sex chromosome evolution in vertebrates institut des sciences de levolution department genome team...
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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
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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.
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1
109 1186
2 3 4 5
12
15
7
1413 16 1817
19 222120 X Y
XY X X
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X and Y chromosomes evolved from an ancestral pair of
autosomes
SRY
proto-X -Y X Y
X > 1000 genes
Y >45 genes (SRY)
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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)
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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)
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• 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
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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…
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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 :
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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
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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
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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
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All Therian mammals have the same sex chromosomes
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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
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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)
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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
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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
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Origin of sex chromosomes in Mammals.
Differentiation of mammalian X-Y started 310 Mya, just after mammal / reptile split (Lahn & Page Science 1999)
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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
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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.
![Page 21: Sex chromosome evolution in Vertebrates Institut des Sciences de lEvolution Department Genome Team Sex & Speciation CNRS / University Montpellier 2 Frédéric](https://reader035.vdocuments.site/reader035/viewer/2022062421/56649b5b550346318e8db510/html5/thumbnails/21.jpg)
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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
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Grutzner et al Nature 2004
An exceptional system (1)
5Xs 5Ys
Extraordinary meiotic chain:
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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
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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
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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
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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?
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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
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EutheriansMarsupialsMonotremes Birds Crocodilians TurtlesSnakesLizards
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
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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.
![Page 32: Sex chromosome evolution in Vertebrates Institut des Sciences de lEvolution Department Genome Team Sex & Speciation CNRS / University Montpellier 2 Frédéric](https://reader035.vdocuments.site/reader035/viewer/2022062421/56649b5b550346318e8db510/html5/thumbnails/32.jpg)
Warren et al Nature 2008
Physical map of the platypus genome
correspondence « karyotype – genotype »
Y2
X2
X3
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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.
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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
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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.
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EutheriansMarsupialsMonotremes Birds Crocodilians TurtlesSnakesLizards
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
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Is homology a relic of shared ancestry or just convergence?
Do particular portions of genome make better sex chromosomes?
Graves & Peichel Genome Biol 2010
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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
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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
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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
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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.
![Page 43: Sex chromosome evolution in Vertebrates Institut des Sciences de lEvolution Department Genome Team Sex & Speciation CNRS / University Montpellier 2 Frédéric](https://reader035.vdocuments.site/reader035/viewer/2022062421/56649b5b550346318e8db510/html5/thumbnails/43.jpg)
Myopus schistocolor
Tokudaia osimensis
Ellobius lutescens
Microtus oregoni
Dicrostonyx torquatus
Ellobius tancrei
Akodon sp.
XX, XY / XYXO / XY
XO / XO
XX / XX
Mus minutoides
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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
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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)
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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
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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
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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
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Modification of sex determining systems (2)
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
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Identification of the Mutation
FIELD TRIPSTemporal survey in natural pop.
TEST ON CANDIDATE GENES
Modification of sex determining systems (3)
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 ?
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Modification of sex determining systems (4)
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
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Modification of sex determining systems (5)
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 !!
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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