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Evolution of the eukaryotic nuclear genome
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The nuclear genome of eukaryotes is thought to have initially evolved
as a mixture of archaeal genes (involved in information transfer) and
eubacterial genes (involved in metabolism and other basic cellular
functions).
As eukaryotes developed into complex multicellular organisms, the
number of genes and size of the nuclear genome increased and various
other properties were altered, notably the amount of repetitive DNA
and the fraction of coding DNA.
The transition from the DNA of a typical simple eukaryotic cell
precursor to the DNA of a mammalian cell is therefore thought to
have involved a huge increase in the size of the genome and a sizeable
increase in gene number and in the percentage of noncoding and
repetitive DNA.
Genetica per Scienze Naturali
a.a. 05-06 prof S. Presciuttini
Ancient genome duplication events
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Genome duplication (tetraploidization) is an effective way of
increasing genome size and is responsible for the extensive polyploidy
of many flowering plants. It can occur naturally when there is a failure
of cell division after DNA duplication, so that a cell has double the
usual number of chromosomes.
Human somatic cells are normally diploid. However, if there is a
failure of the first zygotic cell division, constitutional tetraploidy can
result. Tetraploidy and other forms of polyploidy can be harmful and
is often selected against.
However, whole genome duplication via polyploidy has undoubtedly
occurred relatively recently in maize, yeast, Xenopus and some types
of fish. It is likely therefore that genome duplication occurred several
times in the evolution of all eukaryotic lineages, including our own.
Genetica per Scienze Naturali
a.a. 05-06 prof S. Presciuttini
From diploidy to tetraploidy
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Following genome duplication, an initially diploid cell could have
undergone a transient tetraploid state; subsequent large-scale
chromosome inversions and translocations, etc., could result in
chromosome divergence and restore diploidy, but now with twice the
number of chromosomes
Following duplication of a diploid
genome, each pair of homologous
chromosomes (e.g. chromosome 1)
is now present as a pair of identical
pairs. The resulting tetraploid state,
however, can be restored to diploidy
by chromosome divergence, e.g. by
an interstitial deletion (upper panel,
a), a terminal deletion (lower panel,
c) or by an inversion (b)
Genetica per Scienze Naturali
a.a. 05-06 prof S. Presciuttini
Genome duplication in yeast
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By analysis of the locations of duplicated genes, it was proposed in 1997 that the
entire genome of S. cerevisiae became duplicated at some point in its evolutionary
past and subsequently sustained rearrangements and gene loss.
A recent analysis of gene order information from 14 hemiascomycetes, has
confirmed the hypothesis that S. cerevisiae is a degenerate polyploid. Using gene
order information alone, 70% of the S. cerevisiae genome were mapped into "sister"
regions that tiled together with almost no overlap. Combining gene order and gene
duplication data assigns essentially the whole genome into sister regions.
The 16 centromere regions of S. cerevisiae form eight pairs, indicating that an
ancestor with eight chromosomes underwent complete doubling. Gene arrangements
in Kluyveromyces lactis and four other species agree quantitatively with what would
be expected if they diverged from S. cerevisiae before its polyploidization. In
contrast, Saccharomyces exiguus, Saccharomyces servazzii, and Candida glabrata
show higher levels of gene adjacency conservation, and more cases of imperfect
conservation, suggesting that they split from the S. cerevisiae lineage after
polyploidization.
Genetica per Scienze Naturali
a.a. 05-06 prof S. Presciuttini
Allopolyploidy
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In plants, new genes can be acquired by polyploidization.
Allopolyploidy, which results from interbreeding between two
different species, is also common and, like autopolyploidy, can result
in a viable hybrid. Usually, the two species that form the allopolyploid
are closely related and have many genes in common, but each parent
will possess a few novel genes or at least distinctive alleles of shared
genes.
For example, the bread wheat, Triticum aestivum, is a hexaploid that
arose by allopolyploidization between cultivated emmer wheat, T.
turgidum, which is a tetraploid, and a diploid wild grass, Aegilops
squarrosa. The wild-grass nucleus contained novel alleles for the
high-molecular-weight glutenin genes which, when combined with the
glutenin alleles already present in emmer wheat, resulted in the
superior properties for breadmaking displayed by the hexaploid
wheats. Allopolyploidization can therefore be looked upon as a
combination of genome duplication and interspecies gene transfer.
Genetica per Scienze Naturali
a.a. 05-06 prof S. Presciuttini
Genome evolution in Triticum
The evolution of bread wheat is a
classic example of sympatric
speciation through allopolyploidy.
Modern wheat (Triticum aestivum) is a
hexaploid represented by AABBDD
(Figure 3.12). Its lineage can be traced
to the tetraploid wheat Triticum
dicoccum with an AABB genome that
is produced by the intergeneric cross
between the diploid wheat Triticum
monococcum (AA) and goat grass
Aegilops speltoides (BB). Later, a
second intergeneric cross between T.
dicoccum and Aegilops squarrosa, the
latter contributing the D genome,
occurred to produce modern bread
wheat.
Genetica per Scienze Naturali
a.a. 05-06 prof S. Presciuttini
Ancient tetraploidization events
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If ancient tetraploidization events were rare in the evolution of the
vertebrate genome, much intragenomic DNA shuffling would have
occurred since the last such event. This means that the original
evidence for tetraploidization events would be very largely obscured
by subsequent chromosomal inversions, translocations, etc.
Additionally, traces of gene duplication following genome duplication
are likely to be frequently reduced by silencing of one member of
each duplicated gene pair which then degenerates into a pseudogene.
After hundreds of millions of years without any function, the
nonprocessed pseudogenes generated following the last proposed
genome duplication would have diverged so much in sequence as to
be not recognizably related to the functional gene, even assuming they
have not been lost during occasional rearrangements leading to gene
deletion.
Genetica per Scienze Naturali
a.a. 05-06 prof S. Presciuttini
Patterns of paralogous genes
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Pattern Predicted for the
Relative Locations of
Paralogous Genes from Two
Genome Duplications
(A) Representation of a hypothetical genome that
has 22 genes shown as colored squares.
(B) A genome duplication generates a complete set
of paralogs in identical order.
(C) Many paralogous genes suffer disabling
mutations, become pseudogenes, and are then lost.
(D) A second genome duplication recreates another
set of paralogs in identical order, with multigene
families that retained two copies now present in
four, and those that had lost a member now present
in two copies.
(E) Again, many paralogous genes suffer disabling
mutations, become pseudogenes, and are then lost.
This leaves only a few four-member gene families,
but the patterns of 2- and 3-fold gene families
reveals that the sequential duplications had been of
very large regions.
Genetica per Scienze Naturali
a.a. 05-06 prof S. Presciuttini
Genome duplication events during vertebrate evolution
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In the case of vertebrates, two rounds of genome duplication have
been envisaged at an early stage of vertebrate evolution.
Gene numbers in different species have been taken to provide some
evidence for two rounds of tetraploidization in vertebrates:
invertebrates such as C. elegans, Drosophila and the sea squirt Ciona
intestinalis are estimated to have about 15 000–20 000 genes, about
one quarter that expected in mammalian genomes. In addition, many
single-copy Drosophila genes have four vertebrate homologues and
certain gene clusters appear to have been quadruplicated
Genetica per Scienze Naturali
a.a. 05-06 prof S. Presciuttini