sex chromosome evolution in vertebrates institut des sciences de levolution department genome team...

Sex chromosome evolution in Vertebrates

Institut des Sciences de l’EvolutionDepartment GenomeTeam Sex & SpeciationCNRS / University Montpellier 2

Frédéric VEYRUNES

email: [email protected]

Comparative GenomicsLyon 2011

I. Origin and Evolution of sex chromosomes in Vertebrates.

II. The “weird” sex chromosome system of the platypus.

III. New data from the complete sequencing genome of the platypus

IV. Sex chromosomes and sex determination in African pygmy mice.

1

109 1186

2 3 4 5

12

15

7

1413 16 1817

19 222120 X Y

XY X X

X and Y chromosomes evolved from an ancestral pair of

autosomes

SRY

proto-X -Y X Y

X > 1000 genes

Y >45 genes (SRY)

The Human Y chromosome rapidly degenerates.

Graves Cell 2006

Y = by-product of perverse evolution leading to its

extinction ?

Well… Human Y may disappear, but probably not males

Ellobius lutescens, a species without Y, nor SRY (Just et al Nature Genet 1995)

The ancestral Y of D. pseudoobcura has been lost, and a novel Y has arisen de novo (Carvalho & Clarck Science 2005)

11/11 genes shared between Z and W

(small sex-determining region)

3/11 genes shared between

Z and W

No genes shared between Z and W (W has lost most

genes)

Pythonidae Colubridae

Gradual degeneration of snake W chromosome (Matsubara et al PNAS 2006)

Viperidae

Z W

Non-recombining region has remained small

Large non-recombining region

Ratite bird sex chromosomes are not evolving at the same rate than other birds (Nanda et al Cytogenet Genome Res 2008)

FOUR active genes in human and gorilla became pseudogenes in chimpanzee, suggesting a faster Y degrading process in the chimp than in the other lineages (Goto et al J Mol Evol 2009)

• Most of the gametologues present on the human Y are found in the youngest strata (3 and 4) of the X

• This indicates that the older strata are genetically degenerated and have lost most of the genes that were once on the Y

Lahn & Page Science 1999

The Y chromosome determines the male sex, regardless of which other chromosomes are present

Female development: « default pathway »

AT CONTRARY:

The X chromosome is gene-rich, and notably with an over-representation of genes involved in sex, reproduction, and cognitive (“intelligence genes”) functions.

IN FACT,

Rapid Selection for: - male-advantage recessive mutations on the X chromosome (hemizygous males)

- female-advantage dominant mutations on the X chromosome (ratio 2:1)

The Y chromosome is a by-product of perverse evolution leading to its degeneration

BUT…

In Vertebrates, sex is determined by many different strategies

Environmental Sex Determination

Genetic Sex Determination

Z W

X Y

Z Z

Male heterogametic:

X X

Female heterogametic :

Nile Tilapia

Baroiller & D’Cotta Comp Biochem Phys C 2001

XX/XY species

But temperature induces sex reversal

Platyfish

Polyfactorial Genetic Sex Determination

Females: XX, XW or ZWMales: XY or YY

Volff & Schartl Genetica 2001

Silverside

Conover et al Evolution 1992

sp. with Genetic SDsp. with Environmental SDsp. hermaphrodite

Stickleback

Ross et al PLoS Genet 2009

sp. with XX/XYsp. with ZZ/ZW

In the Japanese frog, some populations are XY and others ZW

The XY pair switched into a ZW pair

Rana rugosa

Uno et al Chrom Res 2008

Pogona vitticeps

Quinn et al Science 2007

Temperature induces sex reversal in a ZZ/ZW lizard

Pokorna & Kratochvil Zool J Linn Soc 2009

- Numerous transitions from TSD to GSD (but GSD > TSD ??)

- A few XY ZW

Sex determining systems mapped onto a molecular phylogeny of Squamates

All Therian mammals have the same sex chromosomes

Why?

Heteromorphic sex chromosomes, with a highly degraded and specialized Y chromosome, are a strong barrier to transitions between sex-determining systems.

And conversely, the lack of necessary Y-specific genes in neo-XX males

The potential adverse effects of Y-specific genes on the feminization process of neo-XY females

But some exceptions exist…

Due to formation of lethal genotypes (YY)

Vs.YY

YY

Murphy et al Genome Res 1999

The X and Y are extremely conserved

Any modifications generally lead to infertility/sterility

The X and Y are very ancient

- Human patients with Klinefelter syndrom (XXY) or Turner (XO)

X

X

5

Graves 1995 BioEssays

Origin of sex chromosomes in Mammals.Large-scale gene-mapping comparisons

Recent autosomal addition on the Eutherian X chromosome

2 Matsubara et al 2006 PNAS

X

1

12

4

Fridolfsson et al 1998 PNAS

Z

4

58

918

Nanda et al 1999 Nature Genet

Independent origin of sex chromosomes in mammals, birds, and snakes

Origin of sex chromosomes in Mammals.

Differentiation of mammalian X-Y started 310 Mya, just after mammal / reptile split (Lahn & Page Science 1999)

EutheriansMarsupialsMonotremes Birds Crocodilians TurtlesSnakesLizards

150mya245mya

270mya220mya

285mya310mya

165mya

ZWZW XY

XY

ZW

XY

ZW

XY

Amniote sex chromosomes systems Mammals

?

Monotremes: pivotal position for genomic comparisons/origin of mammal XY

…But their sex chromosome system remained a long mystery until recently

Rens et al PNAS 2004

X1 X4X2 Y2 Y3X3Y1 Y5X5Y4

Karyotype

10 sex chromosomes !! X1Y1X2Y2X3Y3X4Y4X5Y55 Ys: male-specific5 Xs: in pairs in female

Unprecedented sex chromosome system

Grutzner et al Nature 2004

An exceptional system (1)

5Xs 5Ys

Extraordinary meiotic chain:

absence SRY

X1 X4X2 Y2 Y3X3Y1 Y5X5Y4

orthologuesMammalian X

Watson et al PNAS 1990

An exceptional system (2)

Déterminisme du sexe inconnu

Grutzner et al Nature 2004 El Morghabel et al Genomics 2007

DMRT1 gene Avian Z

X5DMRT1

X5DMRT1

Search for the sex determining switch in Monotremes

SRY absent

DAX115

DAX1

Mapped on autosomesSOX9, DAX1, SF1, WT1, etc…

DMRT1 X5, but in opposite dosage than in birds (2:1 in : )

BUT… On the pseudo-autosomal region (same dose between sexes)

Sex determining gene remains unknown

GATA4

GATA4GATA4X2

Y1/X2

Graphodatskaya et al Chrom Res 2007unpublished data

And the Echidna ?

Need a comparative sex chromosome map between Echidna and Platypus

Chromosome Painting allows to establish the chromosomal homologies according to the DNA content, by fluorescence in situ hybridization

Amplification by DOP-PCR

Labelling with fluorochrome

Chromosome probe

Flow-sorted chromosomes are separated

Pics are isolated

Human chromosome 1Human chromosome 19

Genomic comparison Human/Pangolin

Yang et al Chrom Res 2006

How does it work?

Sex chromosome system still evolved after platypus-echidna divergence

Echidna Y2

Echidna X5

Cross-species Chromosome Painting

Platypus X5 and Y5 are not the last chromosomes in echidna chain

Echidna = “only” 9 sex chromosomes

Rens et al. Genome Biol 2007


150mya245mya

270mya220mya

285mya310mya

165mya

ZWZW XY

XY

ZW

XY

ZW

XY

proto X-Y

Amniote sex chromosomes systems Mammals

A link between the bird ZW and mammal XY systems ?

Ezaz et al Current Biol 2006

Warren et al Nature 2008

Physical map of the platypus genome

correspondence « karyotype – genotype »

Y2

X2

X3

Platypus genome: a patchwork of mammalian, reptilian and avian characters

miRNAs

Some are shared with others mammals but not birds (mammal-specific), and others are bird-specific

Egg

- Only one vitellogenin gene, whereas chicken has 3, but other mammals 0- Formation of zona pellucida: 4 genes shared with other mammals + 2 ZPAX genes present only in birds, fishes, amphibians

Milk

Duplication/Cluster of 5 casein genes

Venom

Like in reptiles, cocktail of variations of 3 peptide families, but arose from duplications of different set of genes convergence with snake venom.

Comparative Genomic : Platypus – Human - Chicken

chicken Z human X

X1 X4X2 Y2 Y3X3Y1 Y5X5Y4 1 3 6 1815

Sex chrom autosomes

Veyrunes et al Genome Res 2008

Sex Chromosomes

the 10 sex chromosomes of the platypus(5 Xs and 5 Ys) had no gene homology with the “mammalian” XY,

while they did have substantial homology with the bird Z chromosome.


150mya245mya

270mya220mya

285mya310mya

165mya

ZWZW XY

XY

ZW

XY

ZW

XY

proto-Z-W

proto-X-Y 145My + jeune

MammalsSex chromosome evolution

Veyrunes et al Genome Res 2008

Z WGekko hokouensis

Kawai et al Chromosoma 2008

Is homology a relic of shared ancestry or just convergence?

Do particular portions of genome make better sex chromosomes?

Graves & Peichel Genome Biol 2010

DMRT1 is homolog of the genes doublesex in Drosophila and mab-3 in C. elegans, both involved in the downstream events of sex differentiation

Review in Ferguson-Smith Sex Dev 2007

In Vertebrates, DMRT1 is expressed specifically in male gonads just after sex determination

DMRT1 is a critical gene near the top of the sex determination cascade in both vertebrates and

invertebrates

Mutations on DMRT1 induce sex reversal in human

In addition to DMRT1 (birds) and SRY (mammals)

Sinclair et al Nature 1990

Smith et al Nature 2009

Only two other vertebrate sex determining genes are known:Both homologs of DMRT1 !

- DMY a duplicated copy of DMRT1 in the Medaka fishMatsuda et al. Nature 2002Nanda et al PNAS 2002

- DM-W a truncated copy of DMRT1 in the frog Xenopus laevis

Yoshimoto et al PNAS 2008

Repeated use of the same gene for sex determinationSome parts of the genome may make better sex chromosomes

Conclusions

The 10 platypus’ sex chromosomes do not share gene homology with the “mammal” X, but with the bird Z chromosome

Two independent sex chromosome systems among mammals

The human XY are 145My younger than previously thought. Consequences on rates of gene evolution and Y degeneration

Platypus genome: genomic features of two separate lineages (mammals and sauropsids) coexist in a single organism

Platypus sex determining gene remains unknown

Warren et al Nature 2008Veyrunes et al Genome Res 2008

Myopus schistocolor

Tokudaia osimensis

Ellobius lutescens

Microtus oregoni

Dicrostonyx torquatus

Ellobius tancrei

Akodon sp.

XX, XY / XYXO / XY

XO / XO

XX / XX

Mus minutoides

Biological Model:African pygmy mice

19 sp.Sub-Saharan Africa

Very low morphological differentiation (species-complexes)

Chromosomal radiation involving in particular the sex chromosomes

Genus : Mus (40 sp.)

Subgenera- Mus sensu stricto- Coelomys- Pyromys- Nannomys

Laboratory mouse

The sex chromosomes of the African pygmy mice show three extraordinary deviations from the norm:

Modifications of sex determination systems

Unusual meiotic behaviour

Addition of genetic material on the sex chromosomes (multiple sex-autosome fusions)

How these species manage to ensure a proper segregation is still under discussion

Unusual meiotic behaviour

During male meiosis, sex chromosomes must pair to ensure balanced gamete formation.

However, in a very few species, the sex chromosomes do not pair (asynaptic).

X

X

Y

Y

Mus mattheyi

Loss of the Pseudo-Autosomal Region ?

Mus minutoides

X Y

1 1

Multiple sex-autosome fusions

a paradox … Sex-autosome fusions :

rare and deleterious among the mammals

- Gametogenesis disruptions- Spreading of X-inactivation to autosome (silencing autosomal genes)

Y-autosome = azoospermiaX-autosome = sterility + other symptoms

(congenital malformations …)

Human pathologic cases:

X chromosome

autosome

Extremely diverse among the Nannomys

but…

11

X Y Y

X

77

1313

1616

X

Y

1 1XX

15 15

Genome modif/plasticity allowing a higher rate of appearance/fixation of these fusions

Multiple formations Neo-sex chromosomes

Veyrunes et al Chrom Res 2004, 2007

deleted X?

Y

Y mouse probe

Y

1 1

XY

X

1 1

Modification of sex determining systems (1)

Mus minutoides:

XY

XXXYVery high proportion of fertile sex-reversed females

Unexplained strong bias in favor of the XY females

Stellenbosch

Caledon NR

Kuruman Belfast

Willem Pretorius NR

Mutanda

Sterkfontein NRSandveld NR

MalesLocalities XY XX XYBelfast 0 1 0Caledon NR 11 0 10Kuruman 1 0 1Mutanda 2 0 1Sandveld NR 1 1 3Stellenbosch 3 4 3Sterkfontein NR 2 0 1Willem Pretorius NR 0 1 0Total 20 7 19

Females

1415 4

24 11 23

Veyrunes et al Proc R Soc B 2010


Novel sex determination system in a Therian species

SRY sequencing = male & female have the same haplotype

Sex reversal is probably not due to a mutation on SRY gene

Females are XX, XX* or X*Y, and Males only XY

Two morphologically different X chromosomes, one always associated to sex-reversed females

X X X* X*Y

female XX female XX* female X*Y

1

X

Y

male XY

… but rather on a X-linked mutation

Male XY Female XX Female XX* Female X*Yasterisk designates the still unknown mutation converting X*Y individuals into females

Veyrunes et al Proc R Soc B 2010

Identification of the Mutation

FIELD TRIPSTemporal survey in natural pop.

TEST ON CANDIDATE GENES


Evolutionary Processes: Impact on sex-ratio Population Dynamics, etc…

Reproductive Cost

Loss YY

+ ovulation?Meiotic drive?

BREEDING PROGRAMLitter sizes & Offspring sex-ratioConsequences on mating system ?


XX XX* X*Y

50% XX females50% XY males

25% XX females25% XX* females25% X*Y females25% XY males

25% XX* females25% X*Y females25% XY males25% dead embryos

1:1 3:1 2:1

Com

ple

x

meio

tic

con

fig

ura

tion

s

bivalent Ring of 4 Chain of 4

Y 113

16

X*16

13

11

X

1

XX

1

1

13

13

1616

X*

Selective pressures favouring such system?

Different fitness for each type of female?

Y

11

X

1

X

1

X

16

X*

16

X*

Sex

ch

rom

oso

mes

How could explain the high prevalence of X*Y females ?

In addition, in one pop., the X* has been translocated to another autosome

1

X* X*

16


Mus triton in Burundi has been described with an XO / XO sex chromosome system (Jotterand-Bellomo 1988)

Mus indutus, among five : three were XX, and two XO

In addition to the standard XX / XY, and the new sex determining system described here:

Maybe four different sex chromosome systems recorded within the African pygmy mice !!

But all new variants restricted to only one species

Evolutionary cul-de-sac species ?

Finally, a few mammal species have evolved to escape convention, and present aberrant sex chromosome

systems

sex chromosome evolution in vertebrates institut des sciences de levolution department genome team...

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