Genome Structure and Evolution 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

There are different classes of eukaryotic DNA based on sequence complexity. Which ones?

Reassociation Kinetics

3 Main Components in Eukaryotic Genomes

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 pg) 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 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

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 - errors in meiosis - can be triggered by Cochicine - Polyploids can not mate with diploids - Polyploids can become diploid by chromosome fusion (diploidization)

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) Simple sequence repeats or SSRs - short sequences of 1- 5 bp, repeated Microsatellites Centromers, Heterochromatin Mobile elements transposons and retrotransposons Telomeres Centromere

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

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.

Mobile DNA Moves within genomes Most of the moderately repeated DNA sequences found throughout higher eukaryotic genomes L1 LINE is ~5% of human DNA (~50,000 copies) Alu is ~5% of human DNA (>500,000 copies) Some encode enzymes that catalyze movement

Transposon derived repeats Long interspersed elements – LINEs Short interspersed elements - SINEs LTR (long terminal repeat) retrotransposons DNA transposons 45% or more of genome

4 million tranposable elements

DNA transposons Terminal inverted repeats Transposase 7 major classes Transposition doesn’t occur in humans anymore Horizontal transfer

Transposons The Ac transposable element of maize Inverted repeat 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.

Mechanisms of duplication Transposons Donor element Target Excision (cut) Integration (paste) DNA repair or

LTR (long terminal repeat) Flank viral retrotransposons and retroviruses Repeats contain genes necessary for movement and replication Retroviruses have acquired a coat protein gene Many fossils

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

LTR retrotransposons Donor element Target Transcription RNA 2nd strand synthesis Reverse transcription Integration (paste)

LINEs LINE1 – active Line2 – inactive Line 3 – inactive Many truncated inactive sequences

LINEs (non-LTR retrotransposons) Donor element Target Transcription Cleavage/insertion/reverse transcription RNA Integration (paste)

Exception – Alu elements Derived from signal recognition particle 7SL Does not share its 3’ end with a LINE Only active SINE in the human genome

Different regions of the genome differ in density of repeats Most LINEs accumulate in AT rich regions Alu elements accumulate in GC rich regions

Mouse: blue Human: red

CpG islands CpG is subject to methylation (and deamination). Most eukaryotes show less of this dinucleotide than base composition would indicate. Defined as regions of DNA of at least 200 bp in length that have a G+C content above 50% and above average CpG content. Used to help predict gene sequences, especially promoter regions. 27.000 in human genome

CpG -> CmpG -> TpG

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

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 1 2 1 1 2  G A 1   Myoglobin Chromosome 16 Chromosome 11 Chromosome 22

A phylogeny of the globins based on sequence data Myoglobin Alpha chains Zeta chains Epsilon chains Gamma chains Delta chains Beta chains 257 81 76 120 49 27 6 32 178 9 Numbers indicate the estimated number of DNA sequence changes along the given branch of a tree 36 11 Date of divergence (mya) 450 370 500 210 150 50

Changes in Chromosome Numbers Polyploidy- more than 2 copies of the haploid chromosomes 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

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 t(8; 14) translocation in Burkitt's lymphoma deregulates immunoglobulin t(4; 11) of acute childhood leukaemia resulting in an formation of ALL1 oncogene

Mouse-human synteni 342 segments

Fig. 1. Arrangement of duplicated protein-encoding genes in Oryza Paterson, A. H. et al. (2004) Proc. Natl. Acad. Sci. USA 101, 9903-9908 Copyright ©2004 by the National Academy of Sciences

Fig. 3. An early phylogenetic tree of genomic duplications for the angiosperms Paterson, A. H. et al. (2004) Proc. Natl. Acad. Sci. USA 101, 9903-9908 Copyright ©2004 by the National Academy of Sciences