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Genomes and their Evolution
Figure 21.1 Chapter 21 Genomes and their Evolution Figure 21.1 What genomic information distinguishes a human from a chimpanzee?
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Overview: Reading the Leaves from the Tree of Life
Genome sequences exist human, chimpanzee, E. coli, brewer’s yeast, corn, fruit fly, house mouse, rhesus macaque, ………. Provides information about the evolutionary history of genes and taxonomic groups © 2011 Pearson Education, Inc.
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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.
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Genome Sequencing Human Genome Project began in 1990 largely completed by 2003 3 stages Genetic (or linkage) mapping Physical mapping DNA sequencing © 2011 Pearson Education, Inc.
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genetic marker gene or other identifiable DNA sequence
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.
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Chromosome bands Cytogenetic map Genes located by FISH Figure 21.2-1
Figure 21.2 Three-stage approach to sequencing an entire genome.
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Chromosome bands Cytogenetic map Genes located by FISH 1
Figure Chromosome bands Cytogenetic map Genes located by FISH 1 Linkage mapping Genetic markers Figure 21.2 Three-stage approach to sequencing an entire genome.
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Overlapping fragments
Figure Chromosome bands Cytogenetic map Genes located by FISH 1 Linkage mapping Genetic markers 2 Physical mapping Figure 21.2 Three-stage approach to sequencing an entire genome. Overlapping fragments
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Overlapping fragments
Figure Chromosome bands Cytogenetic map Genes located by FISH 1 Linkage mapping Genetic markers 2 Physical mapping Figure 21.2 Three-stage approach to sequencing an entire genome. Overlapping fragments 3 DNA sequencing
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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.
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Human genome = 3.2 billion bp
Sequencing determines the complete nucleotide sequence of each chromosome Human genome = 3.2 billion bp © 2011 Pearson Education, Inc.
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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.
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Cut the DNA into overlapping frag- ments short enough for sequencing.
Figure 1 Cut the DNA into overlapping frag- ments short enough for sequencing. 2 Clone the fragments in plasmid or phage vectors. Figure 21.3 Whole-genome shotgun approach to sequencing.
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Cut the DNA into overlapping frag- ments short enough for sequencing.
Figure 1 Cut the DNA into overlapping frag- ments short enough for sequencing. 2 Clone the fragments in plasmid or phage vectors. 3 Sequence each fragment. Figure 21.3 Whole-genome shotgun approach to sequencing.
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Cut the DNA into overlapping frag- ments short enough for sequencing.
Figure 1 Cut the DNA into overlapping frag- ments short enough for sequencing. 2 Clone the fragments in plasmid or phage vectors. 3 Sequence each fragment. Figure 21.3 Whole-genome shotgun approach to sequencing. 4 Order the sequences into one overall sequence with computer software.
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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, $1,000.00 © 2011 Pearson Education, Inc.
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Metagenomics environmental sample is sequenced
Eliminates need to culture species in the lab © 2011 Pearson Education, Inc.
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Using bioinformatics to analyze genomes and their functions
The Human Genome Project has accelerated progress in DNA sequence analysis © 2011 Pearson Education, Inc.
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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.
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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.
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Figure 21.4 Figure 21.4 Bioinformatics tools available on the Internet.
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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.
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Proteomics systematic study of all proteins encoded by a genome
© 2011 Pearson Education, Inc.
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Figure 21.5 Systems biology approach define gene circuits and protein interaction networks Glutamate biosynthesis Serine- related biosynthesis Translation and ribosomal functions Mitochondrial functions Vesicle fusion RNA processing Amino acid permease pathway Peroxisomal functions Transcription and chromatin- related functions Metabolism and amino acid biosynthesis Nuclear- cytoplasmic transport Figure 21.5 The systems biology approach to protein interactions. Nuclear migration and protein degradation Secretion and vesicle transport Mitosis Protein folding, glycosylation, and cell wall biosynthesis DNA replication and repair Cell polarity and morphogenesis
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Translation and ribosomal functions Mitochondrial functions
Figure 21.5a Translation and ribosomal functions Mitochondrial functions RNA processing Peroxisomal functions Transcription and chromatin- related functions Metabolism and amino acid biosynthesis Nuclear- cytoplasmic transport Nuclear migration and protein degradation Secretion and vesicle transport Figure 21.5 The systems biology approach to protein interactions. Mitosis Protein folding, glycosylation, and cell wall biosynthesis DNA replication and repair Cell polarity and morphogenesis
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Glutamate biosynthesis
Figure 21.5b Glutamate biosynthesis Serine- related biosynthesis Vesicle fusion Amino acid permease pathway Figure 21.5 The systems biology approach to protein interactions. Metabolism and amino acid biosynthesis
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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.
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Figure 21.6 Figure 21.6 A human gene microarray chip.
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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.
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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.
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Table 21.1 Table 21.1 Genome Sizes and Estimated Numbers of Genes
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Number of Genes Bacteria and archaea have 1,500 to 7,500 genes
Eukaryotes from 40,000 genes © 2011 Pearson Education, Inc.
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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.
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Multicellular eukaryotes have much noncoding DNA and many multigene families
Previously called “junk DNA” plays important roles in the cell © 2011 Pearson Education, Inc.
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Sequencing of the human genome reveals that 98
Sequencing of the human genome reveals that 98.5% does not code for proteins, rRNAs, or tRNAs © 2011 Pearson Education, Inc.
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Intergenic DNA is noncoding DNA found between genes
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.
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About three-fourths of repetitive DNA is made up of transposable elements
© 2011 Pearson Education, Inc.
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Regulatory sequences (20%)
Figure 21.7 Exons (1.5%) Introns (5%) Regulatory sequences (20%) Repetitive DNA that includes transposable elements and related sequences (44%) Unique noncoding DNA (15%) L1 sequences (17%) Figure 21.7 Types of DNA sequences in the human genome. Repetitive DNA unrelated to transposable elements (14%) Alu elements (10%) Simple sequence DNA (3%) Large-segment duplications (56%)
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Transposable Elements
First evidence came from geneticist Barbara McClintock’s 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.
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Figure 21.8 Figure 21.8 The effect of transposable elements on corn kernel color.
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New copy of transposon Transposon is copied
Figure 21.9 New copy of transposon Transposon DNA of genome Transposon is copied Insertion Figure 21.9 Transposon movement. Mobile transposon
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New copy of retrotransposon Reverse transcriptase
Figure 21.10 New copy of retrotransposon Retrotransposon Formation of a single-stranded RNA intermediate RNA Insertion Reverse transcriptase Figure Retrotransposon movement.
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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.
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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.
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Genes and Multigene Families
Collections of identical or very similar genes © 2011 Pearson Education, Inc.
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Nontranscribed spacer Transcription unit
Figure 21.11 DNA RNA transcripts -Globin Nontranscribed spacer -Globin Transcription unit Heme DNA -Globin gene family -Globin gene family 18S 5.8S 28S Chromosome 16 Chromosome 11 rRNA 5.8S 2 1 G 2 1 A 28S Figure Gene families. Fetus and adult 18S Embryo Embryo Fetus Adult (a) Part of the ribosomal RNA gene family (b) The human -globin and -globin gene families
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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.
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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.
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Chimpanzee chromosomes
Figure 21.12 Human chromosome 2 Chimpanzee chromosomes Telomere sequences Centromere sequences Telomere-like sequences 12 Human chromosome 16 Mouse chromosomes Centromere-like sequences Figure Related chromosome sequences among mammals. 13 7 8 16 17 (a) Human and chimpanzee chromosomes (b) Human and mouse chromosomes
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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.
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Duplication of ancestral gene
Figure 21.14 Ancestral globin gene Duplication of ancestral gene Mutation in both copies Transposition to different chromosomes Evolutionary time Further duplications and mutations Figure A model for the evolution of the human -globin and -globin gene families from a single ancestral globin gene. 2 1 G A 2 1 -Globin gene family on chromosome 16 -Globin gene family on chromosome 11
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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.
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Rearrangements of Parts of Genes: Exon Duplication and Exon Shuffling
Has contributed to genome evolution Mixing and matching of exons © 2011 Pearson Education, Inc.
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Exon shuffling Exon duplication Exon shuffling
Figure 21.15 EGF EGF EGF EGF Epidermal growth factor gene with multiple EGF exons Exon shuffling Exon duplication F F F F Fibronectin gene with multiple “finger” exons F EGF K K Figure Evolution of a new gene by exon shuffling. K Exon shuffling Plasminogen gene with a “kringle” exon Portions of ancestral genes TPA gene as it exists today
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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.
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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.
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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.
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Most recent common ancestor of all living things
Figure 21.16 Bacteria Most recent common ancestor of all living things Eukarya Archaea 4 3 2 1 Billions of years ago Chimpanzee Human Figure Evolutionary relationships of the three domains of life. Mouse 70 60 50 40 30 20 10 Millions of years ago
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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.
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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.
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May explain why humans but not chimpanzees communicate by speech
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.
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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.
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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.
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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.
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Fruit fly embryo (10 hours)
Figure 21.18 Adult fruit fly Fruit fly embryo (10 hours) Fly chromosome Mouse chromosomes Mouse embryo (12 days) Figure Conservation of homeotic genes in a fruit fly and a mouse. Adult mouse
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Fruit fly embryo (10 hours)
Figure 21.18a Adult fruit fly Fruit fly embryo (10 hours) Figure Conservation of homeotic genes in a fruit fly and a mouse. Fly chromosome
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Mouse chromosomes Mouse embryo (12 days) Adult mouse Figure 21.18b
Figure Conservation of homeotic genes in a fruit fly and a mouse. Adult mouse
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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.
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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.
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Genital segments Thorax Abdomen Thorax Abdomen Figure 21.19
Figure Effect of differences in Hox gene expression in crustaceans and insects.
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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.
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Most are 104,000 Mb, but a few are much larger Most are 16 Mb
Figure 21.UN01 Bacteria Archaea Eukarya Genome size Most are 104,000 Mb, but a few are much larger Most are 16 Mb Number of genes 1,5007,500 5,00040,000 Gene density Lower than in prokaryotes (Within eukaryotes, lower density is correlated with larger genomes.) Higher than in eukaryotes Introns None in protein-coding genes Present in some genes Unicellular eukaryotes: present, but prevalent only in some species Multicellular eukaryotes: present in most genes Figure 21.UN01 Summary figure, Concept 21.3 Other noncoding DNA Can be large amounts; generally more repetitive noncoding DNA in multicellular eukaryotes Very little
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Introns and regulatory sequences (26%)
Figure 21.UN02 Human genome Protein-coding, rRNA, and tRNA genes (1.5%) Introns and regulatory sequences (26%) Figure 21.UN02 Summary figure, Concept 21.4 Repetitive DNA (green and teal)
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2 1 -Globin gene family -Globin gene family
Figure 21.UN03 -Globin gene family -Globin gene family Chromosome 16 Chromosome 11 G A 2 1 2 1 Figure 21.UN03 Summary figure, Concept 21.4
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Figure 21.UN04 Figure 21.UN04 Test Your Understanding, question 5
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Crossover point Figure 21.UN05
Figure 21.UN05 Appendix A: answer to Figure legend question
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Figure 21.UN06 Figure 21.UN06 Appendix A: answer to Test Your Understanding, question 5
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