CHAPTER 21 GENOMES AND THEIR EVOLUTION

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1 GENETICS DATE CHAPTER 21 GENOMES AND THEIR EVOLUTION COURSE 213 AP BIOLOGY 1 Comparisons of genomes provide information about the evolutionary history of genes and taxonomic groups Genomics - study of whole sets of genes and their interactions Bioinformatics - application of computational methods to storage and analysis of biological data Tree of Life Cytogenetic map 1 Linkage mapping Genes located by FISH Chromosome bands Genome Project - officially began in 199 and was completed in 23 2 Physical mapping Genetic markers Linkage map - maps location of genes on each chromosome using recombination frequencies Overlapping fragments Physical map - expresses distance between genetic markers by cutting up DNA and arranging them by overlapping fragments 3 DNA sequencing THREE-STAGE PROCESS FIG Whole Genome/Shotgun Approach Skips genetic and physical mapping and random DNA fragments directly 1 Cut the DNA into overlapping fragments short enough for sequencing. 2 Clone the fragments in plasmid or phage vectors. Powerful computer programs are used to order fragments into a continuous sequence 3 Sequence each fragment. 4 Order the into one overall sequence with computer software. FIG

2 Bioinformatics Many new resources since completion of Genome Project FIG Many nations have data resources (National Library of Medicine, NIH (National Center for Biotechnology Information-NCBI), European Molecular Biology Laboratory, DNA Data Bank of Japan) NCBI doubles its database every 18 months and provides 3-D views of all protein structures that have been determined 4 Proteomics Study of all proteins encoded by a genome FIG Glutamate Translation and ribosomal Mitochondrial Vesicle fusion Serinerelated RNA processing Transcription and chromatinrelated Nuclearcytoplasmic transport Nuclear migration and protein degradation Peroxisomal Metabolism and amino acid Secretion and vesicle transport Amino acid permease pathway Mitosis DNA replication and repair Cell polarity and morphogenesis Protein folding, glycosylation, and cell wall FIG Genomes Genomes vary in size, number of genes and gene density By early 21, over 1,2 genomes were completely sequenced (mostly bacteria) Genomes of most bacteria are between 1-6 million base paris (Mb), plants are more than 1 Mb, humans have 3, Mb No relationship between genome size number of genes (alternative splicing) Mammals (including humans) have the lowest gene density 6

3 Multicellular Eukaryotes Most of the eukaryotic genome does not code for proteins or functional RNAs (98.5% of human genome is noncoding) Noncoding DNA plays an important role in cells Pseudogenes - former genes that have accumulated mutations and are nonfunctional L1 (17%) Alu elements (1%) Repetitive DNA that includes transposable elements and related (44%) Simple sequence DNA (3%) s (1.5%) Introns (5%) Repetitive DNA unrelated to transposable elements (14%) Regulatory ( 2%) Unique noncoding DNA (15%) Large-segment duplications (5-6%) Repetitive DNA - present in multiple copies in the genome FIG Transposable Elements First evidence of mobile DNA segments came from research of Barbara McClintock breeding experiments with Indian corn She identified changes in color of corn kernels that only made sense if genetic elements were moving from other locations into the genes for kernel color These transposable elements are present in both prokaryotes and eukaryotes DNA of genome Transposon Transposon is copied Mobile transposon New copy of transposon Insertion Transposons - move via a DNA intermediate Retrotransposons - move via a RNA intermediate Retrotransposon Formation of a single-stranded RNA intermediate RNA Reverse transcriptase New copy of retrotransposon Insertion FIGS Genome Evolution Mutation is the basis for genomic evolution Accidents in meiosis can lead to one or more extra sets of (polyploidy) which can allow for genes in one set to diverge and accumulate mutations which may persist if organism reproduces chromosome 2 Telomere Centromere Telomere-like Centromere-like Chimpanzee 12 (a) and chimpanzee chromosome FIG Combining of also shows evolutionary relationships Gene duplication can be caused by unequal crossing over (Fig ) (b) and mouse 9

4 Globin Genes Evolutionary time Duplication of ancestral gene Mutation in both copies Transposition to different Further duplications and mutations ζ α Ancestral globin gene α α ε γ FIG Caused by gene duplication and subsequent mutation ζ ψ ζ ψ α 2 ψ α 1 α 2 α 1 α-globin gene family on chromosome 16 ψ θ ε G γ A γ ψ δ -Globin gene family on chromosome 11 1 Duplication and Shuffling EGF EGF EGF EGF Epidermal growth factor gene with multiple EGF exons F F F F Fibronectin gene with multiple finger exons shuffling duplication F EGF K K K Plasminogen gene with a kringle exon shuffling FIG Portions of ancestral genes TPA gene as it exists today 11 Transposable Elements Contributions to Evolution Multiple copies of similar elements may cause recombination or crossing over between Insertion of a transposable element within a proteincoding sequence may block, increase, or decrease protein production May carry a gene or groups of genes to a new position May create new sites for alternative splicing Changes are usually detrimental but may prove advantageous 12

5 Comparing Genomes Provides clues of evolutionary relationships Comparing closely related species helps understanding of recent evolutionary events Most recent common ancestor of all living things Billions of years ago 1 Bacteria Eukarya Archaea Allows for correlation with phenotypic differences Comparing distantly related species helps understanding of ancient evolutionary events Millions of years ago 1 Chimpanzee Highly conserved genes change little over time FIG Ex. FOXP2 FIG Involved in vocalization EXPERIMENT Wild type: two normal copies of FOXP2 Heterozygote: one copy of FOXP2 disrupted Homozygote: both copies of FOXP2 disrupted Experiment 1: Researchers cut thin sections of brain and stained them with reagents that allow visualization of brain anatomy in a UV fluorescence microscope. Experiment 2: Researchers separated each newborn pup from its mother and recorded the number of ultrasonic whistles produced by the pup. RESULTS Experiment 1 Experiment 2 Wild type Heterozygote Homozygote Number of whistles Wild type Heterozygote (No whistles) Homozygote 14 Evo-devo Evolutionary developmental biology studies the evolution of developmental processes in multicellular organisms Analysis of homeotic genes in Drosophila show that all include a sequence called a homeobox which is identical or similar in all vertebrates and invertebrates Homeobox genes code for a domain that allows proteins to bind to DNA as transcription regulators Adult fruit fly Fruit fly embryo (1 hours) Fly chromosome embryo (12 days) Adult mouse In animals these homeotic genes are called Hox genes FIG