Réarrangements chromosomiques Evolution des génomes de levures

Réarrangements chromosomiques Evolution des génomes de levures

2ème réunion GTGC Nantes

12 et 13 octobre 2006

Gilles Fischer

Comparative genomics in yeasts:significant results:

- Gene identification and annotation

- Sequence comparison and protein evolution

Saccharomyces cerevisiae

Saccharomyces paradoxus

Saccharomyces mikatae

Saccharomyces kudriavzevii

Saccharomyces bayanus

Saccharomyces exiguus

Saccharomyces servazzii

Saccharomyces castellii

Candida glabrataZygosaccharomyces rouxii

Kluyveromyces thermotolerans

Kluyveromyces waltiiSaccharomyces kluyveri

Kluyveromyces lactisKluyveromyces marxianus

Ashbya gossypii

Pichia angusta

Debaryomyces hanseniiPichia sorbitophila

Candida guilliermondii

Candida lusitaniae

Candida tropicalis

Candida parapsilosis

Candida albicansCandida dubliniensis

Yarrowia lipolytica

Schizosaccharomyces pombe

Cryptococcus neoformans

Hem

iasc

omyc

etes

Archiascomycetes

1

2

3

4

5

6

7

Basidiomycetes

Euascomycetes Neurospora, Magnaporthe, Aspergillus, etc…

Mus musculus

Takifugu rubripesTetraodon negroviridis

Homo sapiens

Ciona intestinalis

100 *

90

70

50* Data from O. Jaillon et al., Nature, 2004

100

85

65

61

51

48

Comparative genomics in yeasts:significant results:

- Gene identification and annotation

- Sequence comparison and protein evolution

- Chromosome rearrangements

1> speciation process

2> level of chromosome reorganisation

3> rates of chromosomal rearrangements

1> speciation process: mechanisms for hybrid sterility

- Chromosomal rearrangements

chromosome imbalance at meiosis

-Genetic incompatibilities

Dominant and/or recessive incompatibilitiesChambers et al., 1996 ; Greig et al., 2002

- DNA sequence divergence and Mismatch repair

prevention of recombination between homologsChambers et al., 1996 ; Hunter et al, 1996 ; Greig et al., 2003

Chromosomal evolution in the Saccharomyces sensu stricto complex:

S. cariocanus

S. paradoxus

S. mikatae

S. kudriavzevii

S. cerevisiae

S. bayanusvar. uvarum







Saccharomyces servazzii

Saccharomyces castellii

Candida glabrataZygosaccharomyces rouxii


Kluyveromyces waltiiSaccharomyces kluyveri

Kluyveromyces lactisKluyveromyces marxianus

Ashbya gossypii

Pichia angusta

Debaryomyces hanseniiPichia sorbitophila

Candida guilliermondii

Candida lusitaniae

Candida tropicalis

Candida parapsilosis


Yarrowia lipolytica



Archiascomycetes

1

2

3

4

5

6

7

Basidiomycetes


• monophyletic group of species• closely related to S. cerevisiae• viable hybrids

Electrophoretic Karyotypes:

sensu stricto speciesS. cerevisiae

S1 S2 S3

S4 S5 S6

S1 S2 S6

S4 S5 S3

Chromosomal Translocations: mechanism of post-zygotic isolation?

4 translocations

4 translocations

2 translocations

Chromosomal evolution in Saccharomyces sensu stricto:

94

81

94

99

S. cariocanus

S. paradoxus

S. cerevisiae (as reference)

S. mikatae

S. kudriavzevii

S. bayanus

(0 translocation)

(0 translocation)

ITS1

Fischer et al., Nature 2000

QuickTime™ et undécompresseur TIFF (non compressé)

sont requis pour visionner cette image. 0.2 to 0.5 X of genome coverage

In 2000: Genolevures I, Genomic exploration of 13 yeast species

3 - 5 kb random genomic fragments cloned in sequencing plasmid

Left sequence tag

Gene 1 Right sequence tag

Gene 2

Souciet et al., FEBS Letters (special issue), 2000

S.bayanus gene 1 gene 2

0.4X about 2000 neighboring gene couples :

=> 35 synteny breakpoints (80 predicted in total)

3 corresponded to translocations

= > 32 breakpoints left ???







Saccharomyces servazziiSaccharomyces castellii

Candida glabrata

Zygosaccharomyces rouxii


Kluyveromyces waltii

Saccharomyces kluyveri

Kluyveromyces lactis

Kluyveromyces marxianus

Ashbya gossypii

Pichia angusta

Debaryomyces hansenii

Pichia sorbitophilaCandida guilliermondii

Candida lusitaniae

Candida tropicalisCandida parapsilosis


Yarrowia lipolytica



Hem

iasc

omyc

etes

Archiascomycetes

1

2

3

4

5

6

7

Basidiomycetes


S.cerevisiae gene 1’ gene 2’Synteny conservation

S.cerevisiae gene 1’

gene 2’

Synteny breakpoint

X

YJR05

2w

YJR05

3w

YJR05

4w

YJR05

5w

YJR05

7w

YJR056c

YJR058c

YML051w

K. thermotolerans :

YJR05

2wYM

L046w

YJR05

5wYM

L051w

YML04

9w

K. lactis :

YJR05

2wYM

L046w

YJR05

3w

YML04

8w

YJR05

2w

YJR05

3w

YJR05

4w

YJR05

5w

YJR05

7w

YJR056c

YJR058c

YML051w

YML046w

YML048w

YML049w

(i) Gene transposition:

YJR05

2w

YJR05

3w

YJR05

4w

YJR05

5w

YJR05

7w

YJR056c

YJR058c

YML051w

YML046w

YML048w

YML049w

DUPLICATION

YJR05

2w

YJR05

3w

YJR05

4w

YJR05

5w

YJR05

7w

YJR056c

YJR058c

YML051w

YML046w

YML048w

YML049w


YJR05

2w

YJR05

3w

YJR05

4w

YJR05

5w

YJR05

7w

YJR056c

YJR058c

YML051w

YML046w

YML048w

YML049w

YJR05

2w

YJR05

3w

YJR05

4w

YJR05

5w

YJR05

7w

YJR056c

YJR058c

YML051w

YML046w

YML048w

YML049w

RECIPROCAL GENE LOSS


YML051w

YML046w

YML048w

YML049w


YJR05

2w

YJR05

3w

YJR05

4w

YJR05

5w

YJR05

7w

YJR056c

YJR058c

YML04

7c

X

XIII

S. cerevisiae

YML046w

YML048w

YML049w


YJR05

2w

YJR05

3w

YJR05

4w

YJR05

5w

YJR05

7w

YJR056c

YJR058c

YML04

7c

X

XIII

S. bayanus

YML051w

Fischer et al., Genome Research 2001

IVtII

SuYBR60c SuYBR061c

SuYDR037w

IItIVSuYDR038c

SuYDR037w

S. uvarum

YBR60c

II

YBR061c

YDR036cIV

YDR038c

YDR037w(KRS1)

S. cerevisiae Relic of YDR037w

paralog

1000 2000 3000 4000 5000

YBR060c YBR061c

YDR

037w

(KR

S1)

Stringency 15/23

(ii) Species specific gene duplication:

Fischer et al., Genome Research 2001

Reciprocal gene loss => SPECIATION by a version of the Bateson-Dobzhansky-Muller mechanism:

duplication

Duplicate gene loss

Reciprocal gene loss

Hybrid 2n

meiosis

1/4 of dead spores

Reciprocal gene loss => SPECIATION by a version of the Bateson-Dobzhansky-Muller mechanism:

Scannell et al., Nature 2006

Sequence divergence and meiotic sterility: sequencing of 6 genes in 41 strains

Liti et al., Genetics in press

S. cariocanus

0,3%

0,15%

0,1%

0,6%

1%

5%

15%



spore viability: - 1 reciprocal translocation=> 50% - 1 non reciprocal translocation => 75% - 4 reciprocal translocations => 6%



Conclusions: speciation results from several mechanisms superimposed?

S. cerevisiae

C. glabrata

K. lactis

S. paradoxusS. cariocanus

S. bayanus

S. castellii

K. waltii

A. gossypii

Increasing DNA divergence

WholeGenome Duplication

Reciprocal gene loss

Chromosomal translocations

2> Level of chromosome reorganisation: Genolevures 2 Dujon et al., Nature, 2004

Human pathogen

Model organism

Cryotolerant, halotolerant marine yeast

Alkane-using yeast

S. cerevisiae

C. glabrata

K. lactis

D. hansenii

Y. lipolytica

ADHoRe sofware ( Vandepoele et al., Genome Res, 2002)

gene 1 gene 2gene 3gene 4gene 5gene 6gene 7gene 8gene 9gene 10gene 11gene 12gene 13gene 14gene 15gene 16

gene a gene b gene c gene d gene e gene f gene g gene h gene i gene j

Genome 1

Genome 2

gap

r2

Synteny blocks

10 pairwise comparisons

Duplication blocks5 intra comparisons

S. cerevisiae C. glabrata

Blocks of ancestral duplications

S. cerevisiae C. glabrata

Total nb of duplicated blocksinternal to chromosomes 56 20sutelomeric 21 0

Block size (kb) mean 42 27max. 243 89

Nb of gene pairs /block mean 5.8 3.8max. 15 6

Dujon et al., Nature 2004

1

2

3

4

S. cerevisiae

C. glabrata

K. lactis

D. hansenii

Y. lipolytica


More extensive loss of duplicated genes and reductive evolution

Extensive loss of duplicated genes

Othe

r mec

hani

sms

of d

uplic

atio

n

Overall genome redundancy

(nb of genes in families over total nb of genes)

44.2 %

35.1 %

31.8 %

51.5 %

41.8 %

GENOME DUPLICATION AND GENOME REDUNDANCY

K. lactis D. hansenii Y. lipolytica

Total nb of duplicated blocksinternal to chromosomes 8 5 2sutelomeric 1 10 0

Block size (kb) mean 9 19 90max. 25 59 148

Nb of gene pairs /block mean 4.3 3.7 4.0max. 11 6 4

K. lactis D. hansenii Y. lipolytica

Sporadic segmental duplications

?

Blocks of ancestral duplications

Example of a tandem repeat array in D. hansenii

D. hansenii_ CONTIG=DEHAOK

Similar to S. cerevisiae YHR179w OYE2 NADPH dehydrogenase (old yellow enzyme), isoform 1

pseudogenes pseudogenes

Amino-acid sequence identity between copies: from 82 % to 95 %

total nb of direct total nb of

tandem pairs orientation arrays

S. cerevisiae 61 79% 50

C. glabrata 47 83% 32

K. lactis 36 72 % 33

D. hansenii 329 92 % 247Y. lipolytica 54 72 % 48

1

2

3

4

S. cerevisiae

C. glabrata

K. lactis

D. hansenii

Y. lipolytica


More extensive loss of duplicated genes and reductive evolution

Extensive loss of duplicated genes

GENOME DUPLICATION AND GENOME REDUNDANCY

Tandem repeat formation

Segmental duplication



WGDsegmental duplicationsgene tandem duplications

LOSS -> sequence degeneration deletion

New functionsGene dosageGene order changes and translocations

Pseudogenes and gene relicsSpeciation

<- DUPLICATION

S. cerevisiae

C. glabrata

K. lactis

S. paradoxusS. cariocanus

S. bayanus

D. hansenii

Y. lipolytica

Low genome reorganization:10 translocations in total

=> High synteny conservation

Synteny conservation among Hemiascomycetes:

S.cerevisiae C. glabrata K. lactis D. hansenii

C. glabrata

K. lactis

D. hansenii

Y. lipolytica

S.cerevisiae

C. glabrata

88% of the genomes are conserved within synteny blocks

0.1

1000

1000

1000

1000

1000

1000

S. paradoxus

S. mikatae

S. bayanus

S. cerevisiae

C. glabrata

K. lactis

D. hansenii

Y. lipolytica

Low genomereorganization

massivereorganization

4 translocations

2 translocations

4 translocations

reference

0

0

S. paradoxus

S. kudriavzevii

S. cariocanus

S. mikatae

S. bayanus

S. cerevisiae 0

Variable rates of rearrangements?

0.1

923

987

1000

1000

1000

1000

1000

1000

1000

S. paradoxus

S. mikatae

S. bayanus

C. albicans

K. waltii

S. cerevisiae

C. glabrata

A. gossypii

K. lactis

D. hansenii

Y. lipolytica

Gene order conservation: GOC

=5

=5Species 1 gene 1 gene 2

Species 2 gene 1’ gene X

?

Rates of genome rearrangements among Hemiascomycetes:

K. waltii

A. gossypi

K. lactis

D. hansenii

Y. lipolytica

S. cerevisiae

S. paradoxus

S. mikatae

S. bayanus

C. glabrata

C. albicans

1

9

8

5

4

2

3

6

7

i

GOC

0.88

GOL

0.12

GOLest

X12+X13+X15+X17+X19

X1

X2X4

X3

X5

X7

X8X9

X10

X11X12

X13X15

X16

X17X18

X19

X14

X6


Fischer et al., PLoS Genetics, 2006

1

1.20

1.891.43

0.98

9

8

5

1.63

0.23

4.090.75

0.43

2.181.13

0.811.00

0.29

0.080.54

0.51

4

2

3

6

7< 10-2

< 10-2

WGD

K. waltii

A. gossyp

K. lactis

D. hansenii

Y. lipolytica

S. cerevisiae

S. paradoxus

S. mikatae

S. bayanus

C. glabrat

C. albicans

GOC

0.88

GOL

0.12

GOLest

X12+X13+X15+X17+X19



Fischer et al., PLoS Genetics, 2006

1

1.20

1.891.43

0.98

9

8

5

1.63

0.23

4.090.75

0.43

2.181.13

0.811.00

0.29

0.080.54

0.51

4

2

3

6

7< 10-2

< 10-2

WGD

K. waltii

A. gossyp

K. lactis

D. hansenii

Y. lipolytica

S. cerevisiae

S. paradoxus

S. mikatae

S. bayanus

C. glabrat

C. albican

0.5

0.6

0.7

0.8

1

C. albicans

C. glabrataD. hansenii

S. cerevisiaeS. mikataeS. paradoxus

K. lactis

Y. lipolytica

S. bayanus

K. waltiiA. gossypii

0.9

Genome instability scale:

Synteny conservation among Hemiascomycetes: Genome reorganization

5 10 15 20 25 30 35 40 45 50 >50

number of genes in synteny blocks

0

50

100

150

200

250

300

Num

ber o

f syn

teny

blo

cks

S. cerevisiae vs C. glabrataK. lactis vs A. gossypii

Synteny conservation among Hemiascomycetes: Constraints onto gene order changes

0 0.1 0.2 0.3 0.4 0.5 0.6

Sc + Kl

Sc + Dh

Sc + Yl

ScSc + Cg

Sc + Cg + Kl

Sc + Cg + Kl + Dh

Sc + Cg + Kl + Dh + Yl

(10/23)

(40/113)

(625/2481)

(58/157)

(101/340)

(886/3814)

(914/4268)

(1176/5807)

Proportion of genes in synteny that are essentials

• Moderate genome reorganization between closely related species Few translocations90% of the synteny breakpoints are due to alternative loss of duplicated genes

• Major role of duplications onto chromosomal dynamics WGD Segmental duplications tandem gene duplications

•Massive genome reorganization at larger evolutionary distances: hundreds of interchromosomal rearrangements Important reshuffling of gene order

•Variable rates of genome rearrangements between lineages but also at different times within a lineage:

pathogenic yeasts having the most unstable genomes

Conclusions :

- Unité de Génétique Moléculaire des LevuresRomain Koszul, Celia Payen, Ingrid Lafontaine, Bernard Dujon

QuickTime™ et undécompresseur TIFF (non compressé)sont requis pour visionner cette image.

- The GénolevuresGénolevures Sequencing Consortium GDR 2354 CNRS Plateforme séquençage, Genopole Institut PasteurGenoscope

Cécile NeuvéglisePascal DurrensJean-Luc Souciet

- Unité de Genetique des Génomes Bactériens Eduardo Rocha

- Unité Génomique des Microorganismes Pathogènes Massimo Vergassola

- Laboratoire de Biologie Moléculaire de la Cellule (ENS Lyon) Frédéric Brunet

- Genome Stability Group (Nottinhgam, UK) Edward J. Louis

QuickTime™ et undécompresseur TIFF (non compressé)

sont requis pour visionner cette image.

Documents

Réarrangements chromosomiques Evolution des génomes de levures