Download Comparative Genomics IV

Comparative Genomics in Eukaryotes
IV.
GENE 330
CHROMOSOMES
Chromosome Number
• Within species, the number of chromosomes is almost always an even multiple of a
basic number
• E.g. in humans the basic number is 23; mature eggs and sperm have this number of
chromosomes. Most other types of human cells have twice as many (46).
• The haploid, or basic chromosome number (n) defines a set of chromosomes called
the haploid genome
• Most somatic cells contain two of each the chromosomes in this set and are therefore
diploid (2n).
• The basic number of chromosomes varies among spicies.
• Chromosome number is not related to the size or biological complexity of an organism,
with most species containing between 10 and 40 chromosomes in their genomes
Numbers of Pairs of Chromosomes in Different Species of Plants and Animals
SEX-DETERMINATION SYSTEM
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A sex-determination system is a biological system that determines
the development of sexual characteristics in an organism.
Most sexual organisms have two sexes.
In many cases, sex determination is genetic: males and females have
different alleles or even different genes that specify their sexual
morphology.
In animals, this is often accompanied by chromosomal differences.
In other cases, sex is determined by environmental variables (such as
temperature) or social variables (the size of organism relative to other
members of its population).
The details of some sex-determination systems are not yet fully
understood.
NON-GENETIC SEX-DETERMINATION SYSTEMS
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In some species of reptiles, including alligators, some turtles, and the
tuatara, sex is determined by the temperature at which the egg is
incubated.
Other species, such as some snails, practice sex change; adults start
out male, then become female.
In tropical clown fish, the dominant individual in a group becomes
female while the other ones are male.
Some species have no sex-determination system. Earthworms and
some snails are hermaphrodites; a few species of lizard, fish, and
insect are all female and reproduce by parthenogenesis.
In some arthropods, sex is determined by infection, as when bacteria of
the genus Wolbachia alter their sexuality; some species consist entirely
of ZZ individuals (males), with sex determined by the presence of
Wolbachia.
EVOLUTION OF SEX CHROMOSOMES
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Sex chromosomes have arisen independently in many taxonomic
groups. It is an interesting question whether the same mechanisms
were involved each time.
Similarities in sex chromosome evolution have been reported between
birds and mammals (although in birds, females are the heterozygous
sex).
In one study has been uncovered striking parallels in the details of sex
chromosome evolution between mammals and a far more distant
group: plants!
The theory of sex chromosome evolution holds that sex chromosomes
were once homologs (a pair of equivalent autosomes) that evolved
different morphology and gene content because they lost their ability to
recombine.
Suppression of recombination is thought to start around the sexdetermining region, but may eventually affect much of the sex
chromosomes.
Recombination is a key genetic process in which two chromosomes
pair and exchange their sequences. In the absence of recombination,
the two chromosomes of a pair evolve separately.
EVOLUTION OF SEX CHROMOSOMES
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Sex chromosomes are an oddity in flowering plants. They are limited to
dioecious species, a subset of plants that carry male and female organs
on separate individuals (most flowering plants are hermaphrodites).
In some genus e.g. Silene , which include the White Campion, includes
both dioecious and hermaphrodite species.
The X and Y chromosomes of dioecious Silene species are
morphologically distinct, like those in mammals, and they also have a
PAR (pseudoautosomal region) and nonrecombining region.
CHROMOSOMAL DETERMINATION
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XX/XY sex chromosomes
In the XY sex-determination system individuals inheriting a Y chromosome
become males, and XX individuals females. The XY sex chromosomes
are different in shape and size from each other unlike the autosomes, and
are termed allosomes/heterochromosomes.
XX/X0 sex determination
In this variant of the XY system, XX individuals are females, and males are
X0 individuals. This system is observed in a number of insects, including
grasshoppers and crickets and in cockroaches.
The nematode C. elegans X0 is male and XX is a hermaphrodite.
ZW sex chromosomes
The ZW sex-determination system is found in birds and some insects.
System is reversed compare to the XY system - ZZ are males and ZW are
females.
Haplodiploidy
System is found in insects – Hymenoptera – such as ants and bees.
Unfertilized eggs develop into haploid males. Diploid individuals are
generally female but may be sterile males.
CHROMOSOMES Cont…
Sex Chromosomes
• In other animals, e.g. human beings, males and females have the same number of
chromosomes
X
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Y
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Y
EVOLUTION OF THE HUMAN SEX CHROMOSOMES
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The X and Y chromosomes of human and other mammalian species
are heteromorphic.
The human X chromosome is a submetacentric chromosome which
contains about 165 Mb of DNA, whereas the Y chromosome is
acrocentric and is much smaller – about 60 Mb of DNA.
The human X chromosome contains numerous important genes: on the
basis of its size alone, it might be expected to contain about 4000
genes.
The bulk of the Y chromosome is genetically inert and is composed of
constitutive heterochromatin consisting of different types of highly and
moderately repetitive noncoding DNA.
Only a very few functional genes are found on the Y chromosome,
including some which have closely related homologues on the X
chromosome. And several which are Y-specific and testis-expressed.
EVOLUTION OF THE HUMAN SEX CHROMOSOMES
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The X and Y chromosomes are able to pair during meiosis in male cells,
and to exchange sequence information. Sequence exchange occur within
certain small region of homology between X and Y chromosomes, known
as pseudoautosomal regions (PAR), which do not show strict sex-linked
inheritance.
In the human sex chromosomes, there are two PARs:
* The PAR1(the major pseudoautosomal region) extends over 2.6 Mb at
the extreme tips of the short arms of the X and Y chromosomes. It is the
site of an obligate crossover during male meiosis which is thought to be
required for correct meiotic segregation. This region is remarkable for its
high recombination frequency – approximately 10 times the normal
recombination frequency.
* The PAR2 (the minor pseudoautosomal region) extends over 320 kb at
the extreme tips of the long arms of the X and Y chromosomes.
Crossover between the X and Y in this region is not so frequent, and is
neither necessary for successful male meiosis.
GENES OUTSIDE PAR
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Although 95% of the Y chromosome lies between the PAR, fewer than
80 genes have been found here.
Over half of this region is genetically-barren heterochromatin.
Of the 80-odd genes found in the euchromatin , some encode proteins
used by all cells.
The others encode proteins that appear to function only in the testes.
A key player in this latter group is SRY.
SRY (for sex-determining region Y) is a gene located on short (p) arm
just outside the pseudoautosomal region. It is the master switch that
triggers the events that converts the embryo into a male.
Without this gene, you get a female instead. So femaleness is the
“default” program.
X-INACTIVATION
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X inactivation occurs early in embryonic development. In a given cell,
which of a female’s X chromosome becomes inactivated and converted
into a Barr body is a matter of chance (except in marsupials like a
kangaroo, where it is always the father’s X chromosome that is
inactivated).
After inactivation has occurred all the descendants of that cell will have
the same chromosome inactivated.
Thus X-inactivation creates clones with differing effective gene content.
An organism whose cells vary in effective gene content and hence in
the expression of a trait, is called a genetic mosaic.
MECHANISM OF X-INACTIVATION
Inactivation of an X chromosome requires a gene on that chromosome
called XIST.
 XIST encodes a large molecule of RNA
 XIST RNA accumulates along the X chromosome containing the active
XIST gene and proceeds to inactive all (or almost all) of the other
hundreds of genes on that chromosome.
 XIST RNA does not travel over to any other X chromosome in the
nucleus.
 Barr bodies are inactive X chromosomes “painted” with XIST RNA.
Bar body in a human female cell stained with cresyl violet
CHROMOSOMES Cont…
Sex Chromosomes
• In other animals, e.g. human beings, males and females have the same number of
chromosomes, due the presence of Y chromosome in males which pairs with X during
meiosis.
• The Y chromosome is morphologically distinct from the X chromosome. e.g. in humans
the Y chromosome is much shorter than X chromosome and its centromere is located
closer to one of the ends.
• The common regions to human X and Y chromosoms is at the extreme tips of the
arms(short and long) near the end of the chromosomes .
• During meiosis in the male, the X and Y chromosomes separate from each other
producing two kinds of sperm, X bearing and Y bearing; the frequencies of the two types
are approximately equal.
• XX females produce only one kind of egg, which is X-bearing.
• If fertilization were to occur randomly, approximately half the zygotes would be XX,
leading to 1:1 sex ratio at conception
CHROMOSOMES Cont…
Sex Chromosomes
• However, in humans, Y-bearing sperm have a fertilization advantage, and the zygotic
sex ratio is about 1.3 : 1.
• During development, the excess of males is diminished by differential viability of XX
and XY embryos, and at birth, males are only slightly more numerous than females (sex
ratio 1.07.1
• By the age of production, the excess of males is essentially eliminated and the sex
ratio is very close to 1:1.
• The X and Y chromosomes are called sex chromosomes and all other chromosomes
in the genome are called autosomes
CHROMOSOMES Cont…
Sex Chromosomes
• Some animals such as grasshoppers females have one or more chromosome than
males This extra chromosome is called the X chromosome
• Females of such chromosomes have 2 X chromosomes and males have only 1. Thus
males are cyctologically XX and males XO
• During meiosis in the female, the two X chromosomes pair and then separate,
producing eggs that contain a single X chromosome.
• In the males, the solitary X chromosome moves independently of all the other
chromosomes and is incorporated into half the sperm; the other half receive no X
chromosome
• Thus, the sperm and eggs unite, two kinds of zygotes are produced: XX, which develop
into females, and XO, which develop into males.
• In these animals, the reproductive mechanism preserves a 1:1 ratio of males to
females in these species
CHROMOSOMES Cont…
Sex Chromosomes
X
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O
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O