Supplementary table S1. Strains and genomes used

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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