A881del. NF. 11bp del. F. F. PRJEB7601. Almeida et al. 2015. ZP 641. Spontaneous red wine fermentationCastelo de Vide, Portugal. Wine. 1484. NF. A881del.
Supplementary table S1. Strains and genomes used in this study and relevant information pertaining to them. Strain
Other designations
Substrate of isolation
AWRI 1631
N 96
Wine
AWRI 796
Active Dry Wine Yeast Commercial wine yeast
Phylogeny
Heterozigous sites (Q >40)
Australia
Wine
n.d.
South Africa
Wine
1041 *
Cuber, Slovenia
Wine
2053
Geographic location
Monosporic (MD) / single cell (SCD) derivative
A
B
AQY2
PAD1
FDC1
FZF1
NF
11bp del
F
F
W
NF
11bp del
F
F
NF
11bp del
F
F
A881del
NF
11bp del
AQY1
AQY1
NF
A881del
17/19
NF
A881del
NF
DUP
BIO1 / BIO6
AQY2
C 8/19
AQY1
F
AQY2
RTM1
W
FZF1 Fig 4
FZF1 Fig S2
SSU1
SSU1R
Reference
Genome data PRJNA30553
Borneman et al. 2008
PRJNA48559
Borneman et al. 2011
PRJEB7601
Almeida et al. 2015 Almeida et al. 2015
EXF 6719
Wine must
ZP 641
Spontaneous red wine fermentation Castelo de Vide, Portugal
Wine
1484
L1374
Wine (must from País variety)
Cauquenes, Chile
Wine
1550
5/5
NF
A881del
NF
11bp del
F F
F F
PRJEB7601 SGRP2
Bergström et al. 2014
L1528
Wine (must from Cabernet variety)Cauquenes, Chile
Wine
1334
5/5
NF
A881del
NF
11bp del
F
F
SGRP2
Bergström et al. 2014
2/19
NF
A881del
NF
11bp del
F
F
PRJEB19382
Almeida et al. 2017
4/19
NF
A881del
NF
11bp del
F
F
PRJEB19382
Almeida et al. 2017
NF
11bp del
F
F
PRJEB19382
Almeida et al. 2017
PRJEB19382
Almeida et al. 2017
Lalvin BM45
AWRI 1486
Commercial yeast (white wine)
Wine
1280
5/5
Lalvin CY-3079
AWRI 2078
Commercial yeast (red wine)
Wine
5/5
Lalvin W15
Commercial yeast (white and red wine)
Wine
1974 2209
PR
Pasteur Red
Wine
1715
NF
A881del
NF
11bp del
F
F
PYCC 4072
commercial wine yeast (Fermivin) Portugal
Wine
1889
NF
A881del
NF
11bp del
F
F
PRJEB19382
Almeida et al. 2017
TUM V1
Bordeaux wine
Wine
NF
A881del
NF
11bp del
F
F
PRJEB19382
Almeida et al. 2017
Uvaferm SGV
Commercial yeast (red wine)
Wine
1827 1734
4/19
NF
A881del
NF
11bp del
F
F
PRJEB19382
Almeida et al. 2017
Uvaferm VRB
Commercial yeast ( red wine)
Wine
19/19
NF
A881del
NF
11bp del
F
F
PRJEB19382
Almeida et al. 2017
NF
11bp del
F
F
PRJNA48563
Borneman et al. 2011
NF
11bp del
F
F
PRJNA48565
Borneman et al. 2011
NF
11bp del
F
F
PRJNA60199
Justin Fay, Washington University
Vin 13
AWRI 1537
Commercial wine yeast
VL3
B 6, AWRI 1688
Commercial wine yeast
5/5
F
Wine
2750 15216 *
Dup
2/19
F
8/19
NF
Wine
9904 *
5/5
WE 372
Commercial wine yeast
Cape Town, South Africa
Wine
4354
5/5
YJM 1332
Wine
Italy
Wine
1660
A881del
F 2/19
W
NF
A881del
NF
11bp del
F
F
PRJNA189896
Strope et al. 2015
Wine
Italy
Wine
1547
NF
A881del
NF
11bp del
F
F
PRJNA189897
Strope et al. 2015
YJM 1341
NRRL Y-12637
Grape must
South Africa
Wine
2350
NF
A881del
NF
11bp del
F
F
PRJNA189899
Strope et al. 2015
YJM 1415
NRRL Y-268
Wine
France
Wine
1256
Strope et al. 2015
Prise de Mousse
Industrial strain isolated from Champagne France
Wine
n.d.
F F
PRJNA189914
EC 1118
F F
W
PRJEA37863
Novo et al. 2009
IOC 18-2007
AWRI 2340
Commercial yeast
Wine Wine
F
F
W
PRJEB19382 PRJNA264372
Almeida et al. 2017
Commercial wine yeast
5/5 5/5
F
IOC 9002
2181 1224
F
Lalvin QA23
Commercial wine yeast
Wine
18861 *
F
F
PRJNA48561
Borneman et al. 2011
Wine
F
F
PRJNA189934
Strope et al. 2015
Slovenia
F F
PRJNA189852
Strope et al. 2015
PRJEB19382
Almeida et al. 2017
YJM 1336
5/5
19/19
NF
A881del
NF
11bp del
5/5
19/19
NF
A881del
NF
11bp del
NF
A881del
F
4/19
NF
A881del
NF
NF
A881del
F
1796
15/15 TRIP 19/19 5/5
NF
A881del
NF
Wine
1662
19/19
NF
A881del
F
commercial wine yeast (Fermichamp) Portugal
Wine
2263
NF
A881del
F
F F
wine
South Armenia
Wine
2121
NF
A881del
F
F
F
PRJEB19382
Almeida et al. 2017
PYCC 6726
Jerez-wine
Spain
Wine
4939
NF
A881del
F
F
F
PRJEB19382
Almeida et al. 2017
PYCC 6729
Jerez-wine
Armenia
Wine
2901
NF
A881del
F
F
F
PRJEB19382
Almeida et al. 2017
Wine
3242 2805
MD
NF
A881del
NF
11bp del
F
F
PRJEB24932
This study
SCD
NF
A881del
NF
11bp del
F
F
PRJEB24932
This study
3394
MD
5/5
17/19
NF
A881del
NF
11bp del
F
F
PRJEB24932
This study
Santa Bárbara, Minas Gerais, Brazil Wine Wine Casa Nova, Bahia, Brazil
3317
MD
5/5
18/19
NF
A881del
NF
11bp del
F
F
PRJEB24932
This study
3036
MD
5/5
F
NF
11bp del
F
F
PRJEB24932
This study
Wine
3277
MD
5/5
F
NF
11bp del
F
F
PRJEB24932 PRJEB7601
This study
YJM 1574
AWRI 1775
Wine
YJM 270
CBS 2807
Wine
PYCC 4074 PYCC 6722
CBS 5155
Portugal
UFMG-CM-Y215
SP9
Cachaça
São Paulo, Brazil
UFMG-CM-Y617
JB 03
Jabuticaba wine
UFMG-CM-Y618
JB 79
Jabuticaba wine
Santa Bárbara, Minas Gerais, Brazil Wine Santa Bárbara, Minas Gerais, Brazil Wine
UFMG-CM-Y619
JB 107
Jabuticaba wine
UFMG-CM-Y620
V68
Wine
UFMG-CM-Y621 PYR 4b
V152
Wine
DBQ 26
15/15
15/15
5/5
11bp del 11bp del
W
Almeida et al. 2015
Quercus pubescens
Casa Nova, Bahia, Brazil Halkidiki, Greece
MO
2738
F
F
F
F
OakRom 3-2a
Oak
Near Bucarest, Romania
MO
2366
F
F
F
PRJEB7675
Almeida et al. 2015
EXF 7200
Quercus robur
Jasenovo polje, Montenegro
MO
3001
F
F
F
F F
PRJNA264372
Almeida et al. 2015
Almeida et al. 2015
HUN 9.1s1
DBS 14
Oak
Hungary
MO
2745
F
F
F
F
PRJEB7601
Almeida et al. 2015
3.10
DBVPG 10100
Quercus cerris
Parco del Monte Subasio, Italy
MO
3800
F
F
F
F
PRJEB7601
Almeida et al. 2015
ZP 541
Fagus sylvatica
Adagoi, Portugal
MO
2684
F
F
F
PRJEB7601
Almeida et al. 2015
ZP 1008
Quercus faginea
Eja, Melres, Douro, Portugal
MO
2409
n.d.
n.d.
PRJNA264372
Almeida et al. 2015
ZP 570
Fraxinus sp.
Paul Boquilobo, Portugal
MO
2813
n.d. F
F n.d.
F
F
F
PRJEB7601
Almeida et al. 2015
ZP 848
Quercus ilex
Alter do Chão, Portugal
MO
2656
F
F
F
F
PRJEB7675
Almeida et al. 2015
ZP 850
Quercus ilex
Alconorales Natural Park, Andaluzia, Spain MO
2869
F
F
F
Almeida et al. 2015
Quercus pubescens
Montbarri, Southern France
MO
3752
PRJNA264372
Almeida et al. 2015
ZP 560
Quercus pyrenaica
Castelo de Vide, Portugal
MO
2553
n.d. F
n.d.
F n.d.
PRJEB7601
MB 7c
F
PRJEB7601
Almeida et al. 2015
BE013
Beer (Ale refermentation)
Belgium
Beer 2
n.d.
5/5
NF
MBZP00000000
Gallone et al. 2016
BE021
Beer (Pale ale)
Canada
Beer 2
n.d.
5/5
BE032
Beer
England
Beer 2
n.d.
5/5
BE063
Beer
England
Beer 2
n.d.
BE083
Beer (Saison)
Belgium
Beer 2
n.d.
BE092
Beer (Strong ale)
Belgium
Beer 2
n.d.
Minas Gerais, Brazil
C1
31074
SCD
15/15
n.d.
n.d.
n.d.
n.d.
F
n.d. F
A881del
F
F
F
NF
A881del
F
F
F
MBZH00000000
Gallone et al. 2016
NF
A881del
NF
F
F
MBYW00000000
Gallone et al. 2016
5/5
NF
V121Mpol
F
F
MBXR00000000
Gallone et al. 2016
5/5
NF
A881del
NF
F
F
MBWX00000000
Gallone et al. 2016
NF
A881del
F
F
F
MBWO00000000
Gallone et al. 2016
5/5
NF
A881del
NF
F
F
PRJEB24932
This study
5/5
NF
T498del
F
F
F
C W W
PRJEB24932
This study
NF
A881del
NF
11bp del
F
F
C
PRJEB24932
This study
NF
11bp del
F
F
C
PRJEB24932
This study
4/19
15/15
11bp del
F 11bp del
W
UFMG-CM-Y030
CAY1007
Cachaça (commercial strain)
UFMG-CM-Y625
CAY2170
Cachaça
Novo Cruzeiro, Minas Gerais, Brazil
C1
4737
SCD
UFMG-CM-Y251
SC1
Cachaça
Santa Catarina, Brazil
C1
12655
SCD
5/5
UFMG-CM-Y630
SC3
Cachaça
Santa Catarina, Brazil
C1
3570
MD
5/5
F
UFMG-CM-Y631
SC7
Cachaça
Santa Catarina, Brazil
C1
4036
MD
5/5
NF
A881del
NF
11bp del
F
F
C
PRJEB24932
This study
UFMG-CM-Y627
RJ1
Cachaça
Rio de Janiero, Brazil
C1
28953
SCD
5/5
NF
A881del
NF
11bp del
F
F
W
PRJEB24932
This study
UFMG-CM-Y629
RJW03
Cachaça
Pernambuco, Brazil
C1
4332
SCD
NF
T498del
NF
11bp del
F
F
C
PRJEB24932
This study
F
F
W
PRJEB24932
This study
F
F
C
PRJEB24932
This study
F
F
W
PRJEB24932
This study
19/19
UFMG-CM-Y624
CAY1834
Cachaça
Salinas, Minas Gerais, Brazil
C1
27658
MD
NF
T498del
F
UFMG-CM-Y632
TO1
Cachaça
Tocantins, Brazil
C2
12225
SCD
NF
A881del
NF
UFMG-CM-Y633
T09
Cachaça
Tocantins, Brazil
C2
6833
MD
NF
A881del
F
G25del
W
11bp del
UFMG-CM-Y634
TOC1301
Cachaça
Tocantins, Brazil
C2
21251
MD
5/5
NF
A881del
NF
11bp del
F
F
C
PRJEB24932
This study
UFMG-CM-Y635
TOC1346
Cachaça
Tocantins, Brazil
C2
22600
MD
5/5
NF
A881del
NF
11bp del
F
F
C
PRJEB24932
This study
UFMG-CM-Y260
YEF034
Tapirira guianensis
Tocantins, Brazil
C2
3236
MD
5/5
F
F
F
W
PRJEB11698
Barbosa et al. 2016
F NF
11bp del
F
F
W
PRJEB11698
Barbosa et al. 2016
NF
11bp del
F
F
W
PRJEB24932
This study
NF
11bp del
F
F
PRJEB24932
This study
F
F
F
C W W
PRJEB24932
This study
F
F
F
W
PRJEB24932
This study
F
F
F
W
PRJEB11698
Barbosa et al. 2016
11bp del
F
F
W
PRJNA60391
Justin Fay, Washington University
NF
11bp del
F
F
W
PRJNA32809
Argueso et al. 2009
A881del
NF
20bp ins
F
F
C
Coutouné 2017
NF
792stop
F
F
W
PRJNA352845 ERS1108635
NF
792stop
F
F
W
ERS1108633
Gonçalves et al. 2016
UFMG-CM-Y636
YEF036
Tapirira guianensis
Tocantins, Brazil
C2
3747
MD
5/5
NF
UFMG-CM-Y623
CAY44
Cachaça
Betim, Minas Gerais, Brazil
?
34631
SCD
5/5
F
UFMG-CM-Y628
RJ15
Cachaça
Rio de Janeiro, Brazil
?
81659
SCD
5/5
NF
UFMG-CM-Y637
PE6
Cachaça
Pernambuco, Brazil
?
4809
MD
4/5
F
UFMG-CM-Y638
TOC1309
Cachaça
Tocantins, Brazil
?
5932
MD
5/5
F
UFMG-CM-Y639
TOC1349-1
Tapirira guianensis
Tocantins, Brazil
?
MD
5/5
F
UFMG-CM-Y626
CBS 7960
Bioethanol-producing strain from sugar Brazilcane
5249 n.d.
4/5
NF
A881del
NF
NF
A881del
NF
Bioethanol
4/19
T498del A817del
JAY 291
Haploid derivative of bioethanol-producing Brazil strain JAY 270
Bioethanol
n.d.
5/5
BG-1 PYCC 4226
Bioethanol Bread
n.d. 30081
4/5
HET
Bioethanol-producing strain from sugar Brazilcane Commercial baker's yeast
4/5
2/19
NF
A881del
Platinum
HET
Commercial baker's yeast
Bread
42278
4/5
15/19
NF
V121Mpol
A822ins
Gonçalves et al. 2016
NF
NF
C W
F
NF
C W W
Baker's yeast
Portugal
Bread
53091
5/5 17/19
NF
V121Mpol
Baker's yeast
Morocco
Bread
61910
5/5
NF
V121Mpol
A822ins
F
TUM 506
British ale
Great Britain
Bread
50225
4/5
NF
V121Mpol
A822ins
NF
11bp del
F
F
TUM 480 BE005
Opaque beer Ale beer
South Africa Belgium
Bread
41556 n.d.
5/5 4/5
A822ins
NF
11bp del
F
NF
F
NF
C W W
AP13.1 Morocco Bread G17
HET
Bread
16/19
NF 17/19
NF
NF
11bp del
F
V121Mpol
NF
PRJEB24932 SRR403236
This study
ERS1108634
Gonçalves et al. 2016
ERS1108636
Gonçalves et al. 2016
MBZX00000000
Gallone et al. 2016
Dunn et al. 2012
BE029
Ale beer (refermentation)
Belgium
Bread
n.d.
4/5
17/19
NF
V121Mpol
NF
11bp del
F
NF
W
MBYZ00000000
Gallone et al. 2016
BR004
Bread
Belgium
Bread
n.d.
5/5
17/19
NF
V121Mpol
NF
11bp del
F
NF
W
MBVV00000000
Gallone et al. 2016
Bread
46892
MD
3/5
NF
V121Mpol
A881del
F
F
F
C
PRJEB24932
This study
Bread
37077
SCD
4/5
17/19
NF
V121Mpol
A822ins
NF
F
F
This study
53617 33689
MD
4/5
17/19
NF
A822ins
NF
11bp del
F
F
C W W
PRJEB24932
Bread
PRJEB24932 ERS1108617
This study
C
UFMG-CM-Y223
PEW01
Cachaça
UFMG-CM-Y622
PE3
Cachaça
Rio de Janeiro, Brazil Pernambuco, Brazil
UFMG-CM-Y228 TUM 208
SP1
Cachaça
São Paulo, Brazil
Alt beer
Rhineland-Palatinate, GermanyBeer 1 - German
TUM 513
California ale
TUM 308 TUM 177
Alt beer Alt / Kölsch beer
Beer 1 - German Unknown Rhineland-Palatinate, GermanyBeer 1 - German
TUM 174 TUM 148
Regional beer similar to Kölsch beerMülheim, Germany Alt beer Düsseldorf, Germany
Beer 1 - German
TUM 338
Alt beer
BE015
786stop
NF
V121Mpol
NF
11bp del
792stop
NF
NF
33061
NF
V121Mpol
NF
11bp del
792stop
NF
NF
ERS1108618
Gonçalves et al. 2016
33689 20371
NF
V121Mpol
NF
11bp del
792stop
NF
NF
ERS1108619
Gonçalves et al. 2016
NF
V121Mpol
NF
11bp del
792stop
NF
NF
ERS1108620
Gonçalves et al. 2016
21227 32602
NF
V121Mpol
NF
11bp del
792stop
NF
NF
ERS1108621
Gonçalves et al. 2016
Beer 1 - German
NF
V121Mpol
NF
11bp del
792stop
NF
NF
ERS1108622
Gonçalves et al. 2016
Düsseldorf, Germany
Beer 1 - German
35423
NF
V121Mpol
NF
11bp del
792stop
NF
NF
ERS1108623
Gonçalves et al. 2016
Beer
Germany
Beer 1 - German
n.d.
NF
V121Mpol
NF
11bp del
792stop
NF
NF
MBZN00000000
Gallone et al. 2016
BE046
Beer
Bergium
Beer 1 - German
n.d.
NF
V121Mpol
NF
11bp del
792stop
NF
NF
MBYI00000000
Gallone et al. 2016
BE073
Beer (Hefeweizen)
Germany
Beer 1 - German
n.d.
NF
V121Mpol
NF
11bp del
792stop
NF
NF
MBXH00000000
Gallone et al. 2016
BE075
Wheat beer
Belgium
Beer 1 - German
n.d.
NF
V121Mpol
A822ins
NF
11bp del
792stop
F
F
MBXF00000000
Gallone et al. 2016
BE077
Beer (Trappist)
Belgium
Beer 1 - German
n.d.
NF
V121Mpol
A822ins
NF
11bp del
792stop
F
F
MBXD00000000
Gallone et al. 2016
TUM 213
British ale / stout
Great Britain
Beer 1 - British
38169
NF
V121Mpol
A822ins
F
NF
NF
ERS1108624
Gonçalves et al. 2016
TUM 510
British ale
Great Britain
Beer 1 - British
37397
NF
V121Mpol
A822ins
F
NF
NF
ERS1108625
Gonçalves et al. 2016
TUM 503 FostersO
California ale Commercial brewing ale strain
Unknown
Beer 1 - British
30324 34874
NF
V121Mpol
A822ins
NF
11bp del
NF
NF
ERS1108626
Gonçalves et al. 2016
NF
V121Mpol
A822ins
NF
11bp del
NF
NF
ERS1108627
Gonçalves et al. 2016
TUM 165
British ale
28301
NF
V121Mpol
A822ins
NF
11bp del
NF
NF
ERS1108628
Gonçalves et al. 2016
NCYC 1044
British ale
Beer 1 - British Burton-upon-Trend, Great Britain Beer 1 - British
43373
NF
V121Mpol
A822ins
NF
11bp del
NF
NF
SRR403240
Dunn et al. 2012
FostersB
Commercial brewing ale strain
Beer 1 - British
43000
NF
V121Mpol
A822ins
NF
11bp del
NF
NF
ERS1108629
Gonçalves et al. 2016
TUM 508 TUM 210
Irish ale / stout British ale / stout
Ireland Great Britain
Beer 1 - British
NF
V121Mpol
A822ins
NF
11bp del
NF
NF
ERS1108630
Gonçalves et al. 2016
Beer 1 - British
44826 29225
NF
V121Mpol
A822ins
NF
11bp del
TUM 211
British ale / stout
Great Britain
Beer 1 - British
26842
NF
V121Mpol
A822ins
NF
BE065
Beer
US (California)
Beer 1 - British
n.d.
NF
V121Mpol
A822ins
NF
11bp del
BE071
Beer
US (San Diego)
Beer 1 - British
n.d.
NF
V121Mpol
A822ins
NF
11bp del
BE055
Beer
England
Beer 1 - British
n.d.
NF
V121Mpol
A822ins
F
BE048
Beer (Pale ale)
England
Beer 1 - British
n.d.
NF
V121Mpol
A822ins
TUM 381
Belgian beer
Belgium
Beer 1 - Wheat
30358
NF
TUM 149 W 205
Wheat beer Hefeweizen ale yeast
Munich, Germany
Beer 1 - Wheat Beer 1 - Wheat
21254 31479
TUM 175
Wheat beer
Freising-Weihenstephan, Germany Beer 1 - Wheat
Krefeld, Germany
Beer 1 - German
Beer 1 - British
C
C
C
Gonçalves et al. 2016
NF
NF
ERS1108631
Gonçalves et al. 2016
792stop
NF
NF
ERS1108632
Gonçalves et al. 2016
792stop
NF
NF
MBXP00000000
Gallone et al. 2016
NF
NF
MBXJ00000000
Gallone et al. 2016
NF
NF
MBXZ00000000
Gallone et al. 2016
F
NF
NF
MBYG00000000
Gallone et al. 2016
V121Mpol
F
F
F
ERS1108612
Gonçalves et al. 2016
NF
V121Mpol
F
F
F
ERS1108613
Gonçalves et al. 2016
NF
V121Mpol
F
F
F
Dunn et al. 2012
29902
NF
V121Mpol
F
F
NF
SRR403241 ERS1108615
V121Mpol
F
NF
NF
ERS1108616
Gonçalves et al. 2016
C
C
Gonçalves et al. 2016
TUM 507 BE074
Ale Beer from wheatmalt Beer (Hefeweizen)
Unknown Germany
Beer 1 - Wheat Beer 1 - Wheat
40936 n.d.
NF NF
V121Mpol
F
F
F
MBXG00000000
Gallone et al. 2016
BE093
Beer (Hefeweizen)
Germany
Beer 1 - Wheat
n.d.
NF
V121Mpol
F
F
F
MBWN00000000
Gallone et al. 2016
BE072
Beer (Hefeweizen)
Germany
Beer 1 - Wheat
n.d.
NF
V121Mpol
F
F
F
MBXI00000000
Gallone et al. 2016
CBS 435
Sake moto
Nakazawa, Japan
Sake
4906
NF
V121Mpol
NF
G25del
F
NF
ERS1108637
Gonçalves et al. 2016
CBS 1585
Sake moto
Nakazawa, Japan
Sake
2960
NF
V121Mpol
NF
G25del
F
NF
ERS1108638
Gonçalves et al. 2016
CBS 1598
Sake moto
Nakazawa, Japan
Sake
3517
NF
V121Mpol
NF
G25del
F
NF
ERS1108639
Gonçalves et al. 2016
Sene sake
Kurashi, Japan
Sake
n.d.
NF
V121Mpol
NF
G25del
F
NF
PRJNA60197
Justin Fay, Washington University
Alt beer
Düsseldorf, Germany
Sake
4558
NF
V121Mpol
NF
G25del
F
NF
ERS1108640
Gonçalves et al. 2016
UC 5
UCD612
TUM 184
C C
Japanese sake brewerie
Japan
Sake
n.d.
NF
V121Mpol
NF
G25del
F
NF
PRJNA45827
Akao et al. 2011
Sake moto
Japan
Sake
3270
NF
V121Mpol
NF
G25del
F
NF
ERS1108641
Gonçalves et al. 2016
Fermentation (ragi)
Indonesia
Sake
2932
NF
V121Mpol
NF
G25del
F
NF
PRJNA60205
Justin Fay, Washington University
YJSH1
Bioethanol-producing strain
China
Sake
3084
NF
V121Mpol
NF
G25del
F
NF
PRJNA72403
Zheng et al. 2012
TUM 380
Starter culture for Lambic beer
Belgium
Sake
6522
NF
V121Mpol
NF
G25del
F
F
ERS1108642
Gonçalves et al. 2016
TUM 68
Wheat beer
Freising-Weihenstephan, Germany
Sake
7094
NF
V121Mpol
NF
G25del
F
F
ERS1108643
Gonçalves et al. 2016
TUM 127
Wheat beer
Freising-Weihenstephan, Germany (progeny Sake of TUM 68) 5979
NF
V121Mpol
NF
G25del
F
F
ERS1108644
Gonçalves et al. 2016
NRRL-Y-12844
Budod
Phillipines
Sake
10363
NF
V121Mpol
NF
G25del
F
NF
ERS1108645
Gonçalves et al. 2016
Sake
NF
V121Mpol
NF
G25del
SGRP2
Bergström et al. 2014
n.d.
PRJNA189929
Strope et al. 2015
PRJNA189911
Strope et al. 2015
PRJNA189912
Strope et al. 2015
ERS1108646
Gonçalves et al. 2016
Kyokai-no.7
K7
NRRL-Y-11572 Y9
NRRL Y-5997
Y12
NRRL Y-12663, CBS 400Fermentation (palm wine)
YJM 1479
NRRL Y-6297
Coconut tuba (palm wine)
Ivory Coast Philippines
Philippines
15534 3264
YJM 1400
NRRL YB-4081
Guava (fruit)
Philippines
Philippines
2960
NF
YJM 1401
NRRL YB-4082
Papaya (fruit)
Philippines
Philippines
2762
n.d.
NRRL-YB-4084
Coconut sap
Phillipines
Philippines
10363
NF
ZP 779
Quercus acutissima
Hirusen highland, Okayama Prefecture, NA / Japan Japan
3509
ZP 781
Quercus serrata
Hirusen highland, Okayama Prefecture, NA / Japan Japan
ZP 785
Quercus dentata
SDO 3s1
A822ins
n.d.
TRIP
n.d.
n.d.
F
F
n.d.
n.d.
F
F
F
F
F
F
F
PRJEB7601
Almeida et al. 2015
3333
F
F
F
F
PRJEB7601
Almeida et al. 2015
Hirusen highland, Okayama Prefecture, NA / Japan Japan
3510
F
F
F
F
PRJEB7601
Almeida et al. 2015
Oak
North Carolina, USA
NA / Japan
3693
F
F
F
F
PRJEB7601
Almeida et al. 2015
YPS 1009
Oak exudate
New Jersey, USA
NA / Japan
2650
n.d.
n.d.
n.d.
n.d.
PRJNA60223
Justin Fay, Washington University
ZP 1050
Quercus ilex
Vendinha, Reguengos de Monsaraz, NABeja, / Japan Portugal
3119
F
F
F
F
PRJEB7675
Almeida et al. 2015
YPS 128
Quercus alba
Pennsylvania, USA
NA / Japan
3118
F
F
F
F
SGRP2
Bergström et al. 2014
ZP 530
Castanea sativa
Marão, Campeã, Portugal
NA / Japan
3661
F
F
F
F
PRJEB7601
Almeida et al. 2015
YPS 163
Quercus rubra
Pennsylvania, USA
NA / Japan
2673
F
F
F
F
PRJNA28813
Doniger et al. 2008
ZP 656
Quercus acuta
Chiba Prefecture, Japan
NA / Japan
3723
F
F
F
F
PRJEB7601
Almeida et al. 2015
ZP 651
Quercus acutissima
Chiba Prefecture, Japan
NA / Japan
3623
F
F
F
F
PRJEB7601
Almeida et al. 2015
ZP 652
Quercus acutissima
Chiba Prefecture, Japan
NA / Japan
3699
F
F
F
F
PRJEB7601
Almeida et al. 2015
V121Mpol
NF
n.d.
n.d. V121Mpol
n.d.
G25del n.d.
n.d.
n.d.
n.d.
C C
C
C C
UFMG-CM-Y255
C2
Non-identified tree
Minas Gerais, Brazil
NA / Japan
5103
F
F
F
F
PRJEB11698
Barbosa et al. 2016
UFMG-CM-Y640 YJM 1447
2TERRAPRETA
Soil
NA / Japan
5426
F
F
F
F
Bertram palm
Malaysia
n.d.
NF
F
F
PRJEB11698 PRJNA189923
Barbosa et al. 2016
UWOPS 05-227.2
Amazonia, Brazil Malaysia
ERS1108647
Gonçalves et al. 2016
SGRP2
Bergström et al. 2014
PRJNA189849
Strope et al. 2015
106bp del
NF
G528del
UWOPS 03-433.3
Nectar of Bertram palm
Malaysia
Malaysia
1908
NF
106bp del
NF
G528del
n.d.
n.d.
C
UWOPS 03-461.4
Nectar of Bertram palm
Malaysia
Malaysia
18636
NF
106bp del
NF
G528del
F
F
C
Palm wine
Nigeria
West Africa
2977
NF
A881del
F
F
F
YJM 195
NCYC 762
Raphia palm wine
Aba, Abia state, Nigeria
West Africa
1175
NF
YJM 1439
NCYC 110
Ginger beer from Z. officinale
West Africa
West Africa
2129
F
YJM 1248
NRRL Y-1546
Bili wine from Osbeckia grandifloraWest Africa
West Africa
2600
NF
PW5
A881del A881del
Strope et al. 2015
F
NF
F
C
PRJNA60181
Justin Fay, Washington University
F
NF
F
C
PRJNA189920
Strope et al. 2015
F
NF
F
C
PRJNA189888
Strope et al. 2015
UFMG-CM-Y643
49-30
Quercus rubra
Minas Gerais, Brazil
B1
6562
F
F
F
F
C
PRJEB11698
Barbosa et al. 2016
UFMG-CM-Y262
C37
Tapirira guianensis
Tocantins, Brazil
B1
7501
F
F
F
F
C
PRJEB11698
Barbosa et al. 2016
UFMG-CM-Y649
TOC1361
Tapirira guianensis
Tocantins, Brazil
B1
6059
F
F
F
F
C
PRJEB11698
Barbosa et al. 2016
UFMG-CM-Y650
TOC1364
Tapirira guianensis
B1
4749
F
F
F
F
C
PRJEB11698
Barbosa et al. 2016
UFMG-CM-Y463
C161B
Non-identified tree
Tocantins, Brazil Roraima, Brazil
B1
6665
F
F
F
F
C
PRJEB11698
Barbosa et al. 2016
UFMG-CM-Y464
C203
Non-identified tree
Roraima, Brazil
B1
7034
F
F
F
F
C
PRJEB11698
Barbosa et al. 2016
UFMG-CM-Y457
C129
Non-identified tree
Roraima, Brazil
B1
6856
F
F
F
F
C
PRJEB11698
Barbosa et al. 2016
UFMG-CM-Y461
C145
Mushroom
Roraima, Brazil
B1
7540
F
F
F
F
C
PRJEB11698
Barbosa et al. 2016
UFMG-CM-Y462
CG192
Mushroom
Roraima, Brazil
B1
6917
F
F
F
F
C
PRJEB11698
Barbosa et al. 2016
UFMG-CM-Y644
C133
Non-identified tree
Roraima, Brazil
B1
6988
F
F
F
F
C
PRJEB11698
Barbosa et al. 2016
UFMG-CM-Y646
TOC1322.1
Tapirira guianensis
Tocantins, Brazil
B1
8246
F
F
F
F
C
PRJEB11698
Barbosa et al. 2016
UFMG-CM-Y647 YPS 1000
TOC1325.1
Tapirira guianensis
B1
8165
F
F
F
F
C
PRJEB11698
Barbosa et al. 2016
Oak exudate
Tocantins, Brazil New Jersey, USA
B1
5103
F
F
F
F
C
PRJEB11698
Barbosa et al. 2016
UFMG-CM-Y257
C4
Quercus rubra
Minas Gerais, Brazil
B1
WINE
F
F
F
F
C
PRJEB11698
Barbosa et al. 2016
UFMG-CM-Y645
TOC 1318
Tapirira guianensis
Tocantins, Brazil
B1
11245
F
F
F
F
C
PRJEB11698
Barbosa et al. 2016
UFMG-CM-Y266
C53
Tapirira guianensis
Tocantins, Brazil
B1
8175
F
F
F
F
C
PRJEB11698
Barbosa et al. 2016
UFMG-CM-Y455
C45
Tapirira guianensis
Tocantins, Brazil
B1
8263
F
F
F
F
C
PRJEB11698
Barbosa et al. 2016
UFMG-CM-Y264
C49
Tapirira guianensis
Tocantins, Brazil
B1
8271
F
F
F
F
C
PRJEB11698
Barbosa et al. 2016
UFMG-CM-Y648
TOC 1355
Cachaça
Tocantins, Brazil
B1
7267
F
F
F
F
C
PRJEB24932
Barbosa et al. 2016
UFMG-CM-Y263
C41
Tapirira guianensis
Tocantins, Brazil
B3
7580
F
F
F
F
W
PRJEB11698
Barbosa et al. 2016
UFMG-CM-Y456
CTP2B
Jequitibá tree
Tocantins, Brazil
B3
46044
F
F
F
F
PRJEB11698
Barbosa et al. 2016
UFMG-CM-Y641
TOC1345
Tapirira guianensis
Tocantins, Brazil
B3
5385
F
F
F
F
C NA R
PRJEB11698
Barbosa et al. 2016
UFMG-CM-Y642
TOC1365
Tapirira guianensis
Tocantins, Brazil
B3
4749
F
F
F
F
R
PRJEB11698
Barbosa et al. 2016
> 20000
F
Cachaça Wine - Brazil
Brazilian strain
MD
* values taken from the literature (see citation)
Bioethanol Wild - Brazil
- functional
NF
- non functional
n.d.
- not determined
References: Akao et al. 2011. Whole-genome sequencing of sake yeast Saccharomyces cerevisiae Kyokai no. 7. DNA Res. 18, 423-434. Almeida et al. 2015. A population genomic insigth into the Mediterranean origins of wine yeast domestication. Mol. Eco. 24, 5412-5427. Almeida et al. 2017. Adaptive divergence in wine yeasts and their wild relatives suggests a prominent role for introgressions and rapid evolution at noncoding sites. Mol. Ecol. 26, 2167-2182. Argueso et al. 2009. Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production. Genome Research 19, 2258-2270. Barbosa et al. 2016. Evidence of natural hybridization in Brazilian wild lineages of Saccharomyces cerevisiae. Gen. Biol. Evol. 8, 317-329. Bergström et al. 2014. A high-definition view of functional genetic variation from natural yeast genomes. Mol Biol Evol 31, 872–888. Borneman et al. 2008. Comparative genome analysis of a Saccharomyces cerevisiae wine strain. FEMS Yeast Res. 8, 1185-1195. Borneman et al. 2011. Whole-genome comparison reveals novel genetic elements that characterize the genome of industrial strains of Saccharomyces cerevisiae. PLoS Genet. 7, E1001287. Coutouné 2017. Draft genome sequence of Saccharomyces cerevisiae Barra Grande (BG-1), a Brazilian industrial bioethanol-producing strain. Genome Announc. 5:e00111-17. Doniger et al. 2008. A Catalog of Neutral and Deleterious Polymorphism in Yeast. PLoS Genet 4, e1000183. Dunn et al. 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. Gallone et al. 2016. Domestication and divergence of Saccharomyces cerevisiae beer yeasts. Cell 6, 1397-1410. Gonçalves et al. 2016. Distinct domestication trajectories in top-fermenting beer yeasts and wine yeasts. Curr Biol 26, 2750-2761. Novo et al. 2009. Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118. PNAS 106, 16333-16338. Strope et al. 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. Zheng et al. 2012. Genome sequencing and genetic breeding of a bioethanol Saccharomyces cerevisiae strain YJS329. BMC Genomics 13, 479.
Sake
Spar allele only
Spar NA Scer+Spar alleles
Cosmopolitan
detected
Wine
not detected
Recombinant
Supplementary table S2. Tolerance to ferulic acid (0.2% w/v, pH 4.5) of cachaça strains with and without PAD1 / FDC1 introgression from S. paradoxus. Growth was assessed in Yeast-Peptone-Glucose agar medium supplemented with ferulic acid. Strong (+++), intermediate (++) or low (+) growth was recorded after inoculation of serially diluted (10-2, 10-3 and 10-4) 10 µl drops of a culture grown in liquid medium without ferulic acid up to a OD640nm of 0.3 – 0.4 and 48h incubation at 25 °C. For comparison the results of two wild Brazilian strains with high resistance to ferulic acid are included. Strain CAY 1007 CAY 1834 CAY 2170 RJ1 TO1 TOC1301 TOC1346 CAY44 RJW03 SC1 SC3 SC7 T09 YEF036 YEF034 RJ15 49-30 TOC 1345
PAD1 / FDC1 S. paradoxus introgressions present present present present present present present present absent absent absent absent absent absent absent absent absent absent
Phylogeny
Tolerance to ferulic acid
cachaça cachaça cachaça cachaça cachaça cachaça cachaça cachaça cachaça cachaça cachaça cachaça cachaça cachaça cachaça cachaça wild Brazil B1 wild Brazil B3
++ + + ++ ++ + ++ + + ++ + + + + ++ + +++ +++
BREAD
BIOETHANOL
Y6
33
UF UF CB JA MG Y UF MG- S 7 -C MG CM 960 B 291 MG -CM Y6 Y6 1 2 32 UF Y624 4.1 UF MG- .0 UF MG-C CM-Y MG M- 62 U -CM Y6 7.1 UFM FMG- -Y62 29 G-C CM-Y 7.0 M-Y 63 UFM 630 1 G-C M-Y 030 .1 UFMG U BE09 FMG-C UFMG -CM BE06 M-Y0 2 -Y2 3 51 30.0 -CM-Y6 25 BE032 BE021 BE083 BE013 ZP560 MB7c ZP848 ZP850 ZP570 ZP541 ZP1008 3-10 EXF7200 HUN9 PYR4b m3-2a o OakR 574 1 YJM QA23 Lalvin 18-2007 IOC C 9002 8 IO 111 EC 074 C4 13 PYC 6726 Vin C 29 PYC C 67 70 20 C -Y6 15 PY JM 2 2 M Y 672 -C in W 21 MG alv -Y6 96 2 CC UF L -CM RI 7 E37 PY MG AW W GV S UF rm afe Uv
17 MBG 3.1 AP1 506
M-
TUM
-C
04 BR0
MG
480
UF
TUM 508 NCYC1044 FostersB BE048 Y228.0 UFMG-CM-Y228.1 UFMG-CM Platinum 4226 P Y CC 5 BE00
TUM
.0 223 22.1 M-Y 029 G-C M-Y6 22.0 BE UFM MG-C -Y6 .1 .1 -CM .1 UF 23 35 MG -Y223 -Y6 3.0 -Y6 4.1 UF -CM 62 CM Y63 5.0 .0 -CM MG M-Y G- M- 63 34 MG UF G-C UFM G-C M-Y -Y6 M -C M M UF UF FMG G-C U FM U UF
CACHAÇA 2
TUM 210 BE055 TUM 211 TUM 165 FostersO TUM 50 3 BE065 BE071 TUM 213 TUM 510 BE0 74 BE0 TUM BE0 93 72 149 TU TU M 175 TU W2 M 38 1 M 5 05 07 BE BE 0 7 5 0 TU BE 77 M 17 TUM 015 4 33 8 TU BE M 07 14 3 8
BEER 1
CACHAÇA 1
BEER 2
Y12
6 04 BE 208 08 177 M UM 3 UM U T T T 3 51 1 . M TU Y628 60 Y2 -CM CMMG MGF U UF 636 M-Y G-C .0 M UF Y628 637 -Y -CM -CM 8 MG MG 63 UF UF -CM-Y -Y639 G -CM 2844 M F U FMG L-Y-1 NRR 127 U M TU 380 TUM 68 TUM
ZP 651 ZP 65 ZP 652 6 YPS 1 28 ZP 7 YPS 8 163 ZP 7 1 7 9 ZP UFM 785 SDO G-CM ZP YPS 3s1 -Y2 55 ZP 1050 1009 530 UF MG -CM -Y6 40 .1 56 Y4 M- .0 -C 456 MG M-Y UF G-C M UF S
OP .4
61
-4
03
UW
M
5
YJ
M
M
M
SAKE
39
19
O 0 14 3-43 3.3 47
PHL YJM 1401
NA-JPN
12
14
41 Y6 2 M4 -C -Y6 MG -CM MG UF 63 Y2
UF
M-
-C
MG
UF
BRAZIL B1
YJ
YJ
YJ
PW
UW 43 -Y6 2 -CM -Y26 49 6 MG M UF MG-C CM-Y 50 UF FMG- M-Y6 U -C MG UF -Y463 4 M 6 G-C M-Y4 UFM MG-C 7 UF -Y45 M G-C 1 UFM M-Y46 2 6 4 G-C UFM MG-CM-Y 644 646 UF -CM-Y MG-CM-Y G UF 647 UFM -CM-Y UFMG
YJ AW M 13 RI 32 16 La 31 lv Uv in C VL3 afe YLa rm 30 lv 7 PY in B VR 9 CC M B EX ZP 6 407 45 F 6 41 2 YJM719 134 L15 1 28 YJM L1374 1 TUM 415 YJM V1 1336 UFMG P -C UFMG M-Y215 R -C UFMG-C M-Y617 M-Y618 UFMG-C M-Y619
0.005
00 YPS 10 M-Y257 UFMG-C G-CM-Y645 UFM Y266 UFMG-CMUFMG-CM-Y648 UFMG-CM-Y455 UFMG-CM-Y264
FIGS1
Y9
YJSH1 Kyokai7 572 NRRL-Y-11 UC5 TUM 184 CBS 1585 CBS 1598 CBS 435 YJM1400 YJM 1479 NRRL-YB-40 84
MO
WINE
CACHAÇA (MOSAICS)
48
WA
5
MY
BRAZIL B3
UFMG-CM-Y257 UFMG-CM-Y456 UFMG-CM-Y648 UFMG-CM-Y264
WINE BEER 2 CACHAÇA C1 CACHAÇA C2 CACHAÇA BIOETHANOL BREAD BEER 1 SAKE PHILIPPINES NA - JP MALAYSIA WEST AFRICA BRAZIL B1 BRAZIL B3
UFMG-CM-Y455 UFMG-CM-Y645 UFMG-CM-Y647 UFMG-CM-Y646 UFMG-CM-Y461 UFMG-CM-Y644 UFMG-CM-Y457 UFMG-CM-Y464 UFMG-CM-Y463 UFMG-CM-Y650 UFMG-CM-Y649 UFMG-CM-Y262 UFMG-CM-Y643 UFMG-CM-Y251 UFMG-CM-Y630 UFMG-CM-Y631 UFMG-CM-Y629 UFMG-CM-Y632 UFMG-CM-Y634 UFMG-CM-Y635 UFMG-CM-Y030 BG-1 YJM 1248 YJM 1439 PW5 TUM 208 UWOPS 03-461.4 UWOPS 03-433.3 UC5 Kyokai7 NRRL-YB-4084 YJM 1400 YPS 128 ZP 652 BE073 TUM 507 TUM 480
C ALLELE
MBG17 FostersO FostersB AP 13.1 TUM 381 S. cerevisiae SGD ZP 656 UFMG-CM-Y223 UFMG-CM-Y622 UFMG-CM-Y628 BE063 BE013 BE029 TUM 480 TUM 506
W ALLELE
UFMG-CM-Y626 UFMG-CM-Y628 UFMG-CM-Y633 AWRI 1631 UFMG-CM-Y625 UFMG-CM-Y030 PYCC 4226 Platinum IOC 9002 UFMG-CM-Y228 UFMG-CM-Y622 UFMG-CM-Y617 EXF 6719 UFMG-CM-Y263 MBG17 PR UFMG-CM-Y639 UFMG-CM-Y623 EC 1118 UFMG-CM-Y636 UFMG-CM-Y638 JAY 291 AP 13.1 BR004 BE005 UFMG-CM-Y627 UFMG-CM-Y637 UFMG-CM-Y624 UFMG-CM-Y260 UFMG-CM-Y641 UFMG-CM-Y642 UFMG-CM-Y456 S. paradoxus NA S. paradoxus FE S. paradoxus SGD HUN9 ZP 850 S. mikatae SGD S. uvarum SGD
0.05
FIGS2
S. eubayanus
BEER 2 CACHAÇA C1 CACHAÇA SAKE PHILIPPINES MALAYSIA WEST AFRICA BRAZIL B1 BRAZIL B3
BIO6
S. paradoxus
S. cerevisiae
0.01
FIGS3
UFMG-CM-Y623 UFMG-CM-Y639 UFMG-CM-Y629 UFMG-CM-Y627 UFMG-CM-Y649 UFMG-CM-Y262 UFMG-CM-Y641 UFMG-CM-Y464 UFMG-CM-Y263 BE083 BE013 S. paradoxus NA (YPS138) S. paradoxus NA (UWOPS91917.1) S. paradoxus EU (ZP526) S. paradoxus EU (Q59) S. paradoxus FE (IFO1804) S. paradoxus FE (N44) UFMG-CM-Y630 UFMG-CM-Y251 YJM 1439 YJM 1248 YJM 1400 CBS 435 UC5 CBS 1598 UFMG-CM-Y268 UWOPS 03-433.3 YJM 1447 S. arboricola
Bread
Bioet
C?
C2
C1
CAY1007 CAY1834 CAY2170 RJ1 RJW03 SC1 SC3 SC7 TO1 TO9 TOC301 TOC1346 YEF034 YEF036C CAY44 RJ15 PE6 JAY291 CBS7960 PE3 PEW01 SP1 AWRI1631 AWRI796 EXF6719 ZP641 L1374 L1528 Lalvin BM45 Lalvin CY-3079 Lalvin W15 PR PYCC 4072 TUM V1 Uvaferm SGV Uvaferm VRB
Vin13
Wine
VL3 WE 372 YJM 1332 YJM 1336 YJM 1341 YJM 1415
EC1118 IOC 18-2007
IOC9002 LalvinQA23 YJM 1574 YJM 270 PYCC 4074 PYCC 6722 PYCC 6726
III
IV
V
VI
VII
IX
X
XV
YOL129W
YOL159C
YOL122C
YJL213W
YJL212C
YIL159W
YIL160C
YIL161W
YIL162W
YIL164C
YIL166C
YGR286C
YGR285C
YGL255W
YGL256W
YFR052W
YER183C
YER182W
YER180C-A
YER180C
YER179W
YER178W
YER177W
YDR539W
YDR538W
YDR536W
YDR342C
YCR010C
YCR009C
YCR008W
YCR004C
YCR003W
YCR002C
YCL001W
YCL004W
YCL002C
YCL005W
YCL009C
YCL008C
Strain
Clade
Supplementary figure S4. Introgressions of Saccharomyces paradoxus in the genomes of Brazilian S. cerevisiae cachaça and wild popula�ons and in bioethanol and wine strains (depicted strain by strain). The presence of introgressions is color coded and refers to the donor popula�on of S. paradoxus: European (light green), North American popula�on B (dark green), unknown popula�on or recombinant sequences (brown).
Spar NA Spar EU unknown
B2
B1
PYCC 6729
SP9 JB03 JB79 JB107 V68 V152 C41 CTP2b TOC1345 TOC1365 49-30 C4 C37 C45 C49 C53 C129 C133 C161b C145 C203 TOC1318 TOC1322.1 TOC1325.1 TOC1355 TOC1361 TOC1364 CG192
