GENOMES AND THEIR EVOLUTION - Weebly
GENETICSCHAPTER 21GENOMES AND THEIR EVOLUTIONDATE2013COURSEAP BIOLOGYTree of LifeComparisons of genomes provideinformation about the evolutionaryhistory of genes and taxonomic groupsGenomics - study of whole sets of genesand their interactionsBioinformatics - application ofcomputational methods to storage andanalysis of biological dataHuman Genome Project - officiallybegan in 1990 and was completed in2003ChromosomebandsCytogenetic mapGenes locatedby FISH1 Linkage mappingGeneticmarkers2 Physical mappingLinkage map - maps location ofgenes on each chromosome usingrecombination frequenciesPhysical map - expresses distancebetween genetic markers by cuttingup DNA and arranging them byoverlapping fragments1Overlappingfragments3 DNA sequencingTHREE-STAGEPROCESSFIG. 21.22Whole Genome/Shotgun ApproachSkips genetic andphysical mappingand sequencesrandom DNAfragments directlyPowerfulcomputerprograms areused to orderfragments into acontinuoussequence1 Cut the DNA intooverlapping fragments short enoughfor sequencing.2 Clone the fragmentsin plasmid or phagevectors.3 Sequence eachfragment.4 Order thesequences intoone overallsequencewith computersoftware.FIG. 21.33
BioinformaticsFIG. 21.4Many new resources sincecompletion of Human GenomeProjectMany nations have dataresources (National Library ofMedicine, NIH (NationalCenter for BiotechnologyInformation-NCBI), EuropeanMolecular Biology Laboratory,DNA Data Bank of Japan)NCBI doubles its databaseevery 18 months and provides3-D views of all proteinstructures that have beendetermined4ProteomicsStudy of all proteins encoded by a genomeFIG. 21.5Translation andribosomal nsVesiclefusionRNA processingPeroxisomalfunctionsTranscriptionand chromatinrelated functionsAmino acidpermease pathwayMetabolismand amino onand vesicletransportNuclear migrationand proteindegradationMitosisDNA replicationand repairSerinerelatedbiosynthesisCell polarity andmorphogenesisProtein folding,glycosylation, andcell wall biosynthesisFIG. 21.65GenomesGenomes vary in size, numberof genes and gene densityBy early 2010, over 1,200genomes were completelysequenced (mostly bacteria)Genomes of most bacteria arebetween 1-6 million base paris(Mb), plants are more than 100Mb, humans have 3,000 MbNo relationship betweengenome size number of genes(alternative splicing)Mammals (including humans)have the lowest gene density6
Multicellular EukaryotesMost of the eukaryoticgenome does not code forproteins or functional RNAs(98.5% of human genome isnoncoding)Exons (1.5%)Regulatorysequences( 20%)RepetitiveDNA thatincludestransposableelementsand relatedsequences(44%)Noncoding DNA plays animportant role in cellsPseudogenes - former genesthat have accumulatedmutations and arenonfunctionalIntrons (5%)L1sequences(17%)UniquenoncodingDNA (15%)RepetitiveDNAunrelated totransposableelements(14%)Alu elements(10%)Large-segmentduplications (5-6%)Simple sequenceDNA (3%)Repetitive DNA - present inmultiple copies in the genomeFIG. 21.77Transposable ElementsFirst evidence of mobile DNA segmentscame from research of BarbaraMcClintock breeding experiments withIndian cornShe identified changes in color of cornkernels that only made sense if geneticelements were moving from otherlocations into the genes for kernel colorThese transposable elements arepresent in both prokaryotes andeukaryotesTransposons - move via a DNAintermediateRetrotransposons - move via a RNAintermediateGenome EvolutionMutation is the basis for genomicevolutionAccidents in meiosis can lead toone or more extra sets ofchromosomes (polyploidy) whichcan allow for genes in one set todiverge and accumulatemutations which may persist iforganism reproducesNew copy oftransposonTransposonDNA ofgenomeTransposonis copiedInsertionMobile transposonRetrotransposonNew copy ofretrotransposonFormation of asingle-strandedRNA 1.821.108Humanchromosome e-likesequences13(a) Human and chimpanzee chromosomesHumanchromosome 16MousechromosomesCombining of chromosomes alsoshows evolutionary relationshipsGene duplication can be causedby unequal crossing over (Fig.21.13)781617(b) Human and mouse chromosomes9
HumanGlobinGenesAncestral globin geneFIG. 21.14Duplication ofancestral geneEvolutionary timeMutation inboth copiesαβTransposition todifferent chromosomesFurther duplicationsand mutationsαζζCaused bygeneduplicationandsubsequentmutationβαεψζ ψα ψα 1 α2 α1 ψθ2γGγεα-Globin gene familyon chromosome 16βAγψβδββ-Globin gene familyon chromosome 1110Exon Duplication andShufflingEGFEGFEGFEGFEpidermal growthfactor gene with multipleEGF exonsFFFFFibronectin gene with multiple“finger” n gene with a“kringle” exonPortions of ancestral genesExonshufflingFIG. 21.15TPA gene as it exists today11Transposable Elements’Contributions to EvolutionMultiple copies of similar elements may causerecombination or crossing over between chromosomesInsertion of a transposable element within a proteincoding sequence may block, increase, or decreaseprotein productionMay carry a gene or groups of genes to a new positionMay create new sites for alternative splicingChanges are usually detrimental but may proveadvantageous12
Comparing GenomesProvides clues ofevolutionary relationshipsBacteriaMost recentcommonancestorof all livingthingsComparing closely relatedspecies helpsunderstanding of recentevolutionary eventsEukaryaArchaea4132Billions of years agoAllows for correlation withphenotypic differences0ChimpanzeeHumanComparing distantly relatedspecies helpsunderstanding of ancientevolutionary eventsMouse706050403010200Millions of years agoHighly conserved geneschange little over timeFIG. 21.1613Ex. FOXP2Involved in vocalizationFIG. 21.17EXPERIMENTWild type: two normalcopies of FOXP2Heterozygote: onecopy of FOXP2disruptedHomozygote: bothcopies of FOXP2disruptedExperiment 1: Researchers cut thin sections of brain and stainedthem with reagents that allow visualization of brain anatomy in aUV fluorescence microscope.RESULTSExperiment 1Experiment 2: Researchers separatedeach newborn pup from its motherand recorded the number ofultrasonic whistles produced by thepup.Number of whistlesExperiment 2Wild )WildtypeHetero- Homozygote zygote14Evo-devoEvolutionary developmentalbiology studies the evolution ofdevelopmental processes inmulticellular organismsAnalysis of homeotic genes inDrosophila show that all includea sequence called a homeoboxwhich is identical or similar in allvertebrates and invertebratesHomeobox genes code for adomain that allows proteinsto bind to DNA astranscription regulatorsIn animals these homeoticgenes are called Hox genesAdultfruit flyFruit fly embryo(10 hours)Fly chromosomeMousechromosomesMouse embryo(12 days)Adult mouseFIG. 21.1815
CHAPTER 21 GENOMES AND THEIR EVOLUTION Comparisons of genomes provide Tree of Life 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 ana
Chapter 21: Genomes & Their Evolution 1. Sequencing & Analyzing Genomes 2. How Genomes Evolve. 1. Sequencing & Analyzing Genomes Chapter Reading – pp. 437-447. Whole Genome Shotgun Sequencing Cut the DNA into overlapping frag-ments short enough for sequencing. 1 Clone the fragments in plasmid or phage vectors. 2 Sequence each
C. sakazakii genomes was 4393kb, with an average of 4055 protein coding genes, and an average genome G C content of 56.9%. The genomes contained genes related to carbohydrate transport and metabolism, amino acid transport and metabolism, and cell wall/membrane biogenesis. In addition, we identified genes encoding proteins
So, what is functional genomics? Where sequence-based genomics looks at the structure and components of genomes, and analyses the similarities and differences between genomes Functional genomics looks at how genomes result in cellular phenotypes , and analyses di
Eukaryotic genomes contain vast amounts of repetitive DNA de-rived from transposable elements (TEs). Large-scale sequencing of these genomes has produced an unprecedented wealth of informa-tion about the origin, diversity, and genomic impact of what was once thought to be “junk DNA.” This has also led to the identifica-
genetic mechanisms that affect viruses. n We finish by looking at representative virus genomes to illustrate the . Because viruses are obligate intracellular parasites only able to replicate inside . genomes and to consider how
Chapter 21 Genomes and Their Evolution. Overview: Reading the Leaves from the Tree of Life Complete genome sequences exist for a human, chimpanzee, E. coli, brewer’s yeast, nematode, fruit fly, house mouse, rhesus macaque, among others – Comparisons of
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