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Genomes and their Evolution
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Page 1: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

Genomes and their Evolution

Page 2: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups

What genomic information distinguishes a human from a chimpanzee?

Page 3: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

New approaches have accelerated the pace of genome sequencing

Page 4: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

Cut the DNAinto overlappingfragments short enoughfor sequencing

1

2

3

4

Clone the fragmentsin plasmid or phagevectors.

Sequence eachfragment.

Order thesequences intoone overallsequencewith computer software.

Whole-Genome Shotgun Approach

to Genome

Sequencing- developed by Craig

Venter

Page 5: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

Scientists use bioinformatics to analyze genomes and their functions

Page 6: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

Bioinformatics resources are provided by a number of sources

Page 7: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

Comparison of sequences of “new” genes with those of known genes in other species may help identify new genes

Page 8: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

Most recentcommonancestorof all livingthings

Billions of years ago4 3 2 1 0

Bacteria

Eukarya

Archaea

Chimpanzee

Human

Mouse

010203040506070Millions of years ago

Genome comparisons of closely related species help us understand recent evolutionary events

Page 9: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

Translation andribosomal functions

Nuclear-cytoplasmic

transport

RNA processing

Transcriptionand chromatin-

related functions

Mitochondrialfunctions

Nuclear migrationand proteindegradation

Mitosis

DNA replicationand repair

Cell polarity andmorphogenesis

Protein folding,glycosylation, and

cell wall biosynthesis

Secretionand vesicletransport

Metabolismand amino acid

biosynthesis

Peroxisomalfunctions

Glutamatebiosynthesis

Serine-related

biosynthesis

Amino acidpermease pathway

Vesiclefusion

Understanding Genes and Gene Expression at the

Systems Level

Danny Hillis Ted TalkStart at 8 minutes

Page 10: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

By summer of 2007, the sequencing of more than 600 genomes hadbeen completed.

Page 11: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

Fig. 21-7Exons (regions of genes coding for protein

or giving rise to rRNA or tRNA) (1.5%)

RepetitiveDNA thatincludestransposableelementsand relatedsequences(44%)

Introns andregulatorysequences(24%)

UniquenoncodingDNA (15%)

RepetitiveDNAunrelated totransposableelements (15%)

L1sequences(17%)

Alu elements(10%)

Simple sequenceDNA (3%)

Large-segmentduplications (5–6%)

•Eukaryotic genomes are larger and have more protein-coding genes.•Eukaryotic genomes have more regulatory sequences. Greater complexity requires more regulation. •Much of eukaryotic DNA is noncoding, including introns, gene control sequences, and repeated sequences.

Page 12: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

Transposable Elements

• The first evidence for wandering DNA segments– Came from

geneticist Barbara McClintock’s breeding experiments with Indian corn

Nobel Prize 1983

Page 13: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

TransposonNew copy of transposon

Insertion

Transposonis copied

Mobile transposon

DNA ofgenome

(a) Transposon movement (“copy-and-paste” mechanism)

RetrotransposonNew copy of

retrotransposon

Insertion

Reversetranscriptase

RNA

(b) Retrotransposon movement

Transposons, move by means of a DNA intermediate

Retrotransposons move by means of an RNA intermediate

Page 14: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

The transposable element can alter the expression of a gene at the new location

Page 15: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

How Transposable Elements Contribute to Genome Evolution

• Movement of transposable elements– Occasionally generates new sequence combinations that

are beneficial to the organism

• Some mechanisms– Can alter the functions of genes or their patterns of

expression and regulation

Page 16: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

Alu inserts as markers of primate evolution(retrotransposon)

Salem, et al. 2003. PNAS 100:12787-12791

Page 17: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

Genes and Multigene Families

• Many eukaryotic genes are present in one copy per haploid set of chromosomes

• The rest of the genome occurs in multigene families, collections of identical or very similar genes

• Some multigene families consist of identical DNA sequences, usually clustered tandemly, such as those that code for RNA products.

Page 18: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

Fig. 21-10a

(a) Part of the ribosomal RNA gene family

18S

28S

28S18S 5.8S

5.8S

rRNA

DNA

DNARNA transcripts

Nontranscribedspacer Transcription unit

Page 19: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

Heme

Hemoglobin

-Globin

-Globin

-Globin gene family-Globin gene family

Chromosome 16 Chromosome 11

2 1

2

1

G A

Embryo Embryo FetusFetus

and adult Adult

α-globins and β-globins are examples of multigene families of nonidentical genes

Page 20: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

Figure 21.14

Duplication ofancestral gene

Mutation inboth copies

Transposition todifferent chromosomes

Further duplicationsand mutations

Ancestral globin gene

-Globin gene familyon chromosome 16

-Globin gene familyon chromosome 11

Evo

luti

on

ary

tim

e

2

1

2 1 G A

ICE FISH GENE DUPLICATION EVOLUTIONARY HISTORYCLIP

Page 21: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

Alterations of Chromosome Structure

Humanchromosome 2

Telomeresequences

Centromeresequences

Chimpanzeechromosomes

12Telomere-likesequences

Centromere-likesequences

Humanchromosome 16

13

(a) Human and chimpanzee chromosomes (b) Human and mouse chromosomes

7 8 16 17

Mousechromosomes

Humans have 23 pairs of chromosomes, while chimpanzees have 24 pairsChromosomal rearrangements are thought to contribute to the generation of new species

Page 22: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

Most recentcommonancestorof all livingthings

Billions of years ago4 3 2 1 0

Bacteria

Eukarya

Archaea

Chimpanzee

Human

Mouse

010203040506070Millions of years ago

The accumulation of changes in the genomeprovides a record of evolutionary history

Page 23: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

Comparing Genomes Within a Species

• As a species, humans have only been around about 200,000 years and have low within-species genetic variation

• Variation within humans is due to single nucleotide polymorphisms, inversions, deletions, and duplications

• These variations are useful for studying human evolution and human health

Page 24: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

Other Repetitive DNA, Including Simple Sequence DNA

• Simple sequence DNA contains many copies of tandemly repeated short sequences

This repeat number can vary from person to person, producing variation useful inforensic science.

Page 25: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

STRBase: a short tandem repeat DNA database for the human identity testing community

Christian M. Ruitberg, Dennis J. Reeder and John M. Butler*

Biotechnology Division, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 8311, Gaithersburg, MD 20899-8311, USA

AbstractThe National Institute of Standards and Technology (NIST) has compiled and maintained a Short Tandem Repeat DNA Internet Database (http://www.cstl.nist.gov/biotech/strbase/) since 1997 commonly referred to as STRBase. This database is an information resource for the forensic DNA typing community with details on commonly used short tandem repeat (STR) DNA markers.From: Nucl. Acids Res. (2001) 29 (1): 320-322.

Page 26: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

Comparing Developmental Processes

• Evolutionary developmental biology, or evo-devo, is the study of the evolution of developmental processes in multicellular organisms

• Genomic information shows that minor differences in gene sequence or regulation can result in major differences in form

Page 27: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

Adultfruit fly

Fruit fly embryo(10 hours)

Flychromosome

Mousechromosomes

Mouse embryo(12 days)

Adult mouse

Molecular analysis of the homeotic genes in Drosophila has shown that they all include a sequence called a homeobox

Hox genes

Neil Shubin and Sean CarrollDiscuss homeobox genes

Page 28: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

GHOSTS

Page 29: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

Fig. 21-3-1Cut the DNAinto overlappingfragments short enoughfor sequencing

1

2 Clone the fragmentsin plasmid or phagevectors.

Whole-Genome Shotgun Approach to Genome Sequencing- developed by Craig Venter

Page 30: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

Fig. 21-3-2Cut the DNAinto overlappingfragments short enoughfor sequencing

1

2

3

Clone the fragmentsin plasmid or phagevectors.

Sequence eachfragment.

Page 31: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

Fig. 21-2-1Cytogenetic map

Genes locatedby FISH

Chromosomebands

Three-Stage Approach to Genome Sequencing

Page 32: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

Fig. 21-2-2Cytogenetic map

Genes locatedby FISH

Chromosomebands

Linkage mapping1

Geneticmarkers

Page 33: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

Fig. 21-2-3Cytogenetic map

Genes locatedby FISH

Chromosomebands

Linkage mapping1

2

Geneticmarkers

Physical mapping

Overlappingfragments

Page 34: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

Fig. 21-2-4Cytogenetic map

Genes locatedby FISH

Chromosomebands

Linkage mapping1

2

3

Geneticmarkers

Physical mapping

Overlappingfragments

DNA sequencing

Page 35: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.
Page 36: Genomes and their Evolution. Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups What.

From: National Academy of Science, 2009

Metagenomics

Genetic diversity is explored without isolating intact organisms.


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