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Overview
Genomics
Martin Polz
[email protected]
I. Genome sizes
II. How to sequence entire genomes
III. Genome evolution
1. Point mutations
2. Regional changes
3. Global changes
IV. Environmental genomics
I. Genome sizes

Bacterial genome: 6×105 to more than 107
Smallest known: Mycoplasma genitalium (480 protein coding genes, 3 rRNA genes,
33 tRNA genes)

Prokaryotes genome sizes are roughly proportional to gene numbers.

Eukayotic genome: 8.8×106~ 6.9×1011
Smallest known include: Saccharomyces cerevisiae and other fungi

Eukaryotes genome sizes are NOT proportional to gene numbers or
anatomical complexity
Genome size (bp)
Chromosome number (n)
Amoeba dubia
670,000,000,000
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Trumpet lily
90,000,000,000
20
Human
3,454,200,000
23
Chicken
1,200,000,000
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Housefly
900,000,000
6
Tomato
655,000,000
12
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Chapter 16
II. How can we sequence entire genomes?
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Figure 16.3 upper
Figure 16.3 middle
SEQUENCING A GENOME
Genomic
DNA
1. Cut DNA into
fragments of ~160 kb,
using different restrictions
enzymes.
4. Cut each 160 kb
fragment into 1 kb
fragments.
“Shotgun
clones”
BAC
library
2. Insert fragments
into bacterial artificial
chromosomes, grow in
E. coli cells.
3. Analyze fragments,
locate each on map of
genome.
5. Insert 1 kb fragments
into plasmids, grow in
E.coli cells.
Shotgun sequence
...ATTTAGACTCGATAA
TAGACTCGATAAGGATGC...
6. Sequence each
fragment (note that
ends of fragments
overlap).
2
Figure 16.3 lower
...ATTTAGACTCGATAAGGATGC...
Figure 16.4
7. Assemble 1 kb
fragments from
within each 160 kb
fragment by
matching
overlapping ends.
Open reading frame (ORF)
Start
Stop
5’ …C T C A A T G G G T A C G T A G G AT C G G G A A T C G T A C A G G A A C G T T T G A A A T C G... 3’
… G A G T T A C C C A T G C A T C C T A G C CC T T A G C A T G T C C T T G C A A A C T T T A G C...
Draft sequence
Genome map
8. Assemble fragments
from different BACs by
matching overlapping
ends.
III. Genome evolution
1. Point mutations
- measure evolutionary relationships
(phylogeny) --> see last lecture
2. “Regional” change
- duplication
- deletion
- mobile elements
- chromosome rearrangements
3. “Global” change
- genome duplication --> not covered
3
Mechanisms of gene deletion or duplication
replication errors
unequal crossing over
Example: evolution of antifreeze gene in arctic fish
5’
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3’
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Ancestral trypsinogen
gene
Deletion
1
5’
6’
3’
Thr Ala Ala Gly
4 fold duplication + addition of spacer sequence
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5’
6’
Internal duplications + addition of intron sequence
Consequences of gene duplication
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5’
1
- part of a gene:
if functional domain is duplicated --> functional enhancement
-complete gene
gene dosage enhanced
New function can evolve due to relaxed selection on one copy
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3’
Spacer: Gly
7
…
37
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6’
3’
Antifreeze glycoprotein gene
Mobile Elements (selfish DNA)
Human genome: gene duplications




5% of the human genome is found
to be recently-duplicated large
segments (>500bp, identity>95%).
[JA Bailey, Science, 2002]
The duplicated regions create
mosaic structure.
Some of the duplicated segments
contain new genes.
Insertion sequences
Only encode for transposase, no exogenous genes.

Transposons
Carry both transposase and exogenous genes (e.g. drug resistant genes).

Non-autonomous transposable elements
Do not carry transposase itself, depend on other autonomous transposable elements.

Retroelements
Carry reverse transcriptase.
-Retrovirus
-Retroposons
-Retrotrnasposons
4
Example: transposons
Chromosome rearrangements
Transposons disrupt genes but can also carry genes around chromosome and among
different cells.
Figure 16.6
Example: comparison of bacterial genomes
Lateral gene transfer - very important mechanisms in prokaryotes!
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When genes are transferred laterally,
they move between species that are
not necessarily closely related
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Recognizing laterally transferred DNA:
- different GC content
- “new” DNA in related organisms
- phylogenetic differences
Mechanisms of lateral gene transfer
Example:
Pathogenicity islands - many pathogens acquire genes from other bacteria
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1 Transformation: uptake of DNA from environment
2 Transduction: DNA transfer by viruses
3 Conjugation: plasmid transfer between bacterial cells
Environmental Genomics - applying genomic sequencing to DNA directly
obtained from the environment
BAC clone obtained directly from environment
16 S rRNA gene
Proteorhodopsin:
Proteorhodopsin:
A new way to convert
solar energy to
chemical energy in
the ocean
Protein coding gene
revealing function of
organism in environment
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