1887

Chapter 53 : Fungi as a Source of Food

Authors: Joëlle Dupont1, Sylvie Dequin2, Tatiana Giraud3, François Le Tacon4, Souhir Marsit5, Jeanne Ropars6, Franck Richard7, Marc-André Selosse8
VIEW AFFILIATIONS HIDE AFFILIATIONS
Affiliations: 1: Institut de Systématique, Evolution et Biodiversité, ISYEB - UMR 7205 – CNRS, MNHN, UPMC, EPHE, Muséum National d’Histoire Naturelle, Sorbonne Universités, CP39, 75231 Paris Cedex 5, France; 2: SPO, INRA, SupAgro, Université Montpellier, 34060 Montpellier, France; 3: Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, F-91400 Orsay, France; 4: INRA, Université de Lorraine, UMR1136 Interactions Arbres-Microorganismes, Laboratoire d’Excellence ARBRE, F-54280 Champenoux, France; 5: SPO, INRA, SupAgro, Université Montpellier, 34060 Montpellier, France; 6: Institut Pasteur, INRA, Unité Biologie et Pathogénicité Fongiques, 75015 Paris, France; 7: CEFE-CNRS, UMR 5175, Equipe Interactions Biotiques, 34 293 Montpellier Cedex 5, France; 8: Institut de Systématique, Evolution et Biodiversité, ISYEB - UMR 7205 – CNRS, MNHN, UPMC, EPHE, Muséum National d’Histoire Naturelle, Sorbonne Universités, CP39, 75231 Paris Cedex 5, France; 9: Department of Plant Taxonomy and Nature Conservation, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
Content Type: Monograph
Publication Year: 2017

Category: Microbial Genetics and Molecular Biology; Environmental Microbiology

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Preview Magnify
Zoom in
Zoomout

Fungi as a Source of Food, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555819583/9781555819576_Chap53-1.gif /docserver/preview/fulltext/10.1128/9781555819583/9781555819576_Chap53-2.gif

Abstract:

Since ancient times, humans have used fungi as food sources ( ). The edible sexual structures of basidiomycetes and ascomycetes (e.g., truffles), the so-called mushrooms, are produced mostly in wood because many fungi are tree symbionts or decayers of tree tissues. These fruiting bodies represent a rich source of proteins, with low fat content and otherwise nutritionally quite poor. In some soils, they accumulate pollution (heavy metals and radioactivity) and should only be eaten in moderate quantities. Some mushroom species are considered delicacies (e.g., truffles, boletus, morels), but cultivation attempts have been unsuccessful, with a few exceptions (e.g., ). Only a few saprobic species can be industrially produced, such as ( ), (shiitake), and , with production having mainly taken place in Asia for thousands of years ( ). Some other fungi, while not really cultured, are inoculated on trees grown in appropriate natural habitats to increase the production of fruiting bodies, such as for shiitake and oyster mushrooms, with, however, sometimes unpredictable success, as is the case for truffles ( ).

Citation: Dupont J, Dequin S, Giraud T, Le Tacon F, Marsit S, Ropars J, Richard F, Selosse M. 2017. Fungi as a Source of Food, p 1063-1085. In Heitman J, Howlett B, Crous P, Stukenbrock E, James T, Gow N (ed), The Fungal Kingdom. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.FUNK-0030-2016
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Fungi as a Source of Food
[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555819583.chap53-1,webId=/content/author/10.1128/9781555819583.chap53-1,properties={foaf_givenname=Joëlle, foaf_name=Joëlle Dupont, foaf_surname=Dupont, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555819583.chap53-aff1]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555819583.chap53-2,webId=/content/author/10.1128/9781555819583.chap53-2,properties={foaf_givenname=Sylvie, foaf_name=Sylvie Dequin, foaf_surname=Dequin, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555819583.chap53-aff2]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555819583.chap53-3,webId=/content/author/10.1128/9781555819583.chap53-3,properties={foaf_givenname=Tatiana, foaf_name=Tatiana Giraud, foaf_surname=Giraud, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555819583.chap53-aff3]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555819583.chap53-4,webId=/content/author/10.1128/9781555819583.chap53-4,properties={foaf_givenname=François, foaf_name=François Le Tacon, foaf_surname=Le Tacon, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555819583.chap53-aff4]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555819583.chap53-5,webId=/content/author/10.1128/9781555819583.chap53-5,properties={foaf_givenname=Souhir, foaf_name=Souhir Marsit, foaf_surname=Marsit, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555819583.chap53-aff5]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555819583.chap53-6,webId=/content/author/10.1128/9781555819583.chap53-6,properties={foaf_givenname=Jeanne, foaf_name=Jeanne Ropars, foaf_surname=Ropars, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555819583.chap53-aff6]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555819583.chap53-7,webId=/content/author/10.1128/9781555819583.chap53-7,properties={foaf_givenname=Franck, foaf_name=Franck Richard, foaf_surname=Richard, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555819583.chap53-aff7]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555819583.chap53-8,webId=/content/author/10.1128/9781555819583.chap53-8,properties={foaf_givenname=Marc-André, foaf_name=Marc-André Selosse, foaf_surname=Selosse, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555819583.chap53-aff8]]}]]
Citation: Dupont J, Dequin S, Giraud T, Le Tacon F, Marsit S, Ropars J, Richard F, Selosse M. 2017. Fungi as a Source of Food, p 1063-1085. In Heitman J, Howlett B, Crous P, Stukenbrock E, James T, Gow N (ed), The Fungal Kingdom. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.FUNK-0030-2016
/content/10.1128/9781555819583.chap53.fig53-1
Figure 1

Relationships between species and their industrial hybrids. Tree topology was obtained using a subset of 25,000 single nucleotide polymorphisms selected after genome alignment.

10.1128/9781555819583/fig53-1_thmb.gif
10.1128/9781555819583/fig53-1.gif
Image of Figure 1
Figure 1

Relationships between species and their industrial hybrids. Tree topology was obtained using a subset of 25,000 single nucleotide polymorphisms selected after genome alignment.

Citation: Dupont J, Dequin S, Giraud T, Le Tacon F, Marsit S, Ropars J, Richard F, Selosse M. 2017. Fungi as a Source of Food, p 1063-1085. In Heitman J, Howlett B, Crous P, Stukenbrock E, James T, Gow N (ed), The Fungal Kingdom. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.FUNK-0030-2016
Permissions and Reprints Request Permissions
Download as Powerpoint
/content/10.1128/9781555819583.chap53.fig53-2
Figure 2

Two hypotheses regarding origins of based on shared chromosomal translocations and differences in ploidy between groups 1 and 2. Hybridization between diploid Sc and Se types occurred before chromosomal translocations, whereas chromosomal deletions occurred only in ancestral group 1 strains. After hybridization between haploid Sc and diploid Se types and chromosomal translocations, ancestral group 2 strains gained another Sc type (i.e., a second hybridization event occurred). Chromosomal deletion or loss of heterozygosity (LOH) explains single nucleotide polymorphisms observed when comparing reference genomes.

10.1128/9781555819583/fig53-2_thmb.gif
10.1128/9781555819583/fig53-2.gif
Image of Figure 2
Figure 2

Two hypotheses regarding origins of based on shared chromosomal translocations and differences in ploidy between groups 1 and 2. Hybridization between diploid Sc and Se types occurred before chromosomal translocations, whereas chromosomal deletions occurred only in ancestral group 1 strains. After hybridization between haploid Sc and diploid Se types and chromosomal translocations, ancestral group 2 strains gained another Sc type (i.e., a second hybridization event occurred). Chromosomal deletion or loss of heterozygosity (LOH) explains single nucleotide polymorphisms observed when comparing reference genomes.

Citation: Dupont J, Dequin S, Giraud T, Le Tacon F, Marsit S, Ropars J, Richard F, Selosse M. 2017. Fungi as a Source of Food, p 1063-1085. In Heitman J, Howlett B, Crous P, Stukenbrock E, James T, Gow N (ed), The Fungal Kingdom. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.FUNK-0030-2016
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555819583.chap53
1. Kurtzman CP . 1983. Fungi: sources of food, fuel and biochemicals. Mycologia 75 : 374– 382.[CrossRef]
2. Silar P,, Malagnac F . 2013. Les Champignons Redécouverts. Belin, Paris, France.
3. Morin E,, Kohler A,, Baker AR,, Foulongne-Oriol M,, Lombard V,, Nagy LG,, Ohm RA,, Patyshakuliyeva A,, Brun A,, Aerts AL,, Bailey AM,, Billette C,, Coutinho PM,, Deakin G,, Doddapaneni H,, Floudas D,, Grimwood J,, Hildén K,, Kües U,, Labutti KM,, Lapidus A,, Lindquist EA,, Lucas SM,, Murat C,, Riley RW,, Salamov AA,, Schmutz J,, Subramanian V,, Wösten HAB,, Xu J,, Eastwood DC,, Foster GD,, Sonnenberg ASM,, Cullen D,, de Vries RP,, Lundell T,, Hibbett DS,, Henrissat B,, Burton KS,, Kerrigan RW,, Challen MP,, Grigoriev IV,, Martin F . 2012. Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. Proc Natl Acad Sci USA 109 : 17501– 17506.[CrossRef]
4. Chang S-T . 1977. The origin and early development of straw mushroom cultivation. Econ Bot 31 : 374– 376.[CrossRef]
5. De Miguel AM,, Águeda B,, Sánchez S,, Parladé J . 2014. Ectomycorrhizal fungus diversity and community structure with natural and cultivated truffle hosts: applying lessons learned to future truffle culture. Mycorrhiza 24( Suppl 1) : 5– 18.[CrossRef]
6. Valverde E,, Hernandez-Perez T,, Paredees-Lopez O, . 2012. Huitlacoche: -a 21st century culinary delight originated in the Aztec times, p 83– 100. In Tunick MH,, D’e Meija EG (ed), Hispanic Foods: Chemistry and Bioactive Compounds, Oxford University Press, New York, NY.
7. Alonso-Aguilar LE,, Montoya A,, Kong A,, Estrada-Torres A,, Garibay-Orijel R . 2014. The cultural significance of wild mushrooms in San Mateo Huexoyucan, Tlaxcala, Mexico. J Ethnobiol Ethnomed 10 : 27.[CrossRef]
8. Carod-Artal FJ . 2015. Hallucinogenic drugs in pre-Columbian Mesoamerican cultures. Neurologia 30 : 42– 49.[CrossRef]
9. McGovern PE,, Zhang J,, Tang J,, Zhang Z,, Hall GR,, Moreau RA,, Nuñez A,, Butrym ED,, Richards MP,, Wang CS,, Cheng G,, Zhao Z,, Wang C . 2004. Fermented beverages of pre- and proto-historic China. Proc Natl Acad Sci USA 101 : 17593– 17598.[CrossRef]
10. McGovern PE,, Glusker DL,, Exner LJ,, Voigt MM . 1996. Neolithic resinated wine. Nature 381 : 480– 481.[CrossRef]
11. Samuel D . 1996. Investigation of ancient Egyptian baking and brewing methods by correlative microscopy. Science 273 : 488– 490.[CrossRef]
12. Salque M,, Bogucki PI,, Pyzel J,, Sobkowiak-Tabaka I,, Grygiel R,, Szmyt M,, Evershed RP . 2013. Earliest evidence for cheese making in the sixth millennium BC in northern Europe. Nature 493 : 522– 525.[CrossRef]
13. Machida M , , et al . 2005. Genome sequencing and analysis of Aspergillus oryzae . Nature 438 : 1157– 1161.[CrossRef] [PubMed]
14. Nout MJR,, Aidoo KE, . 2002. Asian fungal fermented food, p 23– 47. In Osiewacz HD (ed), Industrial Applications. Springer-Verlag, Berlin, Germany.[CrossRef]
15. Fournier E,, Gladieux P,, Giraud T . 2013. The ‘Dr Jekyll and Mr Hyde fungus’: noble rot versus gray mold symptoms of Botrytis cinerea on grapes. Evol Appl 6 : 960– 969.[CrossRef] [PubMed]
16. Bernáldez V,, Córdoba JJ,, Rodríguez M,, Cordero M,, Polo L,, Rodríguez A . 2013. Effect of Penicillium nalgiovense as protective culture in processing of dry-fermented sausage “salchichón.” Food Control 32 : 69– 76.[CrossRef]
17. 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 . 2014. Multiple recent horizontal transfers of a large genomic region in cheese making fungi. Nat Commun 5 : 2876.[CrossRef]
18. Gladieux P,, Ropars J,, Badouin H,, Branca A,, Aguileta G,, de Vienne DM,, Rodríguez de la Vega RC,, Branco S,, Giraud T . 2014. Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes. Mol Ecol 23 : 753– 773.[CrossRef]
19. Ropars J,, Rodríguez de la Vega RC,, López-Villavicencio M,, Gouzy J,, Sallet E,, Dumas É,, Lacoste S,, Debuchy R,, Dupont J,, Branca A,, Giraud T . 2015. Adaptive horizontal gene transfers between multiple cheese-associated Fungi. Curr Biol 25 : 2562– 2569.[CrossRef]
20. Liti G,, Barton DBH,, Louis EJ . 2006. Sequence diversity, reproductive isolation and species concepts in Saccharomyces . Genetics 174 : 839– 850.[CrossRef]
21. Marsit S,, Dequin S . 2015. Diversity and adaptive evolution of Saccharomyces wine yeast: a review. FEMS Yeast Res 15 : fov067.[CrossRef] [PubMed]
22. Marsit S,, Mena A,, Bigey F,, Sauvage F-X,, Couloux A,, Guy J,, Legras J-L,, Barrio E,, Dequin S,, Galeote V . 2015. Evolutionary advantage conferred by an eukaryote-to-eukaryote gene transfer event in wine yeasts. Mol Biol Evol 32 : 1695– 1707.[CrossRef]
23. Naumova ES,, Naumov GI,, Masneuf-Pomarède I,, Aigle M,, Dubourdieu D . 2005. Molecular genetic study of introgression between Saccharomyces bayanus and S. cerevisiae . Yeast 22 : 1099– 1115.[CrossRef]
24. Novo M,, Bigey F,, Beyne E,, Galeote V,, Gavory F,, Mallet S,, Cambon B,, Legras J-L,, Wincker P,, Casaregola S,, Dequin S . 2009. Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118. Proc Natl Acad Sci USA 106 : 16333– 16338.[CrossRef]
25. Burger J,, Kirchner M,, Bramanti B,, Haak W,, Thomas MG . 2007. Absence of the lactase-persistence-associated allele in early Neolithic Europeans. Proc Natl Acad Sci USA 104 : 3736– 3741.[CrossRef]
26. Yang Y,, Shevchenko A,, Knaust A,, Abuduresule I,, Li W,, Hu X,, Wang C,, Shevchenko A . 2014. Proteomics evidence for kefir dairy in Early Bronze Age China. J Archaeol Sci 45 : 178– 186.[CrossRef]
27. McSweeney PL . 2004. Biochemistry of cheese ripening. Int J Dairy Technol 57 : 127– 144.[CrossRef]
28. Mounier J,, Monnet C,, Vallaeys T,, Arditi R,, Sarthou A-S,, Hélias A,, Irlinger F . 2008. Microbial interactions within a cheese microbial community. Appl Environ Microbiol 74 : 172– 181.[CrossRef]
29. Wolfe BE,, Button JE,, Santarelli M,, Dutton RJ . 2014. Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity. Cell 158 : 422– 433.[CrossRef]
30. Ropars J,, Cruaud C,, Lacoste S,, Dupont J . 2012. A taxonomic and ecological overview of cheese fungi. Int J Food Microbiol 155 : 199– 210.[CrossRef] [PubMed]
31. Hermet A,, Méheust D,, Mounier J,, Barbier G,, Jany J-L . 2012. Molecular systematics in the genus Mucor with special regards to species encountered in cheese. Fungal Biol 116 : 692– 705.[CrossRef]
32. Ropars J,, de la Vega RCR,, López-Villavicencio M,, Gouzy J,, Dupont J,, Swennen D,, Dumas E,, Giraud T,, Branca A, . 2016. Diversity and mechanisms of genomic adaptation in Penicillium , p 210. In de Vries RP,, Benoit Gelber I,, Andersen MR (ed), Aspergillus and Penicillium in the Post-Genomic Era. Caister Academic Press, Poole, United Kingdom.[CrossRef]
33. Giraud F,, Giraud T,, Aguileta G,, Fournier E,, Samson R,, Cruaud C,, Lacoste S,, Ropars J,, Tellier A,, Dupont J . 2010. Microsatellite loci to recognize species for the cheese starter and contaminating strains associated with cheese manufacturing. Int J Food Microbiol 137 : 204– 213.[CrossRef]
34. Pitt JI,, Hocking AD . 2009. Fungi and Food Spoilage. Springer US, Boston, MA.[CrossRef]
35. Samson RA . 2000. Introduction to Food- and Airborne Fungi. ASM Press, Washington, DC.
36. Labbe M,, Serres J-P . 2009. Chroniques du Roquefort: des Hommes, des Entreprises, des Marques, Période Moderne. Graphi Imprimeur, La Primaube, France.
37. Labbe M,, Serres J-P . 2004. Chroniques du Roquefort: de la préhistoire à l’Aube Industrielle. Graphi Imprimeur, La Primaube, France.
38. Vabre S . 2015. Le Sacre du Roquefort. Presses Universitaires François-Rabelais, Tours, France.
39. Ropars J,, López-Villavicencio M,, Dupont J,, Snirc A,, Gillot G,, Coton M,, Jany J-L,, Coton E,, Giraud T . 2014. Induction of sexual reproduction and genetic diversity in the cheese fungus Penicillium roqueforti . Evol Appl 7 : 433– 441.[CrossRef]
40. Gillot G,, Jany J-L,, Coton M,, Le Floch G,, Debaets S,, Ropars J,, López-Villavicencio M,, Dupont J,, Branca A,, Giraud T,, Coton E . 2015. Insights into Penicillium roqueforti morphological and genetic diversity. PLoS One 10 : e0129849.[CrossRef]
41. Ropars J,, López-Villavicencio M,, Snirc A,, Lacoste S,, Giraud T . 2017. Blue cheese-making has shaped the population genetic structure of the mould Penicillium roqueforti . PLoS One 12 : e0171387.[CrossRef]
42. Ropars J,, Aguileta G,, de Vienne DM,, Giraud T . 2014. Massive gene swamping among cheese-making Penicillium fungi. Microb Cell 1 : 3.[CrossRef] [PubMed]
43. Lessard M-H,, Viel C,, Boyle B,, St-Gelais D,, Labrie S . 2014. Metatranscriptome analysis of fungal strains Penicillium camemberti and Geotrichum candidum reveal cheese matrix breakdown and potential development of sensory properties of ripened Camembert-type cheese. BMC Genomics 15 : 235.[CrossRef]
44. Larson G,, Fuller DQ . 2014. The evolution of animal domestication. Annu Rev Ecol Evol Syst 45 : 115– 136.[CrossRef]
45. Lu J,, Tang T,, Tang H,, Huang J,, Shi S,, Wu C-I . 2006. The accumulation of deleterious mutations in rice genomes: a hypothesis on the cost of domestication. Trends Genet 22 : 126– 131.[CrossRef]
46. Marsden CD,, Ortega-Del Vecchyo D,, O’Brien DP,, Taylor JF,, Ramirez O,, Vilà C,, Marques-Bonet T,, Schnabel RD,, Wayne RK,, Lohmueller KE . 2016. Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs. Proc Natl Acad Sci USA 113 : 152– 157.[CrossRef]
47. Schubert M,, Jónsson H,, Chang D,, Der Sarkissian C,, Ermini L,, Ginolhac A,, Albrechtsen A,, Dupanloup I,, Foucal A,, Petersen B,, Fumagalli M,, Raghavan M,, Seguin-Orlando A,, Korneliussen TS,, Velazquez AMV,, Stenderup J,, Hoover CA,, Rubin C-J,, Alfarhan AH,, Alquraishi SA,, Al-Rasheid KAS,, MacHugh DE,, Kalbfleisch T,, MacLeod JN,, Rubin EM,, Sicheritz-Ponten T,, Andersson L,, Hofreiter M,, Marques-Bonet T,, Gilbert MTP,, Nielsen R,, Excoffier L,, Willerslev E,, Shapiro B,, Orlando L . 2014. Prehistoric genomes reveal the genetic foundation and cost of horse domestication. Proc Natl Acad Sci USA 111 : E5661– E5669.[CrossRef]
48. Ropars J,, Lo Y-C,, Dumas E,, Snirc A,, Begerow D,, Rollnik T,, Lacoste S,, Dupont J,, Giraud T,, López-Villavicencio M . 2016. Fertility depression among cheese-making Penicillium roqueforti strains suggests degeneration during domestication. Evolution 70 : 2099– 2109.[CrossRef]
49. Piškur J,, Rozpędowska E,, Polakova S,, Merico A,, Compagno C . 2006. How did Saccharomyces evolve to become a good brewer? Trends Genet 22 : 183– 186.[CrossRef] [PubMed]
50. Hagman A,, Säll T,, Compagno C,, Piškur J . 2013. Yeast “make-accumulate-consume” life strategy evolved as a multi-step process that predates the whole genome duplication. PLoS One 8 : e68734.[CrossRef] [PubMed]
51. Kurtzman CP,, Robnett CJ . 1998. Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences. Antonie van Leeuwenhoek 73 : 331– 371.[CrossRef] [PubMed]
52. Replansky T,, Koufopanou V,, Greig D,, Bell G . 2008. Saccharomyces sensu stricto as a model system for evolution and ecology. Trends Ecol Evol 23 : 494– 501.[CrossRef] [PubMed]
53. Dujon B , , et al . 2004. Genome evolution in yeasts. Nature 430 : 35– 44.[CrossRef]
54. Morales L,, Dujon B . 2012. Evolutionary role of interspecies hybridization and genetic exchanges in yeasts. Microbiol Mol Biol Rev 76 : 721– 739.[CrossRef]
55. Giraud T,, Refrégier G,, Le Gac M,, de Vienne DM,, Hood ME . 2008. Speciation in fungi. Fungal Genet Biol 45 : 791– 802.[CrossRef] [PubMed]
56. Hittinger CT . 2013. Saccharomyces diversity and evolution: a budding model genus. Trends Genet 29 : 309– 317.[CrossRef]
57. Gibbons JG,, Rinker DC . 2015. The genomics of microbial domestication in the fermented food environment. Curr Opin Genet Dev 35 : 1– 8.[CrossRef] [PubMed]
58. Libkind D,, Hittinger CT,, Valério E,, Gonçalves C,, Dover J,, Johnston M,, Gonçalves P,, Sampaio JP . 2011. Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast. Proc Natl Acad Sci USA 108 : 14539– 14544.[CrossRef]
59. Wang Q-M,, Liu W-Q,, Liti G,, Wang S-A,, Bai F-Y . 2012. Surprisingly diverged populations of Saccharomyces cerevisiae in natural environments remote from human activity. Mol Ecol 21 : 5404– 5417.[CrossRef]
60. Naumov GI,, Naumova ES,, Sniegowski PD . 1998. Saccharomyces paradoxus and Saccharomyces cerevisiae are associated with exudates of North American oaks. Can J Microbiol 44 : 1045– 1050.[CrossRef]
61. Sniegowski PD,, Dombrowski PG,, Fingerman E . 2002. Saccharomyces cerevisiae and Saccharomyces paradoxus coexist in a natural woodland site in North America and display different levels of reproductive isolation from European conspecifics. FEMS Yeast Res 1 : 299– 306.[PubMed]
62. Sampaio JP,, Gonçalves P . 2008. Natural populations of Saccharomyces kudriavzevii in Portugal are associated with oak bark and are sympatric with S. cerevisiae and S. paradoxus . Appl Environ Microbiol 74 : 2144– 2152.[CrossRef]
63. Bing J,, Han P-J,, Liu W-Q,, Wang Q-M,, Bai F-Y . 2014. Evidence for a Far East Asian origin of lager beer yeast. Curr Biol 24 : R380– R381.[CrossRef] [PubMed]
64. Liti G . 2015. The fascinating and secret wild life of the budding yeast S. cerevisiae . eLife 4 : e05835.[CrossRef] [PubMed]
65. Suh S-O,, Nguyen NH,, Blackwell M . 2008. Yeasts isolated from plant-associated beetles and other insects: seven novel Candida species near Candida albicans . FEMS Yeast Res 8 : 88– 102.[CrossRef]
66. Stefanini I,, Dapporto L,, Legras J-L,, Calabretta A,, Di Paola M,, De Filippo C,, Viola R,, Capretti P,, Polsinelli M,, Turillazzi S,, Cavalieri D . 2012. Role of social wasps in Saccharomyces cerevisiae ecology and evolution. Proc Natl Acad Sci USA 109 : 13398– 13403.[CrossRef]
67. Stefanini I,, Dapporto L,, Berná L,, Polsinelli M,, Turillazzi S,, Cavalieri D . 2016. Social wasps are a Saccharomyces mating nest. Proc Natl Acad Sci USA 113 : 2247– 2251.[CrossRef] [PubMed]
68. Fay JC,, Benavides JA . 2005. Evidence for domesticated and wild populations of Saccharomyces cerevisiae . PLoS Genet 1 : e5.[CrossRef] [PubMed]
69. Legras J-L,, Merdinoglu D,, Cornuet J-M,, Karst F . 2007. Bread, beer and wine: saccharomyces cerevisiae diversity reflects human history. Mol Ecol 16 : 2091– 2102.[CrossRef]
70. Liti G,, Carter DM,, Moses AM,, Warringer J,, Parts L,, James SA,, Davey RP,, Roberts IN,, Burt A,, Koufopanou V,, Tsai IJ,, Bergman CM,, Bensasson D,, O’Kelly MJT,, van Oudenaarden A,, Barton DBH,, Bailes E,, Nguyen AN,, Jones M,, Quail MA,, Goodhead I,, Sims S,, Smith F,, Blomberg A,, Durbin R,, Louis EJ . 2009. Population genomics of domestic and wild yeasts. Nature 458 : 337– 341.[CrossRef]
71. Borneman AR,, Desany BA,, Riches D,, Affourtit JP,, Forgan AH,, Pretorius IS,, Egholm M,, Chambers PJ . 2011. Whole-genome comparison reveals novel genetic elements that characterize the genome of industrial strains of Saccharomyces cerevisiae . PLoS Genet 7 : e1001287.[CrossRef]
72. Tapsoba F,, Legras J-L,, Savadogo A,, Dequin S,, Traore AS . 2015. Diversity of Saccharomyces cerevisiae strains isolated from Borassus akeassii palm wines from Burkina Faso in comparison to other African beverages. Int J Food Microbiol 211 : 128– 133.[CrossRef]
73. Zhu YO,, Sherlock G,, Petrov DA . 2016. Whole genome analysis of 132 clinical Saccharomyces cerevisiae strains reveals extensive ploidy variation. G3 (Bethesda) 6 : 2421– 2434.[PubMed]
74. Borneman AR,, Forgan AH,, Kolouchova R,, Fraser JA,, Schmidt SA . 2016. Whole genome comparison reveals high levels of inbreeding and strain redundancy across the spectrum of commercial wine strains of Saccharomyces cerevisiae . G3 (Bethesda) 6 : 957– 971.[PubMed]
75. Albertin W,, Marullo P,, Aigle M,, Bourgais A,, Bely M,, Dillmann C,, DE Vienne D,, Sicard D . 2009. Evidence for autotetraploidy associated with reproductive isolation in Saccharomyces cerevisiae: towards a new domesticated species. J Evol Biol 22 : 2157– 2170.[CrossRef]
76. Cavalieri D,, McGovern PE,, Hartl DL,, Mortimer R,, Polsinelli M . 2003. Evidence for S. cerevisiae fermentation in ancient wine. J Mol Evol 57( Suppl 1) : S226– S232.[CrossRef]
77. McGovern P . 2003. Ancient Wine: The Search for the Origins of Viniculture. Princeton University Press, Princeton, NJ.
78. Pretorius IS . 2000. Tailoring wine yeast for the new millennium: novel approaches to the ancient art of winemaking. Yeast 16 : 675– 729.[CrossRef]
79. Swiegers JH,, Bartowsky EJ,, Henschke PA,, Pretorius IS . 2005. Yeast and bacterial modulation of wine aroma and flavour. Aust J Grape Wine Res 11 : 139– 173.[CrossRef]
80. Sablayrolles JM, . 2008. Fermented beverages: the example of winemaking, p 322– 347. In Pandey A,, Larroche C,, Soccol CR (ed), Advances in Fermentation Technology. Asiatech Publishers, New Delhi, India.
81. Schacherer J,, Shapiro JA,, Ruderfer DM,, Kruglyak L . 2009. Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae . Nature 458 : 342– 345.[CrossRef]
82. Cromie GA,, Hyma KE,, Ludlow CL,, Garmendia-Torres C,, Gilbert TL,, May P,, Huang AA,, Dudley AM,, Fay JC . 2013. Genomic sequence diversity and population structure of Saccharomyces cerevisiae assessed by RAD-seq. G3 (Bethesda) 3 : 2163– 2171.[CrossRef]
83. Liti G,, Schacherer J . 2011. The rise of yeast population genomics. C R Biol 334 : 612– 619.[CrossRef]
84. Almeida P,, Barbosa R,, Zalar P,, Imanishi Y,, Shimizu K,, Turchetti B,, Legras J-L,, Serra M,, Dequin S,, Couloux A,, Guy J,, Bensasson D,, Gonçalves P,, Sampaio JP . 2015. A population genomics insight into the Mediterranean origins of wine yeast domestication. Mol Ecol 24 : 5412– 5427.[CrossRef]
85. Eberlein C,, Leducq J-B,, Landry CR . 2015. The genomics of wild yeast populations sheds light on the domestication of man’s best (micro) friend. Mol Ecol 24 : 5309– 5311.[CrossRef]
86. Fay JC,, McCullough HL,, Sniegowski PD,, Eisen MB . 2004. Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae . Genome Biol 5 : R26.[CrossRef]
87. Warringer J,, Zörgö E,, Cubillos FA,, Zia A,, Gjuvsland A,, Simpson JT,, Forsmark A,, Durbin R,, Omholt SW,, Louis EJ,, Liti G,, Moses A,, Blomberg A . 2011. Trait variation in yeast is defined by population history. PLoS Genet 7 : e1002111. doi:10.1186/gb-2004-5-4-r26.[CrossRef] [PubMed]
88. Park H,, Bakalinsky AT . 2000. SSU1 mediates sulphite efflux in Saccharomyces cerevisiae . Yeast 16 : 881– 888.[CrossRef]
89. Pérez-Ortín JE,, Querol A,, Puig S,, Barrio E . 2002. Molecular characterization of a chromosomal rearrangement involved in the adaptive evolution of yeast strains. Genome Res 12 : 1533– 1539.[CrossRef]
90. Wenger JW,, Schwartz K,, Sherlock G . 2010. Bulk segregant analysis by high-throughput sequencing reveals a novel xylose utilization gene from Saccharomyces cerevisiae . PLoS Genet 6 : e1000942.[CrossRef]
91. Homann OR,, Cai H,, Becker JM,, Lindquist SL . 2005. Harnessing natural diversity to probe metabolic pathways. PLoS Genet 1 : e80.[CrossRef]
92. Damon C,, Vallon L,, Zimmermann S,, Haider MZ,, Galeote V,, Dequin S,, Luis P,, Fraissinet-Tachet L,, Marmeisse R . 2011. A novel fungal family of oligopeptide transporters identified by functional metatranscriptomics of soil eukaryotes. ISME J 5 : 1871– 1880.[CrossRef]
93. Hyma KE,, Saerens SM,, Verstrepen KJ,, Fay JC . 2011. Divergence in wine characteristics produced by wild and domesticated strains of Saccharomyces cerevisiae . FEMS Yeast Res 11 : 540– 551.[CrossRef]
94. Barrio E,, González SS,, Arias A,, Belloch C,, Querol A, . 2006. Molecular mechanisms involved in the adaptive evolution of industrial yeasts, p 153– 174. In Querol A,, Fleet G (ed), Yeasts in Food and Beverages. Springer-Verlag, Berlin, Germany.
95. Blondin B,, Dequin S,, Querol A,, Legras J-L, . 2009. Genome of Saccharomyces cerevisiae and related yeasts, p 361– 378. In König H,, Unden G,, Fröhlich J (ed), Biology of Microorganisms on Grapes, in Must and in Wine. Springer-Verlag, Berlin, Germany.[CrossRef]
96. Dequin S,, Casaregola S . 2011. The genomes of fermentative Saccharomyces . C R Biol 334 : 687– 693.[CrossRef]
97. Alexandre H . 2013. Flor yeasts of Saccharomyces cerevisiae: their ecology, genetics and metabolism. Int J Food Microbiol 167 : 269– 275.[CrossRef]
98. Guo B,, Styles CA,, Feng Q,, Fink GR . 2000. A Saccharomyces gene family involved in invasive growth, cell-cell adhesion, and mating. Proc Natl Acad Sci USA 97 : 12158– 12163.[CrossRef] [PubMed]
99. Fidalgo M,, Barrales RR,, Ibeas JI,, Jimenez J . 2006. Adaptive evolution by mutations in the FLO11 gene. Proc Natl Acad Sci USA 103 : 11228– 11233.[CrossRef]
100. Guillaume C,, Delobel P,, Sablayrolles JM,, Blondin B . 2007. Molecular basis of fructose utilization by the wine yeast Saccharomyces cerevisiae: a mutated HXT3 allele enhances fructose fermentation. Appl Environ Microbiol 73 : 2432– 2439.[CrossRef]
101. Legras J-L,, Moreno-Garcia J,, Zara S,, Zara G,, Garcia-Martinez T,, Mauricio JC,, Mannazzu I,, Coi AL,, Bou Zeidan M,, Dequin S,, Moreno J,, Budroni M . 2016. Flor yeast: new perspectives beyond wine aging. Front Microbiol 7 : 503.[CrossRef]
102. Strope PK,, Skelly DA,, Kozmin SG,, Mahadevan G,, Stone EA,, Magwene PM,, Dietrich FS,, McCusker JH . 2015. The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen. Genome Res 25 : 762– 774.[CrossRef]
103. Goto-Yamamoto N,, Kitano K,, Shiki K,, Yoshida Y,, Suzuki T,, Iwata T,, Yamane Y,, Hara S . 1998. SSUI-R, a sulfite resistance gene of wine yeast, is an allele of SSUl with a different upstream sequence. J Ferment Bioeng 86 : 427– 433.[CrossRef]
104. Yuasa N,, Nakagawa Y,, Hayakawa M,, Iimura Y . 2004. Distribution of the sulfite resistance gene SSU1-R and the variation in its promoter region in wine yeasts. J Biosci Bioeng 98 : 394– 397.[CrossRef]
105. Dunn B,, Richter C,, Kvitek DJ,, Pugh T,, Sherlock G . 2012. Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments. Genome Res 22 : 908– 924.[CrossRef]
106. Brown SL,, Stockdale VJ,, Pettolino F,, Pocock KF,, de Barros Lopes M,, Williams PJ,, Bacic A,, Fincher GB,, Høj PB,, Waters EJ . 2007. Reducing haziness in white wine by overexpression of Saccharomyces cerevisiae genes YOL155c and YDR055w . Appl Microbiol Biotechnol 73 : 1363– 1376.[CrossRef]
107. Almeida P,, Gonçalves C,, Teixeira S,, Libkind D,, Bontrager M,, Masneuf-Pomarède I,, Albertin W,, Durrens P,, Sherman DJ,, Marullo P,, Hittinger CT,, Gonçalves P,, Sampaio JP . 2014. A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum . Nat Commun 5 : 4044.[CrossRef]
108. Borneman AR,, Forgan AH,, Pretorius IS,, Chambers PJ . 2008. Comparative genome analysis of a Saccharomyces cerevisiae wine strain. FEMS Yeast Res 8 : 1185– 1195.[CrossRef]
109. Marsit S,, Sanchez I,, Galeote V,, Dequin S . 2016. Horizontally acquired oligopeptide transporters favour adaptation of Saccharomyces cerevisiae wine yeast to oenological environment. Environ Microbiol 18 : 1148– 1161.[CrossRef]
110. González SS,, Barrio E,, Gafner J,, Querol A . 2006. Natural hybrids from Saccharomyces cerevisiae, Saccharomyces bayanus and Saccharomyces kudriavzevii in wine fermentations. FEMS Yeast Res 6 : 1221– 1234.[CrossRef]
111. Bradbury JE,, Richards KD,, Niederer HA,, Lee SA,, Rod Dunbar P,, Gardner RC . 2006. A homozygous diploid subset of commercial wine yeast strains. Antonie van Leeuwenhoek 89 : 27– 37.[CrossRef]
112. Lopandic K,, Gangl H,, Wallner E,, Tscheik G,, Leitner G,, Querol A,, Borth N,, Breitenbach M,, Prillinger H,, Tiefenbrunner W . 2007. Genetically different wine yeasts isolated from Austrian vine-growing regions influence wine aroma differently and contain putative hybrids between Saccharomyces cerevisiae and Saccharomyces kudriavzevii . FEMS Yeast Res 7 : 953– 965.[CrossRef]
113. Sipiczki M . 2008. Interspecies hybridization and recombination in Saccharomyces wine yeasts. FEMS Yeast Res 8 : 996– 1007.[CrossRef]
114. Arroyo-López FN,, Orlić S,, Querol A,, Barrio E . 2009. Effects of temperature, pH and sugar concentration on the growth parameters of Saccharomyces cerevisiae, S. kudriavzevii and their interspecific hybrid. Int J Food Microbiol 131 : 120– 127.[CrossRef]
115. Gangl H,, Batusic M,, Tscheik G,, Tiefenbrunner W,, Hack C,, Lopandic K . 2009. Exceptional fermentation characteristics of natural hybrids from Saccharomyces cerevisiae and S. kudriavzevii . N Biotechnol 25 : 244– 251.[CrossRef]
116. Borneman AR,, Desany BA,, Riches D,, Affourtit JP,, Forgan AH,, Pretorius IS,, Egholm M,, Chambers PJ . 2012. The genome sequence of the wine yeast VIN7 reveals an allotriploid hybrid genome with Saccharomyces cerevisiae and Saccharomyces kudriavzevii origins. FEMS Yeast Res 12 : 88– 96.[CrossRef]
117. Erny C,, Raoult P,, Alais A,, Butterlin G,, Delobel P,, Matei-Radoi F,, Casaregola S,, Legras J-L . 2012. Ecological success of a group of Saccharomyces cerevisiae/Saccharomyces kudriavzevii hybrids in the Northern European wine-making environment. Appl Environ Microbiol 78 : 3256– 3265.[CrossRef]
118. Masneuf I,, Hansen J,, Groth C,, Piškur J,, Dubourdieu D . 1998. New hybrids between Saccharomyces sensu stricto yeast species found among wine and cider production strains. Appl Environ Microbiol 64 : 3887– 3892.[PubMed]
119. Masneuf I,, Murat M,, Naumov G,, Tominaga T,, Dubourdieu D . 2002. Hybrids Saccharomyces cerevisiae & Saccharomyces bayanus var. uvarum having a high liberating ability of some sulfur varietal aromas of Vitis vinifera sauvignon blanc wines. J Int Sci Vigne Vin 36 : 205– 212.
120. Le Jeune C,, Lollier M,, Demuyter C,, Erny C,, Legras J-L,, Aigle M,, Masneuf-Pomarède I . 2007. Characterization of natural hybrids of Saccharomyces cerevisiae and Saccharomyces bayanus var. uvarum . FEMS Yeast Res 7 : 540– 549.[CrossRef] [PubMed]
121. González SS,, Gallo L,, Climent MA,, Barrio E,, Querol A . 2007. Enological characterization of natural hybrids from Saccharomyces cerevisiae and S. kudriavzevii . Int J Food Microbiol 116 : 11– 18.[CrossRef]
122. Tronchoni J,, Gamero A,, Arroyo-López FN,, Barrio E,, Querol A . 2009. Differences in the glucose and fructose consumption profiles in diverse Saccharomyces wine species and their hybrids during grape juice fermentation. Int J Food Microbiol 134 : 237– 243.[CrossRef]
123. Belloch C,, Orlic S,, Barrio E,, Querol A . 2008. Fermentative stress adaptation of hybrids within the Saccharomyces sensu stricto complex. Int J Food Microbiol 122 : 188– 195.[CrossRef]
124. Belloch C,, Pérez-Torrado R,, González SS,, Pérez-Ortín JE,, García-Martínez J,, Querol A,, Barrio E . 2009. Chimeric genomes of natural hybrids of Saccharomyces cerevisiae and Saccharomyces kudriavzevii . Appl Environ Microbiol 75 : 2534– 2544.[CrossRef]
125. Dubourdieu D,, Tominaga T,, Masneuf I,, Peyrot des Gachons C,, Murat ML . 2006. The role of yeasts in grape flavor development during fermentation: the example of sauvignon blanc. Am J Enol Vitic 57 : 81– 88.
126. Swiegers JH,, Kievit RL,, Siebert T,, Lattey KA,, Bramley BR,, Francis IL,, King ES,, Pretorius IS . 2009. The influence of yeast on the aroma of sauvignon blanc wine. Food Microbiol 26 : 204– 211.[CrossRef]
127. Legras J-L,, Galeote V,, Camarasa C,, Blondin B,, Dequin S, . 2017. Ecology, diversity and applications of Saccharomyces yeasts in food and beverages, p ••–••. In Kunze G,, Satyanarayana T (ed), Prospects in Utilizing Yeast Diversity for Human Welfare. Springer, in press.
128. Cadière A,, Ortiz-Julien A,, Camarasa C,, Dequin S . 2011. Evolutionary engineered Saccharomyces cerevisiae wine yeast strains with increased in vivo flux through the pentose phosphate pathway. Metab Eng 13 : 263– 271.[CrossRef]
129. Hall JD,, Craven RR,, Fuller JR,, Pickles RJ,, Kawula TH . 2007. Francisella tularensis replicates within alveolar type II epithelial cells in vitro and in vivo following inhalation. Infect Immun 75 : 1034– 1039.[PubMed]
130. Horwitz MA . 1983. The Legionnaires' disease bacterium ( Legionella pneumophila) inhibits phagosome-lysosome fusion in human monocytes. J Exp Med 158 : 2108– 2126.[PubMed]
131. Marquis H,, Bouwer HG,, Hinrichs DJ,, Portnoy DA . 1993. Intracytoplasmic growth and virulence of Listeria monocytogenes auxotrophic mutants. Infect Immun 61 : 3756– 3760.[PubMed]
132. Bellon JR,, Schmid F,, Capone DL,, Dunn BL,, Chambers PJ . 2013. Introducing a new breed of wine yeast: interspecific hybridisation between a commercial Saccharomyces cerevisiae wine yeast and Saccharomyces mikatae . PLoS One 8 : e62053.[CrossRef]
133. Sicard D,, Legras J-L . 2011. Bread, beer and wine: yeast domestication in the Saccharomyces sensu stricto complex. C R Biol 334 : 229– 236.[CrossRef]
134. Reed G,, Nagodawithana TW, . 1990. Baker’s yeast production, p 261– 314. In Reed G,, Nagodawithana TW (ed), Yeast Technology. Springer Netherlands, Dordrecht, The Netherlands.[CrossRef]
135. De Vuyst L,, Van Kerrebroeck S,, Harth H,, Huys G,, Daniel H-M,, Weckx S . 2014. Microbial ecology of sourdough fermentations: diverse or uniform? Food Microbiol 37 : 11– 29.[CrossRef]
136. Lhomme E,, Urien C,, Legrand J,, Dousset X,, Onno B,, Sicard D . 2016. Sourdough microbial community dynamics: an analysis during French organic bread-making processes. Food Microbiol 53( Part A) : 41– 50.
137. Aslankoohi E,, Rezaei MN,, Vervoort Y,, Courtin CM,, Verstrepen KJ . 2015. Glycerol production by fermenting yeast cells is essential for optimal bread dough fermentation. PLoS One 10 : e0119364.[CrossRef]
138. Randez-Gil F,, Córcoles-Sáez I,, Prieto JA . 2013. Genetic and phenotypic characteristics of baker’s yeast: relevance to baking. Annu Rev Food Sci Technol 4 : 191– 214.[PubMed] [CrossRef]
139. Donalies UEB,, Nguyen HTT,, Stahl U,, Nevoigt E, . 2008. Improvement of Saccharomyces yeast strains used in brewing, wine making and baking, p 67– 98. In Stahl U,, Donalies UEB,, Nevoigt E (ed), Food Biotechnology. Springer, Berlin, Germany.[CrossRef]
140. Aguilera J,, Andreu P,, Randez-Gil F,, Prieto JA . 2010. Adaptive evolution of baker’s yeast in a dough-like environment enhances freeze and salinity tolerance. Microb Biotechnol 3 : 210– 221.[CrossRef]
141. Wongkhalaung C,, Boonyaratanakornkit M . 2007. Characterization of new baker’s yeast strains and their leavening ability in bread dough. Kasetsart J 41 : 751– 763.
142. Research and Markets . 2015. Beer: Global Industry Guide. http://www.researchandmarkets.com/reports/53577/beer_global_industry_guide.
143. Wunderlich S,, Back W, . 2009. Overviewof manufacturing beer: ingredients, processes, and quality criteria, p 3– 16. In Preedy VR (ed), Beer in Health and Disease Prevention. Academic Press, San Diego, CA.[CrossRef]
144. Wendland J . 2014. Lager yeast comes of age. Eukaryot Cell 13 : 1256– 1265.[CrossRef]
145. Barnett JA,, Lichtenthaler FW . 2001. A history of research on yeasts 3: Emil Fischer, Eduard Buchner and their contemporaries, 1880–1900. Yeast 18 : 363– 388.[CrossRef]
146. Vaughn Martini A,, Martini A . 1987. Three newly delimited species of Saccharomyces sensu stricto. Antonie van Leeuwenhoek 53 : 77– 84.[CrossRef]
147. Vaughan Martini A,, Kurtzman CP . 1985. Deoxyribonucleic acid relatedness among species of the genus Saccharomyces sensu stricto . Int J Syst Bacteriol 35 : 508– 511.[CrossRef]
148. Dunn B,, Sherlock G . 2008. Reconstruction of the genome origins and evolution of the hybrid lager yeast Saccharomyces pastorianus . Genome Res 18 : 1610– 1623.[CrossRef]
149. Nakao Y,, Kanamori T,, Itoh T,, Kodama Y,, Rainieri S,, Nakamura N,, Shimonaga T,, Hattori M,, Ashikari T . 2009. Genome sequence of the lager brewing yeast, an interspecies hybrid. DNA Res 16 : 115– 129.[CrossRef]
150. Casaregola S,, Nguyen HV,, Lapathitis G,, Kotyk A,, Gaillardin C . 2001. Analysis of the constitution of the beer yeast genome by PCR, sequencing and subtelomeric sequence hybridization. Int J Syst Evol Microbiol 51 : 1607– 1618.[CrossRef]
151. Rainieri S,, Kodama Y,, Kaneko Y,, Mikata K,, Nakao Y,, Ashikari T . 2006. Pure and mixed genetic lines of Saccharomyces bayanus and Saccharomyces pastorianus and their contribution to the lager brewing strain genome. Appl Environ Microbiol 72 : 3968– 3974.[CrossRef]
152. Okuno M,, Kajitani R,, Ryusui R,, Morimoto H,, Kodama Y,, Itoh T . 2016. Next-generation sequencing analysis of lager brewing yeast strains reveals the evolutionary history of interspecies hybridization. DNA Res 23 : 67– 80.
153. Gibson B,, Liti G . 2015. Saccharomyces pastorianus: genomic insights inspiring innovation for industry. Yeast 32 : 17– 27.[PubMed]
154. Bokulich NA,, Bamforth CW . 2013. The microbiology of malting and brewing. Microbiol Mol Biol Rev 77 : 157– 172.[CrossRef]
155. Gibson BR,, Storgårds E,, Krogerus K,, Vidgren V . 2013. Comparative physiology and fermentation performance of Saaz and Frohberg lager yeast strains and the parental species Saccharomyces eubayanus . Yeast 30 : 255– 266.[CrossRef]
156. Walther A,, Hesselbart A,, Wendland J . 2014. Genome sequence of Saccharomyces carlsbergensis, the world’s first pure culture lager yeast. G3 (Bethesda) 4 : 783– 793.[PubMed]
157. Liti G,, Peruffo A,, James SA,, Roberts IN,, Louis EJ . 2005. Inferences of evolutionary relationships from a population survey of LTR-retrotransposons and telomeric-associated sequences in the Saccharomyces sensu stricto complex. Yeast 22 : 177– 192.[CrossRef]
158. Hewitt SK,, Donaldson IJ,, Lovell SC,, Delneri D . 2014. Sequencing and characterisation of rearrangements in three S. pastorianus strains reveals the presence of chimeric genes and gives evidence of breakpoint reuse. PLoS One 9 : e92203.[CrossRef]
159. Baker E,, Wang B,, Bellora N,, Peris D,, Hulfachor AB,, Koshalek JA,, Adams M,, Libkind D,, Hittinger CT . 2015. The genome sequence of Saccharomyces eubayanus and the domestication of lager-brewing yeasts. Mol Biol Evol 32 : 2818– 2831.[CrossRef]
160. Monerawela C,, James TC,, Wolfe KH,, Bond U . 2015. Loss of lager specific genes and subtelomeric regions define two different Saccharomyces cerevisiae lineages for Saccharomyces pastorianus group I and II strains. FEMS Yeast Res 15 : fou008.[CrossRef]
161. Ogata T,, Izumikawa M,, Kohno K,, Shibata K . 2008. Chromosomal location of Lg- FLO1 in bottom-fermenting yeast and the FLO5 locus of industrial yeast. J Appl Microbiol 105 : 1186– 1198.[CrossRef]
162. Mertens S,, Steensels J,, Saels V,, De Rouck G,, Aerts G,, Verstrepen KJ . 2015. A large set of newly created interspecific Saccharomyces hybrids increases aromatic diversity in lager beers. Appl Environ Microbiol 81 : 8202– 8214.[CrossRef]
163. Krogerus K,, Magalhães F,, Vidgren V,, Gibson B . 2015. New lager yeast strains generated by interspecific hybridization. J Ind Microbiol Biotechnol 42 : 769– 778.[CrossRef]
164. Garcia Sanchez R,, Solodovnikova N,, Wendland J . 2012. Breeding of lager yeast with Saccharomyces cerevisiae improves stress resistance and fermentation performance. Yeast 29 : 343– 355.[CrossRef]
165. Machida M, . 2002. Progress of Aspergillus oryzae genomics, p 81– 107. In Laskin AI,, Bennett JW,, Gadd GM (ed), Advances in Applied Microbiology. Academic Press, San Diego, CA.
166. Gibbons JG,, Salichos L,, Slot JC,, Rinker DC,, McGary KL,, King JG,, Klich MA,, Tabb DL,, McDonald WH,, Rokas A . 2012. The evolutionary imprint of domestication on genome variation and function of the filamentous fungus Aspergillus oryzae . Curr Biol 22 : 1403– 1409.[CrossRef]
167. Machida M,, Yamada O,, Gomi K . 2008. Genomics of Aspergillus oryzae: learning from the history of Koji mold and exploration of its future. DNA Res 15 : 173– 183.[CrossRef]
168. Taylor MJ,, Richardson T, . 1979. Applications of microbial enzymes in food systems and in biotechnology, p 7– 35. In Perlman D (ed), Advances in Applied Microbiology. Academic Press, San Diego, CA.[CrossRef]
169. Hesseltine CW . 1965. A millennium of fungi, food, and fermentation. Mycologia 57 : 149– 197.[CrossRef]
170. Kitamoto K, . 2002. Molecular biology of the Koji molds, p 129– 153. In Laskin AI,, Bennett JW,, Gadd GM (ed), Advances in Applied Microbiology. Academic Press, San Diego, CA.
171. Klich MA,, Pitt JI . 1988. Differentiation of Aspergillus flavus from A. parasiticus and other closely related species. Trans Br Mycol Soc 91 : 99– 108.[CrossRef]
172. Kurtzman CP,, Smiley MJ,, Robnett CJ,, Wicklow DT . 1986. DNA Relatedness among wild and domesticated species in the Aspergillus flavus group. Mycologia 78 : 955– 959.[CrossRef]
173. Geiser DM,, Pitt JI,, Taylor JW . 1998. Cryptic speciation and recombination in the aflatoxin-producing fungus Aspergillus flavus . Proc Natl Acad Sci USA 95 : 388– 393.[CrossRef] [PubMed]
174. Barbesgaard P,, Heldt-Hansen HP,, Diderichsen B . 1992. On the safety of Aspergillus oryzae: a review. Appl Microbiol Biotechnol 36 : 569– 572.[CrossRef]
175. Geiser DM,, Dorner JW,, Horn BW,, Taylor JW . 2000. The phylogenetics of mycotoxin and sclerotium production in Aspergillus flavus and Aspergillus oryzae . Fungal Genet Biol 31 : 169– 179.[CrossRef]
176. Payne GA,, Nierman WC,, Wortman JR,, Pritchard BL,, Brown D,, Dean RA,, Bhatnagar D,, Cleveland TE,, Machida M,, Yu J . 2006. Whole genome comparison of Aspergillus flavus and A. oryzae . Med Mycol 44( s1) : S9– S11.[CrossRef]
177. Rokas A,, Payne G,, Fedorova ND,, Baker SE,, Machida M,, Yu J,, Georgianna DR,, Dean RA,, Bhatnagar D,, Cleveland TE,, Wortman JR,, Maiti R,, Joardar V,, Amedeo P,, Denning DW,, Nierman WC . 2007. What can comparative genomics tell us about species concepts in the genus Aspergillus? Stud Mycol 59 : 11– 17.[CrossRef]
178. Tominaga M,, Lee Y-H,, Hayashi R,, Suzuki Y,, Yamada O,, Sakamoto K,, Gotoh K,, Akita O . 2006. Molecular analysis of an inactive aflatoxin biosynthesis gene cluster in Aspergillus oryzae RIB strains. Appl Environ Microbiol 72 : 484– 490.[CrossRef]
179. Akao T,, Sano M,, Yamada O,, Akeno T,, Fujii K,, Goto K,, Ohashi-Kunihiro S,, Takase K,, Yasukawa-Watanabe M,, Yamaguchi K,, Kurihara Y,, Maruyama J,, Juvvadi PR,, Tanaka A,, Hata Y,, Koyama Y,, Yamaguchi S,, Kitamoto N,, Gomi K,, Abe K,, Takeuchi M,, Kobayashi T,, Horiuchi H,, Kitamoto K,, Kashiwagi Y,, Machida M,, Akita O . 2007. Analysis of expressed sequence tags from the fungus Aspergillus oryzae cultured under different conditions. DNA Res 14 : 47– 57.[CrossRef]
180. Keller-Seitz MU,, Certa U,, Sengstag C,, Würgler FE,, Sun M,, Fasullo M . 2004. Transcriptional response of yeast to aflatoxin B1: recombinational repair involving RAD51 and RAD1 . Mol Biol Cell 15 : 4321– 4336.[CrossRef]
181. Rokas A . 2009. The effect of domestication on the fungal proteome. Trends Genet 25 : 60– 63.[CrossRef]
182. Hall IR,, Yun W,, Amicucci A . 2003. Cultivation of edible ectomycorrhizal mushrooms. Trends Biotechnol 21 : 433– 438.[CrossRef]
183. Callot G . 1999. La Truffe, la Terre, la Vie. INRA, Montpellier, France.
184. Rubini A,, Belfiori B,, Riccioni C,, Tisserant E,, Arcioni S,, Martin F,, Paolocci F . 2011. Isolation and characterization of MAT genes in the symbiotic ascomycete Tuber melanosporum . New Phytol 189 : 710– 722.[CrossRef]
185. Selosse M-A,, Taschen E,, Giraud T . 2013. Do black truffles avoid sexual harassment by linking mating type and vegetative incompatibility? New Phytol 199 : 10– 13.[CrossRef]
186. Smith SE,, Read DJ . 2010. Mycorrhizal Symbiosis. Academic Press, San Diego, CA.
187. Comandini O,, Contu M,, Rinaldi AC . 2006. An overview of Cistus ectomycorrhizal fungi. Mycorrhiza 16 : 381– 395.[CrossRef]
188. Taschen E,, Sauve M,, Taudiere A,, Parlade J,, Selosse M-A,, Richard F . 2015. Whose truffle is this? Distribution patterns of ectomycorrhizal fungal diversity in Tuber melanosporum brûlés developed in multi-host Mediterranean plant communities. Environ Microbiol 17 : 2747– 2761.[CrossRef]
189. Pliny the Elder . 77 AD. Natural History Volume I, Books 1-2 (translated by H. Rackham, 1938). Harvard University Press for LOEB Classical Library, Cambridge, MA.
190. Frank AB . 1885. Über die auf Wurzelsymbiose beruhende Ernährung gewisser Bäume durch unterirdische Pilze. Ber Dtsch Bot Ges 3 : 128– 145.
191. Frank AB,, Trappe JM . 2005. On the nutritional dependence of certain trees on root symbiosis with belowground fungi (an English translation of A.B. Frank’s classic paper of 1885). Mycorrhiza 15 : 267– 275.[CrossRef]
192. Fassi B,, Fontana A . 1967. Sintesi micorrizica tra Pinus strobus e Tuber maculatum. I. Micorrize e sviluppo dei semenzali nel secondo anno. Allionia 13 : 177– 186.
193. Fassi B,, Fontana A . 1969. Sintesi micorrizica tra Pinus strobus e Tuber maculatum. II. Sviluppo dei semenzali trapiantati e produzione di ascocarpi. Allionia 15 : 115– 120.
194. Fontana A,, Palenzona M . 1969. Sintesi micorrizica di Tuber albidum in coltura pura, con Pinus strobus e pioppo euroamericano. Allionia 19 : 99– 104.
195. Fontana A,, Fasolo Bonfante P . 1971. Sintesi micorrizica di Tuber brumale Vitt. con Pinus nigra Arnold. Allionia 17 : 15– 18.
196. Palenzona M . 1969. Sintesi micorrizica tra Tuber aestivum Vitt., Tuber brumale Vitt., Tuber melanosporum Vitt. E semenziali di Coryllus avellana . Allionia 15 : 122– 131.
197. Palenzona M,, Chevalier G,, Fontana A . 1972. Sintesi micorrizica tra i miceli in coltura di T. brumale, T. melanosporum, T. rufum e semenzali di conifere e latifoglie. Allionia 18 : 41– 52.
198. Chevalier G,, Grente J . 1979. Application pratique de la symbiose ectomycorrhizienne: production à grande échelle de plants mycorhizés par la truffe. Mushroom Sci 10 : 40.
199. Murat C . 2015. Forty years of inoculating seedlings with truffle fungi: past and future perspectives. Mycorrhiza 25 : 77– 81.[CrossRef]
200. Olivera A,, Fischer CR,, Bonet JA,, Martínez de Aragón J,, Oliach D,, Colinas C . 2011. Weed management and irrigation are key treatments in emerging black truffle ( Tuber melanosporum) cultivation. New For 42 : 227– 239.[CrossRef]
201. Olivera A,, Bonet JA,, Oliach D,, Colinas C . 2014. Time and dose of irrigation impact Tuber melanosporum ectomycorrhiza proliferation and growth of Quercus ilex seedling hosts in young black truffle orchards. Mycorrhiza 24( Suppl 1) : S73– S78.[CrossRef]
202. Rubini A,, Belfiori B,, Riccioni C,, Arcioni S,, Martin F,, Paolocci F . 2011. Tuber melanosporum: mating type distribution in a natural plantation and dynamics of strains of different mating types on the roots of nursery-inoculated host plants. New Phytol 189 : 723– 735.[CrossRef]
203. Murat C,, Rubini A,, Riccioni C,, De la Varga H,, Akroume E,, Belfiori B,, Guaragno M,, Le Tacon F,, Robin C,, Halkett F,, Martin F,, Paolocci F . 2013. Fine-scale spatial genetic structure of the black truffle ( Tuber melanosporum) investigated with neutral microsatellites and functional mating type genes. New Phytol 199 : 176– 187.[CrossRef]
204. Rubini A,, Riccioni C,, Belfiori B,, Paolocci F . 2014. Impact of the competition between mating types on the cultivation of Tuber melanosporum: Romeo and Juliet and the matter of space and time. Mycorrhiza 24( Suppl 1) : S19– S27.[CrossRef]
205. Bonneau L . 2016