Multiple Genetic Origins of Saccharomyces Cerevisiae in Bakery

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Multiple genetic origins of Saccharomyces cerevisiae in bakery Frédéric Bigey, Diego Segond, Lucie Huyghe, Nicolas Agier, Aurélie Bourgais, Anne Friedrich, Delphine Sicard

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Frédéric Bigey, Diego Segond, Lucie Huyghe, Nicolas Agier, Aurélie Bourgais, et al.. Multiple genetic origins of Saccharomyces cerevisiae in bakery. Comparative genomics of eukaryotic microbes: genomes in flux, and flux between genomes, Oct 2019, Sant Feliu de Guixol, Spain. hal-02950887

HAL Id: hal-02950887 https://hal.archives-ouvertes.fr/hal-02950887 Submitted on 28 Sep 2020

HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Multiple genetic origins of Saccharomyces cerevisiae in bakery

Frédéric BIGEY1, Diego SEGOND1, Lucie HUYGHE2‡, Nicolas AGIER3, Aurélie BOURGAIS2, Anne FRIEDRICH4, Delphine SICARD1*

Saccharomyces cerevisiae is an ubiquitous yeast species found in natural and domesticated habitats. It has been domesticated to make a wide diversity of fermented products like wine, sake, beer, cocoa and bread. While bread is of cultural and historical importance, the domestication of S. cerevisiae in bread making is poorly known. Bread can be made either by adding commercial S. cerevisiae strains or by propagating a natural sourdough, which is a mixed of naturally fermented ﬂour, water containing yeast and bacteria. Here we analysed the genetic diversity of 229 S. cerevisiae strains of commercial and sourdough origins to get more insight into bakery yeast domestication.

Table 1 Table 2 Ploidy analysis of a set of 229 bakery strains. Ploidy was determined using a combination of microsatellites typing (at 15 loci) and cytometry origin ploidy total analysis: 31 were commercial yeasts and 198 yeasts were isolated from European sourdoughs in Italy, Belgium and France. A high level of tetraploidy origin ploidy total 2n 4n aneuploidy (40%) and aneuploidy (17%) was observed in bakery strains (Table 1). We found that commercial strains were significantly (two sided Fisher’s exact test, p 2n 4n aneuploid < 0.005) more tetraploid (68%) than sourdough yeasts (35%). On the other hand, we did not observe any significant difference of ploidy distribution France 66 37 26 129 commercial 5 21 5 31 between the 198 sourdough yeasts isolated from Belgium, France and Italy (two sided Fisher’s exact test, p > 0.05, Table 2). Italy 18 24 7 49 sourdough 94 70 34 198 Belgium 10 9 1 20 total 99 91 39 229 total 94 70 34 198

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EF2 TE2 GF3 TF2 Levante Hirondelle B9 RF1 Hirondelle Figure 1 RE3 CLIB215 B5a 12 OF2 CLIB324 MF2 Al28 Pb-29 0.6 OF1 Pb-36 OE2 Pb-38 Sequence data MF3 B7 13 MF1 B9b 19 0.4 QE2 Pb-25 Pa-4 OE3 Pa-1 4 FE3 Pa-2 FE1 Springer F-21 0.2 H-20 F-2 H-2 F-17 H-7 0.0 F-18 H-6 F-11 H-3 1.0 F-12 H-11 H-4 F-5 F-15 MUCL51233 MUCL52901 0.8 F-4 MUCL52909 F-9 CCY-02200-3-46 F-10 0.6 MUCL52905 F-13 DF2 F-14 DF3 0.4 F-16 5 Fermipan F-6 K MUCL51217 F-20 0.2 Elfin Ploidy F-19 GoldenHome F-7 0.0 PROUVY 1.0 F-8 CAPPA Com MUCL 42920

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DBVPG1058DBVPG1058 NE1 B9b 32 NE2 N26 − 1 10:7 5(a)N26 − 1 10:7 5(a)N26 − 1 10:7 5(a)N26 − 1 10:7 5(a)N26 − 1 10:7 5(a)N26 − 1 10:7 5(a)N26 − 1 10:7 5(a)N26 − 1 10:7 5(a) B9b 34 NF4 Isolation B9b 39 P1 P2 P3 P4 P5 P6 NF1 B9b 8 NF2

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B9b 36 Tandaco Population structure of 68 diploid bakery strains. Structure was commercial B9b 7 Mauripan B9b 33 SAFR Instant

B9b 28 Kolin

B9b 4 MUCL51210 obtained from 33,032 biallelic SNPs from 68 bakery strains using B9b 5 MUCL51214 sourdough B9b 21 MUCL51216 B9b 23 Pb-627 fastStructure. The vertical axis depicts the fractional representation of B9b 30 Fleischmann B9b 31 Com P-H11 B9b 6 Finestra Cielo resolved genetic groups (colors) within each strain (horizontal axis) for K B9b 1 Pa-14 Com P-H12 B9b 38 Pa-12 B9b 3 Rapunzel B9b 37 assumed ancestral genetic groups. This analysis yields a population Pa-11 B9b 20 Bioreal Population B9b 16 Pb-26 B9b 15 Pb-28 structure in 6 genetic groups with low level of mosaicism. B9b 29 Pb-31 B9b 10 Pb-727 B9b 35 Pb-32 P1 B9b 18 Pb-18 B14-22 Pb-24 Al15 Pb-17 Al10 Pb-22 Al22 YS2 Al18 LE1 P2 B9c 3 LE3 B9c 2 LF1 Al8 LF5

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Commercial Sourdough Genetic relatedness of 231 diploid and tetraploid bakery strains. NJ tree calculated from

DBVPG1058 Ritland genetic relatedness (Ritland 1996) calculated from 15 microsatellites loci. The tree shows a

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YQ5 B32-1 SBE-1C YS10E Europe YS19 represented by diploid sourdough strains (black squares) while groups P2 and P6 contains mostly 6464 CLIB208-1 YS2 YS15 YS22E CBS1252 commercial tetraploids (white squares). Europe/France YS20 CLIB192-1b CLIB340 Europe/Italy CBS1236-a YS9 Fleischmann 79 Europe/Belgium CBS1385 B10-1 CLIB326-1 Africa MUCL52906 MUCL51209

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Mosaic Tree scale: 0.1

Genomic phylogenetic tree of 68 diploid bakery strains. Maximum Distribution of the 68 bakery strains accross the 1002 genomes strains. The clusters likelyhood phylogenetic tree obtained from 33,032 biallelic SNPs from 68 bakery deﬁned by structure analysis are in agreement with the clades described in the 1002 strains using RAxML (evolution model: GTRGAMMA). The most likely tree from 100 genomes project (Peter et al. 2018). bootstrap replicates was presented. All groups but P3 contains both commercial - Group P1 (7 bakery strains) correspond to Wine/europe and Mosaic region 1 clades. and sourdough strains. However, groups P3 and P4 are composed mostly of - Group P2 and P6 (23 strains; 7 from sourdough) correspond to Mixed origin clade which also sourdough strains while groups P2 and P6 are composed mostly of commercial include beer strains, clinical strains, water, fruits, tree leaves and natural islolates. Not strains. No geographical structuration were found neither for commercial nor for distinguished by fastStructure when K equal 4. sourdough strains. - Groups P3 and P4 (19 strains; 16 from sourdough) are located in the Mozaic region 3 and Asian fermentation clades which includes strains isolated from wine, sake, clinical, fermentation, insect, palm wine, fruit, nature, distillery. These two are closely related and were not distinguished by fastStructure when K equal 5 - Group P5 including 3 bakery strains corresponds to African beer cluster.

The origin of bakery strains is polyphyletic. No geographical structuration were found neither for commercial nor for natural sourdough strains. Selection for commercial strains has maintained autotetraploid. Commercial strains are mostly related to strains of the Mixed origin clade on the 1002 genomes tree, which also includes beer strains. Sourdough strains are mosaic and are genetically related to strains from highly diverse environments like human, wine, sake, fruits, tree, soil...

1 SPO, INRA, Univ. Montpellier, Montpellier SupAgro, Montpellier, France; 2 GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Univ. Paris-Saclay, Gif-sur-Yvette, France; 3 LCQB, Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Paris, France; 4 Université de Strasbourg, CNRS, GMGM, UMR 7156, Strasbourg, France ‡ Present adress: McGill University, Canada funded by ANR: ANR-13-ALID-0005 * Correspondence: [email protected]