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