevisiae to Fermented Food Environments Reveals Remarkable Genome Plasticity and the Footprints of Domestication, Molecular Biology and Evolution, Volume 35 (2018) no. 7, pp. 1712-1727 | DOI

[26] Libkind, D.; Hittinger, C. T.; Valério, E.; Gonçalves, C.; Dover, J.; Johnston, M.; Gonçalves, P.; Sampaio, J. P. Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast, Proceedings of the National Academy of Sciences, Volume 108 (2011) no. 35, pp. 14539-14544 | DOI

[27] Liti, G.; Carter, D. M.; Moses, A. M.; Warringer, J.; Parts, L.; James, S. A.; Davey, R. P.; Roberts, I. N.; Burt, A.; Koufopanou, V.; Tsai, I. J.; Bergman, C. M.; Bensasson, D.; O’Kelly, M. J. T.; van Oudenaarden, A.; Barton, D. B. H.; Bailes, E.; Nguyen, A. N.; Jones, M.; Quail, M. A.; Goodhead, I.; Sims, S.; Smith, F.; Blomberg, A.; Durbin, R.; Louis, E. J. Population genomics of domestic and wild yeasts, Nature, Volume 458 (2009) no. 7236, pp. 337-341 | DOI

[28] Ludlow, C. L.; Cromie, G. A.; Garmendia-Torres, C.; Sirr, A.; Hays, M.; Field, C.; Jeffery, E. W.; Fay, J. C.; Dudley, A. M. Independent Origins of Yeast Associated with Coffee and Cacao Fermentation, Current Biology, Volume 26 (2016) no. 7, pp. 965-971 | DOI

[29] Peter, J.; De Chiara, M.; Friedrich, A.; Yue, J.-X.; Pflieger, D.; Bergström, A.; Sigwalt, A.; Barre, B.; Freel, K.; Llored, A.; Cruaud, C.; Labadie, K.; Aury, J.-M.; Istace, B.; Lebrigand, K.; Barbry, P.; Engelen, S.; Lemainque, A.; Wincker, P.; Liti, G.; Schacherer, J. Genome evolution across 1,011 Saccharomyces cerevisiae isolates, Nature, Volume 556 (2018) no. 7701, pp. 339-344 | DOI

[30] Galagan, J. E.; Calvo, S. E.; Cuomo, C.; Ma, L.-J.; Wortman, J. R.; Batzoglou, S.; Lee, S.-I.; Baştürkmen, M.; Spevak, C. C.; Clutterbuck, J.; Kapitonov, V.; Jurka, J.; Scazzocchio, C.; Farman, M.; Butler, J.; Purcell, S.; Harris, S.; Braus, G. H.; Draht, O.; Busch, S.; D'Enfert, C.; Bouchier, C.; Goldman, G. H.; Bell-Pedersen, D.; Griffiths-Jones, S.; Doonan, J. H.; Yu, J.; Vienken, K.; Pain, A.; Freitag, M.; Selker, E. U.; Archer, D. B.; Peñalva, M. Á.; Oakley, B. R.; Momany, M.; Tanaka, T.; Kumagai, T.; Asai, K.; Machida, M.; Nierman, W. C.; Denning, D. W.; Caddick, M.; Hynes, M.; Paoletti, M.; Fischer, R.; Miller, B.; Dyer, P.; Sachs, M. S.; Osmani, S. A.; Birren, B. W. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae, Nature, Volume 438 (2005) no. 7071, pp. 1105-1115 | DOI

[31] Gibbons, J. G.; Salichos, L.; Slot, J. C.; Rinker, D. C.; McGary, K. L.; King, J. G.; Klich, M. A.; Tabb, D. L.; McDonald, W. H.; Rokas, A. The Evolutionary Imprint of Domestication on Genome Variation and Function of the Filamentous Fungus Aspergillus oryzae, Current Biology, Volume 22 (2012) no. 15, pp. 1403-1409 | DOI

[32] Machida, M.; Asai, K.; Sano, M.; Tanaka, T.; Kumagai, T.; Terai, G.; Kusumoto, K.-I.; Arima, T.; Akita, O.; Kashiwagi, Y.; Abe, K.; Gomi, K.; Horiuchi, H.; Kitamoto, K.; Kobayashi, T.; Takeuchi, M.; Denning, D. W.; Galagan, J. E.; Nierman, W. C.; Yu, J.; Archer, D. B.; Bennett, J. W.; Bhatnagar, D.; Cleveland, T. E.; Fedorova, N. D.; Gotoh, O.; Horikawa, H.; Hosoyama, A.; Ichinomiya, M.; Igarashi, R.; Iwashita, K.; Juvvadi, P. R.; Kato, M.; Kato, Y.; Kin, T.; Kokubun, A.; Maeda, H.; Maeyama, N.; Maruyama, J.-i.; Nagasaki, H.; Nakajima, T.; Oda, K.; Okada, K.; Paulsen, I.; Sakamoto, K.; Sawano, T.; Takahashi, M.; Takase, K.; Terabayashi, Y.; Wortman, J. R.; Yamada, O.; Yamagata, Y.; Anazawa, H.; Hata, Y.; Koide, Y.; Komori, T.; Koyama, Y.; Minetoki, T.; Suharnan, S.; Tanaka, A.; Isono, K.; Kuhara, S.; Ogasawara, N.; Kikuchi, H. Genome sequencing and analysis of Aspergillus oryzae, Nature, Volume 438 (2005) no. 7071, pp. 1157-1161 | DOI

[33] Cheeseman, K.; Ropars, J.; Renault, P.; Dupont, J.; Gouzy, J.; Branca, A.; Abraham, A.-L.; Ceppi, M.; Conseiller, E.; Debuchy, R.; Malagnac, F.; Goarin, A.; Silar, P.; Lacoste, S.; Sallet, E.; Bensimon, A.; Giraud, T.; Brygoo, Y. Multiple recent horizontal transfers of a large genomic region in cheese making fungi, Nature Communications, Volume 5 (2014) no. 1 | DOI

[34] Dumas, E.; Feurtey, A.; Rodríguez de la Vega, R. C.; 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, Molecular Ecology, Volume 29 (2020) no. 14, pp. 2639-2660 | DOI

[35] Ropars, J.; Rodríguez de la Vega, R. C.; López-Villavicencio, M.; Gouzy, J.; Sallet, E.; Dumas, É.; Lacoste, S.; Debuchy, R.; Dupont, J.; Branca, A.; Giraud, T. Adaptive Horizontal Gene Transfers between Multiple Cheese-Associated Fungi, Current Biology, Volume 25 (2015) no. 19, pp. 2562-2569 | DOI

[36] Bigey, F.; Segond, D.; Friedrich, A.; Guezenec, S.; Bourgais, A.; Huyghe, L.; Agier, N.; Nidelet, T.; Sicard, D. Evidence for Two Main Domestication Trajectories in Saccharomyces cerevisiae Linked to Distinct Bread-Making Processes, Current Biology, Volume 31 (2021) no. 4 | DOI

[37] Caron, T.; Piver, M. L.; Péron, A.-C.; 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, International Journal of Food Microbiology, Volume 354 (2021) | DOI

[38] Almeida, P.; Gonçalves, C.; Teixeira, S.; Libkind, D.; Bontrager, M.; Masneuf-Pomarède, I.; Albertin, W.; Durrens, P.; Sherman, D. J.; Marullo, P.; Todd Hittinger, C.; Gonçalves, P.; Sampaio, J. P. A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum, Nature Communications, Volume 5 (2014) no. 1 | DOI

[39] Barros Lopes, M.; Bellon, J. R.; Shirley, N. J.; Ganter, P. F. Evidence for multiple interspecific hybridization inSaccharomycessensu stricto species, FEMS Yeast Research, Volume 1 (2002) no. 4, pp. 323-331 | DOI

[40] Borneman, A. R.; Forgan, A. H.; Kolouchova, R.; Fraser, J. A.; Schmidt, S. A. Whole Genome Comparison Reveals High Levels of Inbreeding and Strain Redundancy Across the Spectrum of Commercial Wine Strains of Saccharomyces cerevisiae, G3 Genes|Genomes|Genetics, Volume 6 (2016) no. 4, pp. 957-971 | DOI

[41] Naumova, E. S.; Naumov, G. I.; Masneuf-Pomarède, I.; Aigle, M.; Dubourdieu, D. Molecular genetic study of introgression betweenSaccharomyces bayanus andS. cerevisiae, Yeast, Volume 22 (2005) no. 14, pp. 1099-1115 | DOI

[42] Novo, M.; Bigey, F.; Beyne, E.; Galeote, V.; Gavory, F.; Mallet, S.; Cambon, B.; Legras, J.-L.; Wincker, P.; Casaregola, S.; Dequin, S. Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118, Proceedings of the National Academy of Sciences, Volume 106 (2009) no. 38, pp. 16333-16338 | DOI

[43] Gillot, G.; Jany, J.-L.; Poirier, E.; Maillard, M.-B.; Debaets, S.; Thierry, A.; Coton, E.; Coton, M. Functional diversity within the Penicillium roqueforti species, International Journal of Food Microbiology, Volume 241 (2017), pp. 141-150 | DOI

[44] Ropars, J.; Caron, T.; Lo, Y.-C.; Bennetot, B.; Giraud, T. La domestication des champignons Penicillium du fromage, Comptes Rendus Biologies, Volume 343 (2020) no. 2, pp. 155-176 | DOI

[45] Alper, I.; Frenette, M.; Labrie, S. Genetic diversity of dairy Geotrichum candidum strains revealed by multilocus sequence typing, Applied Microbiology and Biotechnology, Volume 97 (2013) no. 13, pp. 5907-5920 | DOI

[46] Jacques, N.; Mallet, S.; Laaghouiti, F.; Tinsley, C. R.; Casaregola, S. Specific populations of the yeastGeotrichum candidumrevealed by molecular typing, Yeast, Volume 34 (2016) no. 4, pp. 165-178 | DOI

[47] Perkins, V.; Vignola, S.; Lessard, M.-H.; Plante, P.-L.; Corbeil, J.; Dugat-Bony, E.; Frenette, M.; Labrie, S. Phenotypic and Genetic Characterization of the Cheese Ripening Yeast Geotrichum candidum, Frontiers in Microbiology, Volume 11 (2020) | DOI

[48] Tinsley, C. R.; Jacques, N.; Lucas, M.; Grondin, C.; Legras, J.-L.; Casaregola, S. Molecular Genetic Analysis with Microsatellite-like Loci Reveals Specific Dairy-Associated and Environmental Populations of the Yeast Geotrichum candidum, Microorganisms, Volume 10 (2022) no. 1 | DOI

[49] Boutrou, R.; Guéguen, M. Interests in Geotrichum candidum for cheese technology, International Journal of Food Microbiology, Volume 102 (2005) no. 1, pp. 1-20 | DOI

[50] Morel, G.; Sterck, L.; Swennen, D.; Marcet-Houben, M.; Onesime, D.; Levasseur, A.; Jacques, N.; Mallet, S.; Couloux, A.; Labadie, K.; Amselem, J.; Beckerich, J.-M.; Henrissat, B.; Van de Peer, Y.; Wincker, P.; Souciet, J.-L.; Gabaldón, T.; Tinsley, C. R.; Casaregola, S. Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts, Scientific Reports, Volume 5 (2015) no. 1 | DOI

[51] Felsenstein, J. The Evolutionary Advantage Of Recombination, Genetics, Volume 78 (1974) no. 2, pp. 737-756 | DOI

[52] Giannakou, K.; Cotterrell, M.; Delneri, D. Genomic Adaptation of Saccharomyces Species to Industrial Environments, Frontiers in Genetics, Volume 11 (2020) | DOI

[53] Gao, M.; Glenn, A. E.; Blacutt, A. A.; Gold, S. E. Fungal Lactamases: Their Occurrence and Function, Frontiers in Microbiology, Volume 8 (2017) | DOI

[54] Baduel, P.; Quadrana, L.; Hunter, B.; Bomblies, K.; Colot, V. Relaxed purifying selection in autopolyploids drives transposable element over-accumulation which provides variants for local adaptation, Nature Communications, Volume 10 (2019) no. 1 | DOI

[55] McSweeney, P. L. H. Biochemistry of cheese ripening, International Journal of Dairy Technology, Volume 57 (2004) no. 2-3, pp. 127-144 | DOI

[56] Penland, M.; Falentin, H.; Parayre, S.; Pawtowski, A.; Maillard, M.-B.; Thierry, A.; Mounier, J.; Coton, M.; Deutsch, S.-M. Linking Pélardon artisanal goat cheese microbial communities to aroma compounds during cheese-making and ripening, International Journal of Food Microbiology, Volume 345 (2021) | DOI

[57] Monnet, C.; Back, A.; Irlinger, F. Growth of Aerobic Ripening Bacteria at the Cheese Surface Is Limited by the Availability of Iron, Applied and Environmental Microbiology, Volume 78 (2012) no. 9, pp. 3185-3192 | DOI

[58] Bonnarme, P.; Arfi, K.; Dury, C.; Helinck, S.; Yvon, M.; Spinnler, H.-E. Sulfur compound production by Geotrichum candidum from l-methionine: importance of the transamination step, FEMS Microbiology Letters, Volume 205 (2001) no. 2, pp. 247-252 | DOI

[59] Collins, Y. F.; McSweeney, P. L.; Wilkinson, M. G. Lipolysis and free fatty acid catabolism in cheese: a review of current knowledge, International Dairy Journal, Volume 13 (2003) no. 11, pp. 841-866 | DOI

[60] Dugat-Bony, E.; Straub, C.; Teissandier, A.; Onésime, D.; Loux, V.; Monnet, C.; Irlinger, F.; Landaud, S.; Leclercq-Perlat, M.-N.; Bento, P.; Fraud, S.; Gibrat, J.-F.; Aubert, J.; Fer, F.; Guédon, E.; Pons, N.; Kennedy, S.; Beckerich, J.-M.; Swennen, D.; Bonnarme, P. Overview of a Surface-Ripened Cheese Community Functioning by Meta-Omics Analyses, PLOS ONE, Volume 10 (2015) no. 4 | DOI

[61] Kumura, H.; Takagaki, K.; Sone, T.; Tsukahara, M.; Tanaka, T.; Shimazaki, K.-I. Casein Digestion by Debaryomyces hansenii Isolated from Cheese, Bioscience, Biotechnology, and Biochemistry, Volume 66 (2002) no. 6, pp. 1370-1373 | DOI

[62] Adams, D. J. Fungal cell wall chitinases and glucanases, Microbiology, Volume 150 (2004) no. 7, pp. 2029-2035 | DOI

[63] Rocha, R. O.; Wilson, R. A. Essential, deadly, enigmatic: Polyamine metabolism and roles in fungal cells, Fungal Biology Reviews, Volume 33 (2019) no. 1, pp. 47-57 | DOI

[64] Pitt, J.; Cruickshank, R.; Leistner, L. Penicillium commune, P. camembertii, the origin of white cheese moulds, and the production of cyclopiazonic acid, Food Microbiology, Volume 3 (1986) no. 4, pp. 363-371 | DOI

[65] Gallone, B.; Mertens, S.; Gordon, J. L.; Maere, S.; Verstrepen, K. J.; Steensels, J. Origins, evolution, domestication and diversity of Saccharomyces beer yeasts, Current Opinion in Biotechnology, Volume 49 (2018), pp. 148-155 | DOI

[66] Price, E. O. Animal domestication and behavior, CAB International, UK, 2002 | DOI

[67] Liu, S.-Q.; Holland, R.; Crow, V. Esters and their biosynthesis in fermented dairy products: a review, International Dairy Journal, Volume 14 (2004) no. 11, pp. 923-945 | DOI

[68] Urbach, G. The flavour of milk and dairy products: II. Cheese: contribution of volatile compounds, International Journal of Dairy Technology, Volume 50 (1997) no. 3, pp. 79-89 | DOI

[69] Curioni, P.; Bosset, J. Key odorants in various cheese types as determined by gas chromatography-olfactometry, International Dairy Journal, Volume 12 (2002) no. 12, pp. 959-984 | DOI

[70] Mayo, B.; Rodríguez, J.; Vázquez, L.; Flórez, A. B. Microbial Interactions within the Cheese Ecosystem and Their Application to Improve Quality and Safety, Foods, Volume 10 (2021) no. 3 | DOI

[71] Monnet, C.; Landaud, S.; Bonnarme, P.; Swennen, D. Growth and adaptation of microorganisms on the cheese surface, FEMS Microbiology Letters, Volume 362 (2015) no. 1, pp. 1-9 | DOI

[72] Dieuleveux, V.; Van Der Pyl, D.; Chataud, J.; Gueguen, M. Purification and Characterization of Anti- Listeria Compounds Produced by Geotrichum candidum, Applied and Environmental Microbiology, Volume 64 (1998) no. 2, pp. 800-803 | DOI

[73] Nielsen, M. S.; Frisvad, J. C.; Nielsen, P. V. Colony Interaction and Secondary Metabolite Production of Cheese-Related Fungi in Dual Culture, Journal of Food Protection, Volume 61 (1998) no. 8, pp. 1023-1029 | DOI

[74] Omeike, S. O.; Kareem, S. O.; Nandanwar, H.; Lasisi, A. A.; Oluwafemi, F.; Jangra, M. Purification, De Novo Characterization and Antibacterial Properties of a Novel, Narrow-Spectrum Bacteriostatic Tripeptide from Geotrichum candidum OMON-1, Arabian Journal for Science and Engineering, Volume 46 (2020) no. 6, pp. 5275-5283 | DOI

[75] von Gastrow, L.; Michel, E.; Legrand, J.; Amelot, R.; Segond, D.; Guezenec, S.; Rué, O.; Chable, V.; Goldringer, I.; Dousset, X.; Serpolay‐Bessoni, E.; Taupier‐Letage, B.; Vindras‐Fouillet, C.; Onno, B.; Valence, F.; Sicard, D. Microbial community dispersal from wheat grains to sourdoughs: A contribution of participatory research, Molecular Ecology (2022) | DOI

[76] Lo, Y.-C.; Bruxaux, J.; Rodríguez de la Vega, R. C.; O’Donnell, S.; Snirc, A.; Coton, M.; Piver, M. L.; Prieur, S. L.; Roueyre, D.; Dupont, J.; Houbraken, J.; Debuchy, R.; Ropars, J.; Giraud, T.; Branca, A. Domestication in dry-cured meatPenicilliumfungi: convergent specific phenotypes and horizontal gene transfers without strong genetic subdivision, bioRxiv, 2022 | DOI

[77] Ropars, J.; Giraud, T. Convergence in domesticated fungi used for cheese and dry-cured meat maturation: beneficial traits, genomic mechanisms, and degeneration, Current Opinion in Microbiology, Volume 70 (2022) | DOI

[78] Crequer, E.; Ropars, J.; Jany, J.-L.; Caron, T.; Coton, M.; Snirc, A.; Vernadet, J.-P.; Branca, A.; Giraud, T.; Coton, E. A new cheese population in Penicillium roqueforti and adaptation of the five populations to their ecological niche, bioRxiv, 2023 | DOI

[79] Janzen, G. M.; Hufford, M. B. Crop Domestication: A Sneak-Peek into the Midpoint of Maize Evolution, Current Biology, Volume 26 (2016) no. 23 | DOI

[80] Lin, T.; Zhu, G.; Zhang, J.; Xu, X.; Yu, Q.; Zheng, Z.; Zhang, Z.; Lun, Y.; Li, S.; Wang, X.; Huang, Z.; Li, J.; Zhang, C.; Wang, T.; Zhang, Y.; Wang, A.; Zhang, Y.; Lin, K.; Li, C.; Xiong, G.; Xue, Y.; Mazzucato, A.; Causse, M.; Fei, Z.; Giovannoni, J. J.; Chetelat, R. T.; Zamir, D.; Städler, T.; Li, J.; Ye, Z.; Du, Y.; Huang, S. Genomic analyses provide insights into the history of tomato breeding, Nature Genetics, Volume 46 (2014) no. 11, pp. 1220-1226 | DOI

[81] Carreira, A.; Dillinger, K.; Eliskases-Lechner, F.; Loureiro, V.; Ginzinger, W.; Rohm, H. Influence of selected factors on browning of Camembert cheese, Journal of Dairy Research, Volume 69 (2002) no. 2, pp. 281-292 | DOI

[82] Alberto, F. J.; Boyer, F.; Orozco-terWengel, P.; Streeter, I.; Servin, B.; de Villemereuil, P.; Benjelloun, B.; Librado, P.; Biscarini, F.; Colli, L.; Barbato, M.; Zamani, W.; Alberti, A.; Engelen, S.; Stella, A.; Joost, S.; Ajmone-Marsan, P.; Negrini, R.; Orlando, L.; Rezaei, H. R.; Naderi, S.; Clarke, L.; Flicek, P.; Wincker, P.; Coissac, E.; Kijas, J.; Tosser-Klopp, G.; Chikhi, A.; Bruford, M. W.; Taberlet, P.; Pompanon, F. Convergent genomic signatures of domestication in sheep and goats, Nature Communications, Volume 9 (2018) no. 1 | DOI

[83] Cresko, W. A.; Amores, A.; Wilson, C.; Murphy, J.; Currey, M.; Phillips, P.; Bell, M. A.; Kimmel, C. B.; Postlethwait, J. H. Parallel genetic basis for repeated evolution of armor loss in Alaskan threespine stickleback populations, Proceedings of the National Academy of Sciences, Volume 101 (2004) no. 16, pp. 6050-6055 | DOI

[84] Dyer, A. G.; Boyd-Gerny, S.; McLoughlin, S.; Rosa, M. G. P.; Simonov, V.; Wong, B. B. M. Parallel evolution of angiosperm colour signals: common evolutionary pressures linked to hymenopteran vision, Proceedings of the Royal Society B: Biological Sciences, Volume 279 (2012) no. 1742, pp. 3606-3615 | DOI

[85] Elmer, K. R.; Fan, S.; Kusche, H.; Luise Spreitzer, M.; Kautt, A. F.; Franchini, P.; Meyer, A. Parallel evolution of Nicaraguan crater lake cichlid fishes via non-parallel routes, Nature Communications, Volume 5 (2014) no. 1 | DOI

[86] Lin, Z.; Li, X.; Shannon, L. M.; Yeh, C.-T.; Wang, M. L.; Bai, G.; Peng, Z.; Li, J.; Trick, H. N.; Clemente, T. E.; Doebley, J.; Schnable, P. S.; Tuinstra, M. R.; Tesso, T. T.; White, F.; Yu, J. Parallel domestication of the Shattering1 genes in cereals, Nature Genetics, Volume 44 (2012) no. 6, pp. 720-724 | DOI

[87] Macías, L. G.; Flores, M. G.; Adam, A. C.; Rodríguez, M. E.; Querol, A.; Barrio, E.; Lopes, C. A.; Pérez-Torrado, R. Convergent adaptation of Saccharomyces uvarum to sulfite, an antimicrobial preservative widely used in human-driven fermentations, PLOS Genetics, Volume 17 (2021) no. 11 | DOI

[88] O'Quin, K. E.; Hofmann, C. M.; Hofmann, H. A.; Carleton, K. L. Parallel Evolution of Opsin Gene Expression in African Cichlid Fishes, Molecular Biology and Evolution, Volume 27 (2010) no. 12, pp. 2839-2854 | DOI

[89] Thorpe, R. S.; Barlow, A.; Malhotra, A.; Surget-Groba, Y. Widespread parallel population adaptation to climate variation across a radiation: implications for adaptation to climate change, Molecular Ecology, Volume 24 (2015) no. 5, pp. 1019-1030 | DOI

[90] Harlan, J. R.; et al. Biodiversity in agriculture: domestication, evolution, and sustainability, Cambridge University Press, 2012, 606 pages

[91] Vilgalys, R.; Hester, M. Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species, Journal of Bacteriology, Volume 172 (1990) no. 8, pp. 4238-4246 | DOI

[92] Bolger, A. M.; Lohse, M.; Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, Volume 30 (2014) no. 15, pp. 2114-2120 | DOI

[93] Koren, S.; Walenz, B. P.; Berlin, K.; Miller, J. R.; Bergman, N. H.; Phillippy, A. M. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation, Genome Research, Volume 27 (2017) no. 5, pp. 722-736 | DOI

[94] Salmela, L.; Rivals, E. LoRDEC: accurate and efficient long read error correction, Bioinformatics, Volume 30 (2014) no. 24, pp. 3506-3514 | DOI

[95] Walker, B. J.; Abeel, T.; Shea, T.; Priest, M.; Abouelliel, A.; Sakthikumar, S.; Cuomo, C. A.; Zeng, Q.; Wortman, J.; Young, S. K.; Earl, A. M. Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement, PLoS ONE, Volume 9 (2014) no. 11 | DOI

[96] Antipov, D.; Korobeynikov, A.; McLean, J. S.; Pevzner, P. A. hybridSPAdes: an algorithm for hybrid assembly of short and long reads, Bioinformatics, Volume 32 (2015) no. 7, pp. 1009-1015 | DOI

[97] Prjibelski, A.; Antipov, D.; Meleshko, D.; Lapidus, A.; Korobeynikov, A. Using SPAdes De Novo Assembler, Current Protocols in Bioinformatics, Volume 70 (2020) no. 1 | DOI

[98] Crusoe, M. R.; Alameldin, H. F.; Awad, S.; Boucher, E.; Caldwell, A.; Cartwright, R.; Charbonneau, A.; Constantinides, B.; Edvenson, G.; Fay, S.; Fenton, J.; Fenzl, T.; Fish, J.; Garcia-Gutierrez, L.; Garland, P.; Gluck, J.; González, I.; Guermond, S.; Guo, J.; Gupta, A.; Herr, J. R.; Howe, A.; Hyer, A.; Härpfer, A.; Irber, L.; Kidd, R.; Lin, D.; Lippi, J.; Mansour, T.; McA'Nulty, P.; McDonald, E.; Mizzi, J.; Murray, K. D.; Nahum, J. R.; Nanlohy, K.; Nederbragt, A. J.; Ortiz-Zuazaga, H.; Ory, J.; Pell, J.; Pepe-Ranney, C.; Russ, Z. N.; Schwarz, E.; Scott, C.; Seaman, J.; Sievert, S.; Simpson, J.; Skennerton, C. T.; Spencer, J.; Srinivasan, R.; Standage, D.; Stapleton, J. A.; Steinman, S. R.; Stein, J.; Taylor, B.; Trimble, W.; Wiencko, H. L.; Wright, M.; Wyss, B.; Zhang, Q.; zyme, e.; Brown, C. T. The khmer software package: enabling efficient nucleotide sequence analysis, F1000Research, Volume 4 (2015) | DOI

[99] Stanke, M.; Diekhans, M.; Baertsch, R.; Haussler, D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding, Bioinformatics, Volume 24 (2008) no. 5, pp. 637-644 | DOI

[100] Palmer, J. M.; Stajich, J. Funannotate v1.8.1: Eukaryotic genome annotation, Zenodo, 2020 | DOI

[101] Blum, M.; Chang, H.-Y.; Chuguransky, S.; Grego, T.; Kandasaamy, S.; Mitchell, A.; Nuka, G.; Paysan-Lafosse, T.; Qureshi, M.; Raj, S.; Richardson, L.; Salazar, G. A.; Williams, L.; Bork, P.; Bridge, A.; Gough, J.; Haft, D. H.; Letunic, I.; Marchler-Bauer, A.; Mi, H.; Natale, D. A.; Necci, M.; Orengo, C. A.; Pandurangan, A. P.; Rivoire, C.; Sigrist, C. J. A.; Sillitoe, I.; Thanki, N.; Thomas, P. D.; Tosatto, S. C. E.; Wu, C. H.; Bateman, A.; Finn, R. D. The InterPro protein families and domains database: 20 years on, Nucleic Acids Research, Volume 49 (2020) no. D1 | DOI

[102] Eddy, S. R. Accelerated Profile HMM Searches, PLoS Computational Biology, Volume 7 (2011) no. 10 | DOI

[103] Huang, L.; Zhang, H.; Wu, P.; Entwistle, S.; Li, X.; Yohe, T.; Yi, H.; Yang, Z.; Yin, Y. dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation, Nucleic Acids Research, Volume 46 (2017) no. D1 | DOI

[104] Mistry, J.; Chuguransky, S.; Williams, L.; Qureshi, M.; Salazar, G. A.; Sonnhammer, E. L. L.; Tosatto, S. C. E.; Paladin, L.; Raj, S.; Richardson, L. J.; Finn, R. D.; Bateman, A. Pfam: The protein families database in 2021, Nucleic Acids Research, Volume 49 (2020) no. D1 | DOI

[105] Rawlings, N. D.; Barrett, A. J.; Thomas, P. D.; Huang, X.; Bateman, A.; Finn, R. D. The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database, Nucleic Acids Research, Volume 46 (2017) no. D1 | DOI

[106] The UniProt Consortium UniProt: the universal protein knowledgebase in 2021, Nucleic Acids Research, Volume 49 (2021) no. D1 | DOI

[107] Cantalapiedra, C. P.; Hernández-Plaza, A.; Letunic, I.; Bork, P.; Huerta-Cepas, J. eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale | DOI

[108] Huerta-Cepas, J.; Szklarczyk, D.; Heller, D.; Hernández-Plaza, A.; Forslund, S. K.; Cook, H.; Mende, D. R.; Letunic, I.; Rattei, T.; Jensen, L. J.; von Mering, C.; Bork, P. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses, Nucleic Acids Research, Volume 47 (2018) no. D1 | DOI

[109] Langmead, B.; Salzberg, S. L. Fast gapped-read alignment with Bowtie 2, Nature Methods, Volume 9 (2012) no. 4, pp. 357-359 | DOI

[110] Li, H.; Handsaker, B.; Wysoker, A.; Fennell, T.; Ruan, J.; Homer, N.; Marth, G.; Abecasis, G.; Durbin, R. The Sequence Alignment/Map format and SAMtools, Bioinformatics, Volume 25 (2009) no. 16, pp. 2078-2079 | DOI

[111] Minh, B. Q.; Schmidt, H. A.; Chernomor, O.; Schrempf, D.; Woodhams, M. D.; von Haeseler, A.; Lanfear, R. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era, Molecular Biology and Evolution, Volume 37 (2020) no. 5, pp. 1530-1534 | DOI

[112] Minh, B. Q.; Nguyen, M. A. T.; von Haeseler, A. Ultrafast Approximation for Phylogenetic Bootstrap, Molecular Biology and Evolution, Volume 30 (2013) no. 5, pp. 1188-1195 | DOI

[113] Huson, D. H.; Bryant, D. Application of Phylogenetic Networks in Evolutionary Studies, Molecular Biology and Evolution, Volume 23 (2005) no. 2, pp. 254-267 | DOI

[114] Bougeard, S.; Dray, S. Supervised Multiblock Analysis in R with the ade4 Package, Journal of Statistical Software, Volume 86 (2018) no. 1 | DOI

[115] Chessel, D.; Dufour, A.-B.; Thioulouse, J. The ade4 Package - I: One-Table Methods, R News, Volume 4 (2004), pp. 5-10

[116] Dray, S.; Dufour, A.-B.; Chessel, D. The ade4 Package - II: Two-Table and K-Table Methods, R News, Volume 7 (2007), pp. 47-52

[117] Dray, S.; Dufour, A.-B. The ade4 Package: Implementing the Duality Diagram for Ecologists, Journal of Statistical Software, Volume 22 (2007) no. 4 | DOI

[118] Thioulouse, J.; Dray, S.; Dufour, A.-B.; Siberchicot, A.; Jombart, T.; Pavoine, S. Multivariate Analysis of Ecological Data with ade4, Springer New York, New York, NY, 2018 | DOI

[119] Jørsboe, E.; Hanghøj, K.; Albrechtsen, A. fastNGSadmix: admixture proportions and principal component analysis of a single NGS sample, Bioinformatics, Volume 33 (2017) no. 19, pp. 3148-3150 | DOI

[120] Korneliussen, T. S.; Albrechtsen, A.; Nielsen, R. ANGSD: Analysis of Next Generation Sequencing Data, BMC Bioinformatics, Volume 15 (2014) no. 1 | DOI

[121] Hudson, R. R.; Slatkin, M.; Maddison, W. P. Estimation of levels of gene flow from DNA sequence data, Genetics, Volume 132 (1992) no. 2, pp. 583-589 | DOI

[122] Nei, M.; Li, W. H. Mathematical model for studying genetic variation in terms of restriction endonucleases, Proceedings of the National Academy of Sciences, Volume 76 (1979) no. 10, pp. 5269-5273 | DOI

[123] Watterson, G. On the number of segregating sites in genetical models without recombination, Theoretical Population Biology, Volume 7 (1975) no. 2, pp. 256-276 | DOI

[124] Pfeifer, B.; Wittelsbürger, U.; Ramos-Onsins, S. E.; Lercher, M. J. PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R, Molecular Biology and Evolution, Volume 31 (2014) no. 7, pp. 1929-1936 | DOI

[125] Cingolani, P.; Platts, A.; Wang, L. L.; Coon, M.; Nguyen, T.; Wang, L.; Land, S. J.; Lu, X.; Ruden, D. M. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff, Fly, Volume 6 (2012) no. 2, pp. 80-92 | DOI

[126] Flynn, J. M.; Hubley, R.; Goubert, C.; Rosen, J.; Clark, A. G.; Feschotte, C.; Smit, A. F. RepeatModeler2 for automated genomic discovery of transposable element families, Proceedings of the National Academy of Sciences, Volume 117 (2020) no. 17, pp. 9451-9457 | DOI

[127] Goubert, C.; Craig, R. J.; Bilat, A. F.; Peona, V.; Vogan, A. A.; Protasio, A. V. A beginner’s guide to manual curation of transposable elements, Mobile DNA, Volume 13 (2022) no. 1 | DOI

[128] Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM, arXiv (2013) | DOI

[129] Pavlidis, P.; Živković, D.; Stamatakis, A.; Alachiotis, N. SweeD: Likelihood-Based Detection of Selective Sweeps in Thousands of Genomes, Molecular Biology and Evolution, Volume 30 (2013) no. 9, pp. 2224-2234 | DOI

[130] Ekseth, O. K.; Kuiper, M.; Mironov, V. orthAgogue: an agile tool for the rapid prediction of orthology relations, Bioinformatics, Volume 30 (2013) no. 5, pp. 734-736 | DOI

[131] Ranwez, V.; Douzery, E. J. P.; Cambon, C.; Chantret, N.; Delsuc, F. MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons, Molecular Biology and Evolution, Volume 35 (2018) no. 10, pp. 2582-2584 | DOI

[132] Kritikos, G.; Banzhaf, M.; Herrera-Dominguez, L.; Koumoutsi, A.; Wartel, M.; Zietek, M.; Typas, A. A tool named Iris for versatile high-throughput phenotyping in microorganisms, Nature Microbiology, Volume 2 (2017) no. 5 | DOI

[133] Wickham, H. Getting Started with ggplot2, ggplot2: Elegant Graphics for Data Analysis. Use R! (ed Wickham H), Springer International Publishing, Cham, 2016, pp. 11-31 | DOI

[134] Fraïsse, C. Diverse outcomes in cheese fungi domestication, Peer Community in Evolutionary Biology (2023) | DOI

[135] Bennetot, B.; jpvernadet; BastienBennetot/Article_Geotrichum_2022: Script_and_data (Version V1), Zenodo, 2023 | DOI

[136] Bennetot, B.; Vernadet, J.-P.; Perkins, V.; Hautefeuille, S.; Rodríguez de la Vega, R. C.; O’Donnell, S.; Snirc, A.; Grondin, C.; Lessard, M.-H.; Peron, A.-C.; Labrie, S.; Landaud, S.; Giraud, T.; Ropars, J. Domestication of different varieties in the cheese-making fungus Geotrichum candidum, bioRxiv, 2022.05.17.492043, ver. 4 peer-reviewed and recommended by Peer Community in Evolutionary Biology, 2023 | DOI

Cited by Sources: