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Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 21.1 Chapter 21 Genomes and their Evolution.

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Presentation on theme: "Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 21.1 Chapter 21 Genomes and their Evolution."— Presentation transcript:

1 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 21.1 Chapter 21 Genomes and their Evolution

2 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Overview: Reading the Leaves from the Tree of Life Genome sequences exist human, chimpanzee, E. coli, brewers yeast, corn, fruit fly, house mouse, rhesus macaque, ………. Provides information about the evolutionary history of genes and taxonomic groups © 2011 Pearson Education, Inc.

3 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Genomics is the study of whole sets of genes and their interactions Bioinformatics is the application of computational methods to the storage and analysis of biological data © 2011 Pearson Education, Inc.

4 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Genome Sequencing Human Genome Project began in 1990 largely completed by stages – Genetic (or linkage) mapping – Physical mapping – DNA sequencing © 2011 Pearson Education, Inc.

5 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Linkage Mapping maps location of several thousand genetic markers on each chromosome genetic marker gene or other identifiable DNA sequence Recombination frequencies used to determine the order & relative distances between genetic markers © 2011 Pearson Education, Inc.

6 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure Cytogenetic map Genes located by FISH Chromosome bands

7 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure Cytogenetic map Genes located by FISH Chromosome bands Linkage mapping Genetic markers 1

8 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure Cytogenetic map Genes located by FISH Chromosome bands Linkage mapping Genetic markers 1 Physical mapping 2 Overlapping fragments

9 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure Cytogenetic map Genes located by FISH Chromosome bands Linkage mapping Genetic markers 1 Physical mapping 2 Overlapping fragments DNA sequencing3

10 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Physical Map distance between genetic markers, (number of bp) Constructed by cutting DNA molecule into short fragments and arranging them in order by identifying overlaps © 2011 Pearson Education, Inc.

11 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Sequencing determines the complete nucleotide sequence of each chromosome Human genome = 3.2 billion bp © 2011 Pearson Education, Inc.

12 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Whole-Genome Shotgun Approach to Genome Sequencing Developed by J. Craig Venter (1992) Skips genetic and physical mapping and sequences random DNA fragments directly Powerful computer programs are used to order fragments © 2011 Pearson Education, Inc.

13 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Cut the DNA into overlapping frag- ments short enough for sequencing. 1 Clone the fragments in plasmid or phage vectors. 2 Figure

14 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Cut the DNA into overlapping frag- ments short enough for sequencing. 1 Clone the fragments in plasmid or phage vectors. 2 Sequence each fragment. 3 Figure

15 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Cut the DNA into overlapping frag- ments short enough for sequencing. 1 Clone the fragments in plasmid or phage vectors. 2 Sequence each fragment. 3 Order the sequences into one overall sequence with computer software. 4 Figure

16 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 3-stage process and shotgun used for the Human Genome Project and for genome sequencing of other organisms Newer sequencing techniques massive increases in speed and decreases in cost $3,000,000, $1, © 2011 Pearson Education, Inc.

17 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Metagenomics environmental sample is sequenced Eliminates need to culture species in the lab © 2011 Pearson Education, Inc.

18 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Using bioinformatics to analyze genomes and their functions The Human Genome Project has accelerated progress in DNA sequence analysis © 2011 Pearson Education, Inc.

19 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Centralized Resources for Analyzing Genome Sequences – National Library of Medicine and the National Institutes of Health (NIH) created the National Center for Biotechnology Information (NCBI) – BGI in Shenzhen, China – European Molecular Biology Laboratory – DNA Data Bank of Japan © 2011 Pearson Education, Inc.

20 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Genbank, the NCBI database of sequences, doubles its data approximately every 18 months Software is available that allows online visitors to search Genbank for matches to – A specific DNA sequence – A predicted protein sequence – Common stretches of amino acids in a protein The NCBI website also provides 3-D views of all protein structures that have been determined © 2011 Pearson Education, Inc.

21 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 21.4

22 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Identification of protein coding genes within DNA sequences in a database is called gene annotation Comparison of unknown genes to known genes in other species provides clues about function © 2011 Pearson Education, Inc.

23 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Proteomics systematic study of all proteins encoded by a genome © 2011 Pearson Education, Inc.

24 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Translation and ribosomal functions Nuclear- cytoplasmic transport RNA processing Transcription and chromatin- related functions Mitochondrial functions Nuclear migration and protein degradation Mitosis DNA replication and repair Cell polarity and morphogenesis Protein folding, glycosylation, and cell wall biosynthesis Secretion and vesicle transport Metabolism and amino acid biosynthesis Peroxisomal functions Glutamate biosynthesis Serine- related biosynthesis Amino acid permease pathway Vesicle fusion Figure 21.5 Systems biology approach define gene circuits and protein interaction networks

25 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 21.5a Translation and ribosomal functions Nuclear- cytoplasmic transport RNA processing Transcription and chromatin- related functions Mitochondrial functions Nuclear migration and protein degradation Mitosis DNA replication and repair Cell polarity and morphogenesis Protein folding, glycosylation, and cell wall biosynthesis Secretion and vesicle transport Metabolism and amino acid biosynthesis Peroxisomal functions

26 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Glutamate biosynthesis Serine- related biosynthesis Amino acid permease pathway Vesicle fusion Metabolism and amino acid biosynthesis Figure 21.5b

27 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Systems Biology in Medicine – The Cancer Genome Atlas project is currently seeking all the common mutations in three types of cancer by comparing gene sequences and expression in cancer versus normal cells – Silicon and glass chips have been produced that hold a microarray of most known human genes © 2011 Pearson Education, Inc.

28 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 21.6

29 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Genomes By early 2010, 1,200 genomes were completely sequenced, including 1,000 bacteria, 80 archaea, and 124 eukaryotes Sequencing of over 5,500 genomes and over 200 metagenomes is currently in progress © 2011 Pearson Education, Inc.

30 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Genome Size Bacteria and archaea 1 to 6 million base pairs (Mb) Plant & animal greater than 100 Mb; humans 3,000 Mb Within each domain there is no systematic relationship between genome size and phenotype © 2011 Pearson Education, Inc.

31 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Table 21.1

32 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Number of Genes Bacteria and archaea have 1,500 to 7,500 genes Eukaryotes from 40,000 genes © 2011 Pearson Education, Inc.

33 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Number of genes is not correlated to genome size Vertebrate genomes can produce more than one polypeptide per gene because of alternative splicing of RNA transcripts © 2011 Pearson Education, Inc.

34 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Multicellular eukaryotes have much noncoding DNA and many multigene families Previously called junk DNA plays important roles in the cell © 2011 Pearson Education, Inc.

35 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Sequencing of the human genome reveals that 98.5% does not code for proteins, rRNAs, or tRNAs © 2011 Pearson Education, Inc.

36 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings About 25% of the human genome introns and gene-related regulatory sequences (5%) Intergenic DNA is noncoding DNA found between genes – Pseudogenes are former genes that have accumulated mutations and are nonfunctional – Repetitive DNA is present in multiple copies in the genome © 2011 Pearson Education, Inc.

37 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings About three-fourths of repetitive DNA is made up of transposable elements © 2011 Pearson Education, Inc.

38 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 21.7 Exons (1.5%) Introns (5%) Regulatory sequences ( 20%) Unique noncoding DNA (15%) Repetitive DNA unrelated to transposable elements (14%) Large-segment duplications (5 6%) Simple sequence DNA (3%) Alu elements (10%) L1 sequences (17%) Repetitive DNA that includes transposable elements and related sequences (44%)

39 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Transposable Elements First evidence came from geneticist Barbara McClintocks breeding experiments with Indian corn Identified changes in the color of kernels that made sense only by mobile genetic elements Present in both prokaryotes and eukaryotes © 2011 Pearson Education, Inc.

40 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 21.8

41 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 21.9 Transposon Transposon is copied DNA of genome Mobile transposon Insertion New copy of transposon

42 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure Retrotransposon New copy of retrotransposon Insertion Reverse transcriptase RNA Formation of a single-stranded RNA intermediate

43 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Sequences Related to Transposable Elements In primates, a large portion are a family called Alu elements Function, if any, is unknown © 2011 Pearson Education, Inc.

44 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Other Repetitive DNA, Including Simple Sequence DNA Many copies of tandemly repeated short sequences Series of repeating units of 2 to 5 nucleotides is called a short tandem repeat (STR) © 2011 Pearson Education, Inc.

45 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Genes and Multigene Families Collections of identical or very similar genes © 2011 Pearson Education, Inc.

46 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure DNA RNA transcripts Nontranscribed spacer Transcription unit DNA 18S 5.8S 28S 5.8S 18S (a) Part of the ribosomal RNA gene family - Globin -Globin gene family Chromosome 16 -Globin gene family Chromosome 11 - Globin Heme G A (b) The human -globin and -globin gene families Embryo Fetus and adult Fetus Adult rRNA Embryo

47 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Duplication, rearrangement, and mutation of DNA contribute to genome evolution Earliest forms of life minimal number of genes, (only those necessary for survival and reproduction) Size of genomes has increased over evolutionary time, (extra genetic material raw material for gene diversification) © 2011 Pearson Education, Inc.

48 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Alterations of Chromosome Structure Humans have 23 pairs of chromosomes, while chimpanzees have 24 pairs 2 ancestral chromosomes fused in the human line © 2011 Pearson Education, Inc.

49 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure Human chromosome 2 Telomere sequences Centromere sequences Chimpanzee chromosomes 12 Telomere-like sequences Centromere-like sequences Human chromosome (a) Human and chimpanzee chromosomes(b) Human and mouse chromosomes Mouse chromosomes

50 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Evolution of Genes with Related Functions: The Human Globin Genes Globin genes evolved from common ancestral globin gene, which duplicated and diverged about 450–500 mya Differences arose from accumulation of mutations © 2011 Pearson Education, Inc.

51 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure Ancestral globin gene -Globin gene family on chromosome 16 -Globin gene family on chromosome 11 Duplication of ancestral gene Mutation in both copies Transposition to different chromosomes Further duplications and mutations Evolutionary time G A

52 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Evolution of Genes with Novel Functions Some duplicated genes have diverged so much that the functions of encoded proteins are now very different e.g. lysozyme gene was duplicated and evolved into the gene that encodes α-lactalbumin in mammals (milk production role) © 2011 Pearson Education, Inc.

53 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Rearrangements of Parts of Genes: Exon Duplication and Exon Shuffling Has contributed to genome evolution Mixing and matching of exons © 2011 Pearson Education, Inc.

54 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Exon duplication Exon shuffling Exon shuffling FEGFK K K FFFF Epidermal growth factor gene with multiple EGF exons Fibronectin gene with multiple finger exons Plasminogen gene with a kringle exon Portions of ancestral genes TPA gene as it exists today Figure 21.15

55 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings How Transposable Elements Contribute to Genome Evolution Multiple copies of similar transposable elements may facilitate recombination, or crossing over, between different chromosomes Insertion of transposable elements within a protein-coding sequence may block protein production Insertion of transposable elements within a regulatory sequence may increase or decrease protein production © 2011 Pearson Education, Inc.

56 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Transposable elements may carry a gene or groups of genes to a new position Transposable elements may also create new sites for alternative splicing in an RNA transcript In all cases, changes are usually detrimental but may on occasion prove advantageous © 2011 Pearson Education, Inc.

57 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Comparing genome sequences provides clues to evolution and development Genome comparisons of closely related species help us understand recent evolutionary events Genome comparisons of distantly related species help us understand ancient evolutionary events Relationships among species can be represented by a tree-shaped diagram © 2011 Pearson Education, Inc.

58 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Most recent common ancestor of all living things Bacteria Eukarya Archaea Chimpanzee Human Mouse Millions of years ago Billions of years ago Figure 21.16

59 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Comparing Distantly Related Species Highly conserved genes have changed very little over time Clarify relationships among species Bacteria, archaea, and eukaryotes diverged from each other between 2 and 4 billion years ago Results from model organisms applied to other organisms © 2011 Pearson Education, Inc.

60 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Comparing Closely Related Species Human and chimpanzee genomes differ by 1.2%, at single base-pairs, and by 2.7% because of insertions and deletions Several genes are evolving faster in humans than chimpanzees These include genes involved in defense against malaria and tuberculosis, regulation of brain size, and genes that code for transcription factors © 2011 Pearson Education, Inc.

61 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Humans and chimpanzees differ in the expression of the FOXP2 gene, (vocalization gene) May explain why humans but not chimpanzees communicate by speech © 2011 Pearson Education, Inc.

62 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Comparing Genomes Within a Species Human species only 200,000 years old low within-species genetic variation Variation due to single nucleotide polymorphisms, inversions, deletions, and duplications Variations useful for studying human evolution and human health © 2011 Pearson Education, Inc.

63 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Comparing Developmental Processes Evolutionary developmental biology, or evo-devo, is the study of the evolution of developmental processes in multicellular organisms Minor differences in gene sequence or regulation can result in striking differences in form © 2011 Pearson Education, Inc.

64 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Widespread Conservation of Developmental Genes Among Animals Molecular analysis of the homeotic genes in Drosophila has shown that they all include a sequence called a homeobox An identical or very similar nucleotide sequence has been discovered in the homeotic genes of both vertebrates and invertebrates Homeobox genes code for a domain that allows a protein to bind to DNA and to function as a transcription regulator Homeotic genes in animals are called Hox genes © 2011 Pearson Education, Inc.

65 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure Adult fruit fly Fruit fly embryo (10 hours) Fly chromosome Mouse chromosomes Mouse embryo (12 days) Adult mouse

66 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 21.18a Adult fruit fly Fruit fly embryo (10 hours) Fly chromosome

67 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 21.18b Mouse chromosomes Mouse embryo (12 days) Adult mouse

68 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Related homeobox sequences have been found in regulatory genes of yeasts, plants, and even prokaryotes In addition to homeotic genes, many other developmental genes are highly conserved from species to species © 2011 Pearson Education, Inc.

69 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Sometimes small changes in regulatory sequences of certain genes lead to major changes in body form For example, variation in Hox gene expression controls variation in leg-bearing segments of crustaceans and insects In other cases, genes with conserved sequences play different roles in different species © 2011 Pearson Education, Inc.

70 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure ThoraxAbdomen Genital segments Thorax Abdomen

71 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Comparison of Animal and Plant Development In both plants and animals, development relies on a cascade of transcriptional regulators turning genes on or off in a finely tuned series Molecular evidence supports the separate evolution of developmental programs in plants and animals Mads-box genes in plants are the regulatory equivalent of Hox genes in animals © 2011 Pearson Education, Inc.

72 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Archaea Most are 1 6 Mb Eukarya Genome size Number of genes Gene density Introns Other noncoding DNA Very little None in protein-coding genes Present in some genes Higher than in eukaryotes 1,500 7,500 5,000 40,000 Most are 10 4,000 Mb, but a few are much larger Lower than in prokaryotes (Within eukaryotes, lower density is correlated with larger genomes.) Unicellular eukaryotes: present, but prevalent only in some species Multicellular eukaryotes: present in most genes Can be large amounts; generally more repetitive noncoding DNA in multicellular eukaryotes Bacteria Figure 21.UN01

73 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Protein-coding, rRNA, and tRNA genes (1.5%) Human genome Introns and regulatory sequences ( 26%) Repetitive DNA (green and teal) Figure 21.UN02

74 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 21.UN03 -Globin gene family Chromosome 16 -Globin gene family Chromosome G A

75 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 21.UN04

76 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 21.UN05 Crossover point

77 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 21.UN06


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