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Genes and Evolution
Genome Structure and Evolution
The C-value paradox- differences in genome size
Types of DNA- genes, pseudogenes and repetitive DNA
Gene duplication- The importance of pseudogenes in evolution
and diversity
Changes in chromosome number- polyploidy, chromosome
abnormalities
Chromosomal rearrangements- Inversions and translocations
The C-value paradox
Among multicellular eukaryotes, the size of the genome varies
enormously, and cannot be explained by differences in the number
of functional genes
Units of Genome size
C-vaule is the weight of the genome (in g)
Length is measured in base pairs
kilobase (kb) =
1,000 base pairs =
103
megabase (Mb) = 1,000,000 base pairs = 106
gigabase (Gb) = 1,000,000,000 =
109
The C-value paradox
Species
Common
name
Genome size
in bp
 phage
5.0 x 104
Escherichia coli
4.6 x 106
Saccharomyces cerevisiae
Yeast
1.3 x 107
Caenorhabditis elegans
Drosophila melanogaster
Homo sapiens
Amphiuma species
A nematode
Fruit fly
Human
Salamander
9.7 x 107
1.8 x 108
3.0 x 109
7.6 x 1010
Arabidopsis thalina
Oryza sativa
Hordeum vulgare
Triticum aestivum
Thale cress
Rice
Barley
BreadWheat
1.4 x 108
4.2 x 108
4.9 x 109
1.6 x 1010
Explaining the C-paradox
1- genomes differ in the amount of repetitive DNA
2- some species have more than 2 copies of each chromosome
Polyploidy
Types of DNA in a genome
Single or Low-Copy sequences -genes including promoters, exons and introns
pseudogenes
Repetitive DNA (middle-repetitive and highly repetitive sequences)
Multiple copy genes
Telomeres- (CCCTAAA - repeated many times)
Mobile elements
transposons and retrotransposons
Simple sequence repeats or SSRs - short sequences of 1- 5 bp, repeated
AKA Microsatellites
Centromere
Telomeres
Multiple copy genes
A few genes are present in multiple copies, principally because the
cell needs a lot of the gene-product
e.g.
Ribosomal RNA genes are arranged in large clusters, and organisms
have many copies of each (200 in humans)
Histone genes have multiple copies
Telomeres
Stretches of repeated sequence at either end of each chromosome
that facilitate accurate copying of the linear DNA molecule
Vertebrates
(CCCTAA) n …………….(TTAGGG) n
(GGGATT) n …………….(AATCCC) n
Arabidopsis
(CCCTAAA) n ………….(TTTAGGG) n
(GGGATTT) n ………….(AAATCCC)n
Transposons and retrotranposons
Mobile DNA elements that can move from one place to another
(transposons) or can increase in copy number via the production
of an RNA intermediate followed by insertion of a DNA copy
into the genome (retrotransposon)
Transposons
The Ac transposable element of maize
11-bp inverted
repeats
Exons of
transposase gene
Introns
Inverted repeat
CCAGGTGTACAAGT …………….ACTTGTACACCTGG
GGTCCACATGTTCA …………….TGAACATGTGGACC
A transposon can move at random throughout a plant genome. It is
cut out of its site and reinserted into another site by the action of a
transposase which it itself encodes.
Retrotransposons
The copia retrotransposable element of Drosophila
Coding sequence (5kb) with transposase, reverse transcriptase
and RNase genes
17 base
inverted repeats
Direct repeats of 267 bases
1 Single stranded RNA copy is made
2 Single stranded DNA copy is made using reverse transcriptase
3 The RNA copy is removed using the RNase
4 The DNA is made double stranded
5 The double stranded DNA is inserted using the transposase
Simple Sequence Repeats
(microsatellite DNA)
Short sequences (1-5 bases), sometimes in tandem, repeated
many times and often widely distributed over the genome.
Eg. (AT)n, (GAT)n,
(CTACTA)n
25% of the DNA of one crab species is AT repeats.
In replication, the number of repeats is not well copied because
of slippage
Heterochromatin (regions of the chromosome that condense early
in prophase) are mostly microsatellites.
Centromeres generally contain large tracts of microsatellites.
Gene Duplication
Gene duplication occurs by two quite different processes
One is duplication of large parts or whole chromosomes or even
the whole genome (this last process is polyploidy)
The other is the duplication of short sections of sequence
presumably due to mistakes in recombination. Unequal
crossing over
A B C
A B
A B
C
C
A B
CC
A B
Chiasma
in meiosis
A B
A B
C
C
Gametes
A B
C
Gene Duplication
Gene duplication leads to multiple copies of genes
Some of these are free to mutate
Mutation will normally lead to loss of function- to pseudogenes
Rarely, mutations in duplicate genes or pseudogenes produces
novel, useful, products. These are new genes
Accumulated gene duplications leads to gene clusters
Gene duplication and evolution
The globin gene family
The human globin gene family. 15 genes, two gene clusters
2
2 1
 1 1

2 
G A
1
 
Myoglobin
Chromosome 16
Chromosome 11
Chromosome 22
A phylogeny of the globins based on sequence data
257
81
Myoglobin
Alpha chains
76
120
49
Zeta chains
27
Epsilon chains
32
Gamma chains
6
178
Numbers indicate the estimated
number of DNA sequence changes
along the given branch of a tree
500
450
370
9
Delta chains
11
Beta chains
36
210
150
50 Date of divergence
(mya)
Changes in Chromosome Numbers
Polypoidy- more than 2 copies of the haploid chromosomes
Euploidy- containing a chromosome number that is a multiple of
the haploid number
Aneuploidy- extra or fewer copies of one chromosome or part of
a chromosome
Dosage effect
The more copies of genes there are, the
greater the dosage
Balanced changes in gene dosage are
generally OK. Unbalanced are not.
Polyploidy is important in plant evolution
Chrysanthemum species illustrate the phenomenon
Monoploid number (the basic set) = 9 chromosomes
In Chrysanthemum species, the number of chromosomes found
fall into 5 categories.
18 chromosomes = diploid (2 copies of the monoploid)
36 chromosomes = tetrapoid (4 copies of the monoploid)
54 chromosomes = hexapoid (6 copies of the monoploid)
72 chromosomes = octaploid (8 copies of the monploid)
90 chromosomes = decaploid (10 copies of the monoploid)
50% of flowering plants are polyploid
Polyploidy is important in plant evolution
A tetraploid can be formed by failure of chromosomal separation
in either mitosis or meiosis (endoreplication) and this can result
in a new, autopolyploid species (one that has more than 2 copies
of each chromosome of the ancestral diploid).
Hybridisation between two closely related plant species
occasionally results in an new allopolyploid species. This requires
endoreplication, after hybridisation.
The Ancestry of Bread Wheat
Triticum uratu
wild wheat
(AA, 2n = 14)
X
Aegilops speltoides
goat grass
(BB, 2n = 14)
Endoreplication
Triticum turgidum
Cultivated tetraploid wheat
(AA BB, 2n = 28)
X
Aegilops tauschii
goat grass
(DD, 2n = 14)
Endoreplication
Triticum aestivum
hexaploid bread wheat
(AA BB DD, 2n = 42)
Chromosomal Rearrangements
Inversions
a b
c
d
e
f
g
Double break in chromosome
a b
c
d
e
f
g
Repair inverts the inner section
a b
e
d
c
f
g
Chromosomal Rearrangements
Translocations
Heterozygous
reciprocal
translocation
Homozygous
reciprocal
translocation
semisterile
fertile