S. cerevisiae S. mikatae S. kudriavzevii S. arboricolus S. uvarum S ...

S. cerevisiae

pan-genome

0.03

S. eubayanus* S. mikatae S. arboricolus S. paradoxus S. uvarum S. kudriavzevii

B

AWRI939 | UCD_62-9 253AA_Sc_Y12 YPS128 97A_Sc_Y55 SK1 AWRI1082 | NCYC_761 60A_Sc_DBVPG6044 UWOPS05_227_2 278A_Sc_UWOPS03-461.4 Sc_SardSourdoughtS11 AWRI931 | UCD_C-14 Sc_MoroccoBreadG17 AWRI1722 | CBS_7045 AWRI2865 | Collec_Cepage_Pinot AWRI739 AWRI1493 | Lalvin_71B AWRI2912 | Maurivin_Primeur AWRI2906 | TOP_FLORAL WLP862 | WLP862 Sc_HefeAleW205 WLP800 WLP028 WLP001 WLP023 WLP002 WLP004 WY1084 Sc_BritAleNCYC1044 WLP013 378604X S288C 281_Sc_W303 AWRI934 273614N AWRI1729 | YW8003 Sc_BrazFuelBG1 WLP500 AWRI735 AWRI1083 | NCYC_738 AWRI1910 | NCYC_738 AWRI1776 AWRI834 AWRI814 AWRI947 AWRI1918 AWRI1436 | Lalvin_S6U AWRI1474 AWRI1899 | Fermichamp AWRI2904 | EZFERM_44 AWRI2868 | Fermichamp AWRI778 AWRI763 AWRI723 AWRI740 AWRI292 AWRI722 AWRI81 AWRI1915 Sc_SardCannonau1446 AWRI767 | WE_14 AWRI795 | Isolate_WE_14 AWRI935 | UCD_C-9 AWRI1432 | Vin_7 AWRI2880 | NT_50 AWRI2872 | Fermicru_LVCB AWRI2878 | NT_112 AWRI2879 | NT_202 AWRI2776 | NT_116 AWRI2871 | Fermicru_LS2 AWRI1902 AWRI1796 AWRI1428 | Uvaferm_PM AWRI1795 AWRI1616 | PDM AWRI1639 | Distinction AWRI1638 | Platinum AWRI2881 | Vin_2000 AWRI2850 | Actiflore_RMS2 AWRI2905 | TOP_15 AWRI2901 | Vintage_White AWRI2902 | Perlage AWRI1504 AWRI1503 AWRI1962 AWRI1498 | Lalvin_EC1118 AWRI1429 | Lalvin_DV10 AWRI2873 | Fermicru_Rose AWRI1505 | Cerebray AWRI2869 | Fermicru_4F9 AWRI1501 AWRI1912 AWRI1001 AWRI2910 | Maurivin_Elegance AWRI1642 | Advantage AWRI1502 | Fusion AWRI2260 | Lalvin_QA23 AWRI1775 AWRI1762 AWRI1575 | N96 AWRI1697 | N96 AWRI838 AWRI2340 AWRI1939 AWRI1451 | Levuline_CHP AWRI1625 | Levuline_C19 AWRI2903 | EZFERM AWRI2848 | Actiflore_B0213 AWRI2921 | Lalvin_C WLP775 AWRI2896 | REDFRUIT AWRI1496 | Enoferm_SYRAH AWRI1482 AWRI2914 | Maurivin_Maxithiol AWRI1487 | Lalvin_Rhone_L2056 AWRI2928 | Enoferm_RP15 AWRI2768 AWRI1781 AWRI2860 | Zymaflore_X16 AWRI2858 | Zymaflore_VL1 AWRI2856 | Zymaflore_RX60 AWRI2861 | Zymaflore_X5 AWRI1688 | Zymaflore_VL3c AWRI2913 | Maurivin_Sauvignon AWRI1427 | Lalvin_WSK 27 AWRI1744 AWRI1758 AWRI1761 AWRI1778 | Massey_GF8C AWRI2866 | Collec_Cepage_Sauv_Blanc AWRI1709 AWRI1784 AWRI1491 | Uvaferm_BDX AWRI2908 | Maurivin_BP_725 AWRI1946 | UCD_725 AWRI1756 | DBVPG6765 221A_Sc_L1528 Sc_AnconaWine28-AN 150A_Sc_DBVPG1106 91A_Sc_DBVPG1373 AWRI932 | UCD_C-237 AWRI937 | UCD_55-97 AWRI2907 | Maurivin_B AWRI266 AWRI2308 AWRI793 | Isolate_AWRI792 AWRI792 | Isolate_WE_1 AWRI766 | WE_1 AWRI2013 | Blastocel_Grand_Cru AWRI2895 | VINTAGE_RED AWRI1492 | Enoferm_CSM AWRI1485 | Lalvin_RC212 AWRI1483 | Lalvin_ICV_D254 AWRI2255 | Uvaferm_HPS AWRI2855 | Zymaflore_RB2 AWRI1486 | Lalvin_BM45 AWRI2853 | Zymaflore_F83 AWRI2898 | ES_454 AWRI2875 | Fermicru_XL AWRI2882 | WE_14 AWRI1017 AWRI1727 AWRI1714 AWRI1754 AWRI1712 AWRI1743 AWRI1706 AWRI1921 AWRI796 AWRI1494 | Enoferm_M2 AWRI1431 | Lalvin_W15 AWRI1742 AWRI833 AWRI1719 AWRI1716 AWRI1724 AWRI213 AWRI170 AWRI1942 | UCD_713 AWRI2078 | Lalvin_CY3079 AWRI1077 | UCD_513 WLP705 AWRI1686 AWRI2079 | Enoferm_T306 AWRI1484 AWRI971 AWRI1759 AWRI2876 | Fermirouge AWRI2897 | ES_181 AWRI1537 | Vin_13 AWRI1490 | Lalvin_Rhone_L2323 AWRI1489 | Levuline_BRG AWRI2874 | Fermicru_VR5 AWRI2927 | Lalvin_R-HST AWRI1782 AWRI228 AWRI724 AWRI1629 | Lalvin_BA11 AWRI1833 | Uvaferm_43 AWRI1435 | Oenoferm_Klosternenberg AWRI1736 AWRI2849 | Actiflore_F33 AWRI1495 | UvafermCM_522 AWRI2077 | Lalvin_ICV_D21 AWRI2933 | Lalvin_Barolo_BRL97 AWRI1488 | Lalvin_ICV_D47 AWRI2909 | Maurivin_Cru_Blanc AWRI2859 | Zymaflore_VL2 WLP099 AWRI2900 | ES_123 AWRI2899 | Aroma_White AWRI2870 | Fermicru_AR2 AWRI2851 | Actiflore_Rose AWRI2006 AWRI2854 | Zymaflore_FX10 AWRI2852 | Zymaflore_F15 AWRI2864 | Collec_Cepage_Merlot AWRI2867 | Collec_Cepage_Syrah AWRI1757 AWRI2863 | Collec_Cepage_Chardonnay AWRI1901 AWRI896 AWRI2877 | Fermivin AWRI1787 AWRI1950 | Oenoferm_LWE317-28 AWRI858 | Oenoferm 308A_Sc_YJM975 | 308A_Sc_YJM975 YJM978 | YJM978 YJM981 | YJM981 AWRI1497 | Lalvin_T73 AWRI1705 AWRI2931 | Lalvin_CLOS AWRI1760 AWRI1078 | UCD_514 AWRI1430 | Enoferm_Assmunshansen AWRI2911 | Maurivin_EP2

2 uM plasmid YJM798 chrI EC1118 chr6L JAY291 chr6L killertoxin QA23 chr12L wine circle tyrosine perm aspartic prot EC1118 chr15 796 aryl-alc RTM1 EC1118 1M36 YJM-GNAT MPR1 AWA1 BIO6 BIO1 EHL K7 chrIV Spar IRC7 160 161 162 89:1-5495 65:1-8000

A

AFDC01000

Figure S2. Genomic content across strains. (A) Sequence coverage was used to determine the genomic contribution of sequences from the Saccharomyces sensu stricto group in each strain. Each tile represents one of the sixteen chromosomes of each species, except for the S. cerevisiae sequence set which also contains 26 strain-variable accessory (pan-genome) loci. Strains are ordered according to the genome-wide SNP phylogeny and colored according to clade (ale, red; wine, blue and green; PdM, dark green, VIN7, light green). (B) A detailed display of the S. cerevisiae accessory elements of the pangenome.