Genome evolution and adaptation in yeast : examplfhi tlt ... · Genome evolution and adaptation in yeast : examplfhi tlt fi i tle of horizontal transfer in wine yeasts Sylvie Dequin

Genome evolution and adaptation in yeast : l f h i t l t f i i texample of horizontal transfer in wine yeasts

Sylvie Dequin

UMR1083 SPO Montpellier p

Colloque France-Brésil 2012Des recherches pour l'agronomie, la biodiversité et la santé

17 octobre 2012, Agropolis International, Montpellier

Saccharomyces cerevisiae

FermentationsBread

Wine

Bread

Man

BeerCider

Man

Oak

Lab

Various ecological niches in relation to human activities (fermentations,

Lab

g (bread, wine, beer, cheese, laboratory, clinical…)

High phenotypic diversity within the species

Colloque France‐Brésil 2012 : Des recherches pour l'agronomie, la biodiversité et la santé Montpellier, le 17 octobre 2012

Wine yeasts: a unique originExpansion of populations through human activities

Microsatellite analysis Low coverage genome sequence

Legras et al, Mol Ecol, 2007Liti et al, Nature, 2009


Saccharomyces cerevisiaewine yeasts

Adaptation to wine making

Association to winemaking 7 000

acidic stress

nutrientsstarvationosmotic

tAssociation to winemaking 7,000 years BC (Mc Govern et al, 2004) ethanol toxicitystress

Selected for optimal traitsfermentation performance

th l t lethanol tolerancelow acetic acid productionlow H2S formation, etc

High [glucose/fructose]low pH Limitation N lipids vitamins

C tl th 200

Limitation N, lipids, vitaminsanaerobiosisSO2

Currently more than 200 commercial strains Multiple and sequential

stressesstresses Colloque France‐Brésil 2012 : Des recherches

pour l'agronomie, la biodiversité et la santé Montpellier, le 17 octobre 2012

Whole genome sequence of EC1118

EC1118® Champagne yeastEC1118® Champagne yeastp g yused worldwide as starter

Diploid heterozygous

p g yused worldwide as starter

Diploid heterozygousDiploid, heterozygousMixed WGS (5X) + 454 (17X)Diploid, heterozygousMixed WGS (5X) + 454 (17X)

59A, haploid derivativeIllumina 43X59A, haploid derivativeIllumina 43XIllumina, 43XIllumina, 43X

Novo et al, PNAS, 2009


Comparative analysis of EC1118/S288C genomes

Wine LabDivergence with other S. cerevisiae0 2 to 0 5 %

20,000 heterozygous positions

0.2 to 0.5 %

Chromosomal rearrangements

Gene repertoireSNPs: ~ 50,000rearrangements Missing genes (111, Ty)

Several novel genes

GTCATAGTCATGCCAGTATCAGTACG

Ex: increased expression of SSU1

Several novel genes clusters acquired by

HGTIndels: ~ 5,000

Resistance to sulfites

Perez‐Ortin et al (2002)


Several HGT events of eucaryote origin3 gene clusters carrying 34 genes, 120 kb in totalIndependent events

Zygosaccharomyces bailii

Non Saccharomyces

Zygosaccharomyces bailii

Saccharomyces

Novo et al, PNAS, 2009


Z. bailii, a major contaminant yeast of wine

Highly resistant to stress (acidity, ethanol)

Major cause of alteration of wine in bottle

Horizontal gene transfer could be favoured by common ecological niche


Z. bailii: donor of cluster B

SaccharomycesEC1118

A B C D E

99,7 % nucleotide identity

Zygosaccharomyces A B C D E

Z bailii

Recent transfer from Z bailii to

Z. bailii

Recent transfer from Z. bailii to S. cerevisiae


Several variants of Z. bailii cluster in S cerevisiae strainsS. cerevisiae strains

Z. bailiiChromosomal

XIV

Chromosomal positions

EC1118 XII

X

RM11

M22

XIII

XIVM22

JAY291

XIV

XI

Galeote et al, PLoS One, 2011Colloque France‐Brésil 2012 : Des recherches


Extrachromosomal circular (ECC) DNA

Galeote et al, PLoS One, 2011

Amplification by formation of circular DNA and integration


WU

IL01

Distribution of A, B, C clusters in S. cerevisiae

3 7D

W30

3

03

YS4

NCY

C110

S2 DB6044

WU PW5Mosaic genomes

African palm wineA

2 N DBVPG1853

WU FL1

00

WU Y

JM65

3 si

g127

8b

CPK1

13

S

288C

Max

P W

3

S2

W30

Fors

ters

O

ster

sB

YS

9

YS

2

YS 3

7860

4XDB

VPG

6040

NCY

C361

YJM

789

WU

YJM

320

WU

YJM

421

WU YJM32

6

WU Y

JM42

8

EC9-8

WU YJM45

1

S2 SK1

S2 Y55

WU Y10

YJM269

BC

WU I14 JAY291

W CBS7960

WU T73

W CLIB324

WU YJM280

322134S

W

CLIB382

YIIc17 E

5 273

614N DB

Fors S2

WU YJM

S2U872421

UW05 2173

UW05 2272

S2U034614

WU Y12

S2 Y12 WU Y9

1014-F5

S2 DB6765

DBVPG1788

L1374

S2 L1528

22A4JM

981

975 V

L3 Vin1

3

59A

QA23

EC1118 FS2D F25 7-7

TS12-A7

GUF54-A1

TA12-2

P3-D5

F12-3B

I14

Y9

K11

WU UC5 Kyokai7S2U837873 WU

Japan Sake

2

YJM

b Y

JM97

8

S2 YJM

97

S2

DB11

06

L1

414

WU

WE3

72

AW

RI79

6S2

DB1

373

W

U M

22

G

E7-

4AB

215

AW

RI1

631

632

0-A

7

2

0B2

BC18

7

RM

11-1

A

D47-6-

4A

K1-2

8-1A

59A WU T7W YPS1009

WU NC02 YPS606S2 YPS128

WU YPS163

0.00

05

Wine

US oak

W C

LIB

Found in most wine yeasts and mosaic genomes

96 S i i f96 S. cerevisiae genomes from SGRP, SGD, SPO Colloque France‐Brésil 2012 : Des recherches


Functional distribution of the transferred genes

Metabolic functions: carbon, nitrogen, vitamins


Fsy1, a fructose transporter

Ext

I t

H+ Fructose

Complementation of

IntFructoseH+

0.2% Fructose 0.2% Glucose

Complementation of a hxt null mutant FSY1 encodes a high affinity

fructose/H+ symporter (Km 0.24 mM)

Highly expressed on ethanol

May confer an advantage at the end of fermentation

Residual sugar = fructose

WTHxt1 7Δ

FSY1 WTHxt1-7Δ

FSY1

Residual sugar = fructose

Galeote et al, 2010 MicrobiologyHxt1-7Δ Hxt1-7Δ


The oligopeptide transporters Fot1 & Fot2 FOT1 & FOT2

FOT1/FOT2

Nb dipetides utilized

FOT family, recently identified in the

FOT1 & FOT2 encode dipeptide100

120118

FOT family, recently identified in the genome of fungi

FOT1 & FOT2 encode dipeptide transporters

M f d t60

80

100

46 May confer an advantage when classical nitrogen

sources are depleted during 20

40

60 46

28

p gwinemaking process

Damon et al, ISME J, 2011Wine Wine

fot1-2∆Lab

fot1 2∆Colloque France‐Brésil 2012 : Des recherches


Summary

Role of HGT in the evolution of wine yeast genomes

Several transfer events from distant yeasts, some sharing the same ecological nicheSpreading amplification function of novel genes: suggestSpreading, amplification, function of novel genes: suggest selective advantages during fermentation

SNPs, a main source of variation - a frame for identification of genetic bases of strains properties (QTL approaches)

ABZ1 allele controls the fermentation rate (Ambroset et al, G3 2011)

On going projectsOn going projectsAnalysis of 56 genomes: wine/flor, rum, baking, cheese, oakExperimental evolution (short time-scale)


Acknowledgments

CollaborationsINRA Montpellier

Genoscope, Evry, FranceFrédéric Gavory

k k

Frédéric BigeyVirginie Galeote

Virginie Galeote Patrick Wincker

INRA Grignon, CIRM‐Levures, France Sandrine Mallet

Jean‐Luc LegrasBruno Blondin Brigitte Cambon

Sandrine MalletSerge Casaregola

Pascale Brial

Maité Novo (Post doc) Universidade de Lisboa Portugal

Université Lyon France

a é o o ( os doc)Emmanuelle Beyne (Post doc)Souhir Marsit (PhD student)Annalisa Coi (PhD student)

Universidade de Lisboa, PortugalPaola Gonçalves

Université Lyon, FranceRoland Marmeisse

Annalisa Coi (PhD student)


Documents

Genome evolution and adaptation in yeast : examplfhi tlt ... · Genome evolution and adaptation in yeast : examplfhi tlt fi i tle of horizontal transfer in wine yeasts Sylvie Dequin