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Multiple Genetic Origins of Saccharomyces Cerevisiae in Bakery

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Multiple Genetic Origins of Saccharomyces Cerevisiae in Bakery Multiple genetic origins of Saccharomyces cerevisiae in bakery Frédéric Bigey, Diego Segond, Lucie Huyghe, Nicolas Agier, Aurélie Bourgais, Anne Friedrich, Delphine Sicard To cite this version: 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. genetic diversity of229 propagating a natural sourdough, which is a of mixed naturally fermented domestication of wide diversity of fermented products like wine, Saccharomyces cerevisiae sake, beer, cocoa and bread. While bread is of cultural and historical importance, the highly diverse environments like human, wine, sake, fruits, tree, soil... fruits, tree, human, wine, sake, like highly diverse environments clade on the 1002 genomes whichtree, also includes beer strains. Sourdough strains mosaic are and genetically are to related strains from strains. Selection for strains commercial has maintained autotetraploid. strains mostly to Commercial are related strains of origin the Mixed The origin of bakery strains is polyphyletic. No geographical structuration were found neither for commercial nor for natural sourdough commercial 5 21 5 31 sourdough 94 70 34 198 sourdough strains. sourdough strains. No geographical structuration were found neither for commercial nor for sourdough strains while groups P2 and P6 are and composed mostly sourdough of strains. commercial However, bootstrap groups replicates was presented. All P3 groups but P3 and contains both P4 strains using (evolution commercial RAxML model: The GTRGAMMA). most tree from 100 likely are composed mostly of likelyhood phylogenetic tree obtained from 33,032 biallelic SNPs from 68 bakery Genomic phylogenetic tree of 68 diploid bakery strains origin ploidy total Mosaic Population Origin Isolation Microsatellite total 99 91 39 229 Table 1 Table Figure 1 Figure Mosaic P6 P5 P4 P3 P2 P1 NA Oceania America Asia Africa Europe/Belgium Europe/Italy Europe/France Europe Sourdough Commercial structure in 6 genetic groups with lowlevelofmosaicism. in6genetic groups structure assumed ancestral genetic resolved genetic groups. groups (colors) within This each strain (horizontal analysis axis) for fastStructure. K yields The vertical a axis population obtained depicts the from fractional representation 33,032 of Population structure biallelic of 68 SNPs diploid from bakery strains 68 bakery strains using 2n 4n aneuploidy S. cerevisiae CLIB889 CLIB889 CLIB889 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 YQ5 YQ5 YQ5 YQ5 YQ5 DBVPG1058B29_1 B29_1 DBVPG1058 B29_1 B29_1 CLIB889B32_1 B32_1 CLIB889 B32_1 B32_1 Red_Star Red_Star Red_Star MUCL52906 YQ5YS2 YS2YQ5 YS2 YQ5 YS2 YS2 YS2 MUCL51236 MUCL51226 P1 Red_Star Red_Star CBS1385YS20 YS20 CBS1385 YS20 YS20 CBS1385 YS20 B10-1 CBS1236 a−a QE1 NF1 LE3 CBS1236-a CLIB192_1b CLIB192_1b YS15 YS15 YS15 YS15 YS15 CLIB192-1b YS2 YS2 YS10(E) YS10(E) YS10(E) 2). test, p> 0.05, Table exact and Italy (twosided Fisher’s Belgium,France yeasts isolatedfrom between the 198 sourdough < 0.005) more tetraploid (68%) than sourdough yeasts (35%). found that strainssigni commercial were 1). We On (40%) and aneuploidy (17%) was strains observed (Table the in bakery other hand, we did not observe any signi analysis: 31 were commercial yeasts and 198 yeasts were isolated from Ploidy European sourdoughs analysis in of Italy, Belgium a and France. set A high of level 229 of tetraploidy bakery strains. YA3 CBS1385YS19 YS19 CBS1385 YS19 YS19 YS19 SBD YS20 YS20 YS20 CBS1428 CBS1236− AE1 CBS1252 CLIB340YS10(E)YS15 YS15 YS10(E)CLIB340 YS15 CLIB340 CBS1387 CLIB208-1 YS1979 79 YS19 79 79 YS19 79 79 79 79 MUCL51223 YS22(E) YS22(E) YS22(E) CLIB340 CLIB340 MUCL51215 YS9 YS9 YS9 YS9 YS9 YS9 N26-1-10-7-5a YS22(E) YS22(E) CBS1252 CBS1252 CBS1252 S. cerevisiae YS2 Fleischmann Fleischmann P26464SBE P3 6464 1C−1C 6464 6464 6464 * ‡ 4 3 2 1 N134-7-1a Frédéric BIGEY Frédéric CBS1252SBE− CBS1252 Aurélie BOURGAIS IE1 6464YS9 YS9 6464 6464 Saccharomyces cerevisiae Multiple genetic origins of Université de Strasbourg, CNRS, GMGM, UMR 7156, Strasbourg, France CNRS, GMGM, UMR 7156, Strasbourg, Université deStrasbourg, Montpellier, France; Montpellier, Montpellier SupAgro, Univ. SPO,INRA, CLIB274_1 CLIB274_1 N34-2-4a CLIB326_1 CLIB326_1 B9b-1 is an ubiquitous yeast species found in natural and domesticated habitats. It has been domesticated to make a Correspondence: [email protected] Correspondence: McGill University, Canada adress: Present LCQB, Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Paris, France; Paris, LCQB, Sorbonne Université, CNRS, UMR7238, Institut Paris-Seine, de Biologie France; Gif-sur-Yvette, Paris-Saclay, Univ. CNRS, AgroParisTech, Paris-Sud, Univ. Moulon,INRA, GQE-Le MUCL51209 MUCL51209 B9c-1 646 3B−3B RedStar Aline20IE1 IE1 Aline20 IE1 IE1 Aline20 IE1 IE1 IE1 Aline20 646− B9b 1−1 MUCL51223 MUCL51223 CLIB889 B9c 1−1 Aline20 Aline20 B9b− B25_1PA3Y A3Y B25_1P A3Y A3Y B25_1P A3Y A3Y B25-1P MUCL51215B9cSBD− SBD MUCL51215 SBD SBD SBD DBVPG1058 CBS1387B25_1P B25_1P CBS1387 CBS1387 CBS1254 SBD SBD SBD CBS1428IE1 CBS1428 CBS1428 in bread making is poorly known. Bread can be made either by adding commercial B29-1 MUCL51226 MUCL51226 QE1 QE1 QE1 QE1 QE1 CBS1387A3Y A3Y CBS1387 77 LE3 LE3 LE3 LE3 LE3 LE3 CBS1428 CBS1428 YS4 YQ5 MUCL52906QE1 QE1 MUCL52906 QE1 AE1 AE1 AE1 AE1 AE1 AE1 P4 P5 319-5C B32-1 NF1 NF1 NF1 NF1 NF1 NF1 MUCL51236 MUCL51236 LE3B10 LE3 1−1 MUCL42920 SBE-1C N26 5(a)−1−10:7−5(a) B10N34:2− 4(a)−4(a) CLIB215-3B YS10E AE1 AE1 NF1N134:7 NF1 1(a)−1(a) Bruggeman YS19 CLIB318_1 CLIB318_1 N34:2− CLIB324_2YS8(E) YS8(E) CLIB324_2 YS8(E) YS8(E) N26−1Bruggeman−10:7− Bruggeman CLIB215 6464 MUCL30387N134:7− MUCL30387 MUCL30388 MUCL30388 YS8E YS15 CLIB215 CLIB215 CLIB215 324-6C YS22E yeast domestication. insight into bakery origins togetmore and sourdough strains ofcommercial . Maximum YS5(E)SD YS5(E) 15−15 YS5(E) YS5(E) B16-4 YS20 CLIB215_3B324 6C− CLIB215_3B6C CLIB215 CLIB215 MUCL52901 MUCL52901 MUCL30387 CLIB340 SDB16_4− B16_4 B16_4 B16_4 . Structure was P6 324− SD-15 YS9 YS4 YS4 YS4 YS4 YS4 YS4 MUCL52901 Fleischmann 319 5C−5C MUCL42920 MUCL42920 MUCL30388 79 YS11(E) YS11(E) YS11(E) 77 77 77 77 77 77 77 77 CLIB324-2 CBS1385 YS5E 319− CLIB326-1 CBS1254 CBS1254 CBS1254 CLIB318-1 MUCL51209 YS11E 646-3B CLIB274-1 YS11(E) YS11(E) YS4 YS4 CLIB208_1 CLIB208_1 CBS1254 CBS1254 4 6 5 Figure 2 Figure K 1 , DiegoSEGOND Ploidy was determined using a combination of microsatellites typing (at 15 loci) and cytometry 2 , AnneFRIEDRICH commercial tetraploids (whitesquares). commercial represented by diploid sourdough strains (black squares) while groups P2 and P6 contains mostly clustering concordant with the 6 genomic shows a loci. The tree 15 (Ritland microsatellites Ritland 1996) geneticcalculated relatedness from groups (Figures 1 and 2). Groups Genetic P3, relatedness of P4 231 diploid are and mostly tetraploid bakery strains Tree scale: 0.1 scale: Tree Population Isolation Ploidy Sequence data - Group when Kequal 5 notdistinguished by fastStructure were fermentation, insect, palm wine, fruit, nature, Asian distillery. These two are fermentation closely related and clades - Groups which includes when Kequal 4. distinguished byfastStructure strains isolated include beer from strains, clinical wine, - Group strains, water, sake, fruits, tree clinical, - Group leaves and natural islolates. et al.2018). (Peter genomes project Not de Distribution of the 68 bakery strains accross the 1002 genomes strains fl fi our, water containing yeast and bacteria. Here we analysed the P6 P4 P3 P2 P1 sourdough commercial 4N 2N ned by structure analysis are in agreement with the clades described in the 1002 1 , Lucie HUYGHE Tree scale:0.1 Tree Isolation Population P5 P2 P1 P3 P6 P5 P4 P3 P2 P1 Sourdough Commercial and (7 bakery strains) correspond to Wine/europe and Mosaic region 1clades. andMosaic region toWine/europe strains) correspond (7bakery including 3 bakery strains corresponds to African beercluster. to African strains corresponds including3 bakery and P6 4 P4 , Delphine SICARD (23 strains; 7 from sourdough) correspond to Mixed origin (23 to clade strains; Mixed which correspond 7 sourdough) also from (19 strains; 16 from sourdough) are located in the Mozaic region 3 and B9b 36 B9b 39 B9b B9b 33 34 B9b B9b 28 B9b 32 B9b 9 B9b B9b 8 B9b B9b 7 B9b 27 B9b B9b 26 B9b fi B9b 4 B9b 21 24 B9b B9b 5 B9b 23 22 B9b B9b 30 17 B9b B9b 31 14 B9b B9b 11 B9b B9b 6 B9b 12 B9b cant di B9b 38 B9b 1 B9b 3 B9b 37 B9b 20 B9b 16 B9b 15 B9b 29 B9b 10 B9b 35 F-8 B9b 18 F-7 B14-22 F-19 F-20 Al15 F-6 Al10 F-16 F-14 Asian fermentation Al22 Al18 F-13 B9c 3 F-10 ff B9c 2 F-9 Al8 F-4 erence erence of ploidy distribution Al19 F-15 fi Al36 F-5 Al30 F-12 cantly (two sided Fisher’s exact test, exact p cantly (two sided Fisher’s B9c 7 F-11 F-18 Al4 B9c 1 F-17 B9c 9 F-2 B9c 4 F-21 Al3 FE1 B9c 10 FE3 OE3 ANR-13-ALID-0005 funded by ANR: Al20 B9c 8 QE2 B9c 16 MF1 B9c 15 MF3 B9c 17 OE2 Mosaic region 3 Mosaic region B9c 12 OF1 2‡ B9c 13 MF2 B9c 11 OF2 B9c 14 RE3 Al39 RF1 YQ5 GF3 , Nicolas AGIER MUCL51221 B1a 33 V-23 CE3 MUCL51219 GF2 MUCL51215 GF4 MUCL51213 GF6 MUCL51223 GF1 IE2 EF3 EE2 Wine/European IE1 IF6 EF2 B10L-15 TE2 B10L-13 TF2 B10L-21 Levante in bakery B10L-36 Hirondelle B9 B10L-30 Hirondelle B10L-29 CLIB215 B10L-16 B5a 12 B10L-17 CLIB324 S.
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