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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
Species Common Genome size
name in bp
phage 5.0 x 104
Escherichia coli 4.6 x 106
Saccharomyces cerevisiae Yeast 1.3 x 107
Caenorhabditis elegans A nematode 9.7 x 107 Drosophila melanogaster Fruit fly 1.8 x 108 Homo sapiens Human 3.0 x 109 Amphiuma species Salamander 7.6 x 1010
Arabidopsis thalina Thale cress 1.4 x 108 Oryza sativa Rice 4.2 x 108 Hordeum vulgare Barley 4.9 x 109 Triticum aestivum BreadWheat 1.6 x 1010
The C-value paradox
Explaining the C-paradox
1- genomes differ in the amount of repetitive DNA
2- some species have more than 2 copies of each chromosomePolyploidy
Single or Low-Copy sequences -genes including promoters, exons and introns pseudogenes
Repetitive DNA (middle-repetitive and highly repetitive sequences)Multiple copy genesTelomeres- (CCCTAAA - repeated many times)Mobile elements
transposons and retrotransposons Simple sequence repeats or SSRs - short sequences of 1- 5 bp, repeated
AKA Microsatellites
Telomeres
Centromere
Types of DNA in a genome
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
Vertebrates
(CCCTAA) n …………….(TTAGGG) n
(GGGATT) n …………….(AATCCC) n
Stretches of repeated sequence at either end of each chromosome that facilitate accurate copying of the linear DNA molecule
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
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.
Inverted repeatCCAGGTGTACAAGT …………….ACTTGTACACCTGGGGTCCACATGTTCA …………….TGAACATGTGGACC
Retrotransposons
The copia retrotransposable element of Drosophila
17 base inverted repeats
Direct repeats of 267 bases
Coding sequence (5kb) with transposase, reverse transcriptase and RNase genes
1 Single stranded RNA copy is made2 Single stranded DNA copy is made using reverse transcriptase3 The RNA copy is removed using the RNase4 The DNA is made double stranded5 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.
Heterochromatin (regions of the chromosome that condense early in prophase) are mostly microsatellites.
Centromeres generally contain large tracts of microsatellites.
In replication, the number of repeats is not well copied because of slippage
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
A B C C
A B C
A B C
A B C
A B CA B C
A B C
Chiasmain meiosis Gametes
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 evolutionThe globin gene family
2
12
11
2 G A 1
Myoglobin
Chromosome 16
Chromosome 11
Chromosome 22
The human globin gene family. 15 genes, two gene clusters
Myoglobin
Alpha chains
Zeta chains
Epsilon chains
Gamma chains
Delta chains
Beta chains
49
76
178
257
6
36
120
81
27
32
9
11Numbers indicate the estimatednumber of DNA sequence changesalong the given branch of a tree
500 450 370 150 50210 Date of divergence(mya)
A phylogeny of the globins based on sequence data
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 effectThe 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 Aegilops speltoides wild wheat X goat grass(AA, 2n = 14) (BB, 2n = 14)
Triticum turgidum Aegilops tauschiiCultivated tetraploid wheat X goat grass (AA BB, 2n = 28) (DD, 2n = 14)
Triticum aestivumhexaploid bread wheat(AA BB DD, 2n = 42)
Endoreplication
Endoreplication
Chromosomal RearrangementsInversions
a b c d e f g
a b c d e f g
a b e d c f g
Double break in chromosome
Repair inverts the inner section
Chromosomal RearrangementsTranslocations
Heterozygousreciprocal
translocation
semisterile
Homozygousreciprocal
translocation
fertile