1. 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

2. 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 = 10 3 megabase (Mb) = 1,000,000 base pairs = 10 6 gigabase (Gb) = 1,000,000,000 = 10 9

3. SpeciesCommonGenome size name in bp phage 5.0 x 10 4 Escherichia coli 4.6 x 10 6 Saccharomyces cerevisiae Yeast 1.3 x 10 7 Caenorhabditis elegans A nematode 9.7 x 10 7 Drosophila melanogasterFruit fly 1.8 x 10 8 Homo sapiensHuman 3.0 x 10 9 Amphiuma speciesSalamander 7.6 x 10 10 Arabidopsis thalinaThale cress 1.4 x 10 8 Oryza sativaRice 4.2 x 10 8 Hordeum vulgareBarley 4.9 x 10 9 Triticum aestivumBreadWheat 1.6 x 10 10 The C-value paradox

4. 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

5. 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 Telomeres Centromere Types of DNA in a genome

6. 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

7. 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

8. 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)

9. 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 repeat CCAGGTGTACAAGT …………….ACTTGTACACCTGG GGTCCACATGTTCA …………….TGAACATGTGGACC

10. 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 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

11. 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

12. 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 Chiasma in meiosis Gametes

13. 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

14. Gene duplication and evolution The globin gene family    2  1 22 11 11  2  GG AA  1   Myoglobin Chromosome 16 Chromosome 11 Chromosome 22 The human globin gene family. 15 genes, two gene clusters

15. Myoglobin Alpha chains Zeta chains Epsilon chains Gamma chains Delta chains Beta chains 49 76 178 257 6 36 120 81 27 32 9 11 Numbers indicate the estimated number of DNA sequence changes along the given branch of a tree 500 450370 15050210 Date of divergence (mya) A phylogeny of the globins based on sequence data

16. 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.

17. 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

18. 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.

19. The Ancestry of Bread Wheat Triticum uratu Aegilops speltoides wild wheat X goat grass (AA, 2n = 14) (BB, 2n = 14) Triticum turgidum Aegilops tauschii Cultivated tetraploid wheat X goat grass (AA BB, 2n = 28) (DD, 2n = 14) Triticum aestivum hexaploid bread wheat (AA BB DD, 2n = 42) Endoreplication

20. Chromosomal Rearrangements Inversions a b c d e f g a b e d c f g Double break in chromosome Repair inverts the inner section

21. Chromosomal Rearrangements Translocations Heterozygous reciprocal translocation semisterile Homozygous reciprocal translocation fertile