lecture 20 evolutionary genomics - division of physical &...
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Lecture 20 Evolutionary genomics
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A. Genomic approaches
B. DNA gels
C. Sanger sequencing
D. Microarrays
E. New Generation Sequencing
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A. Genomic approaches
1. Cot, melting, renaturation
2. Cesium Chloride gradients
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Evolution of genome size
Species C-value (in kilobases, kb)
diatom 35,000
fruit fly 180,000
chicken 1,200,000
carp 1,700,000
snake 2,100,000
human 3,400,000
onion 18,000,000
lily 36,000,000
fern 160,000,000
amoeba 670,000,000
The lack of a correlation between organismal complexity and genome size became known as the “C-value paradox”
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Genome sizes are also highly variable within groups
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Cot, and melting curves
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Isochores
(low GC)
L Cold-blooded vertebrates
L L L H3 H2 H1
(low GC) (high GC)
Warm-blooded vertebrates
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Isochores
L L L H3 H2 H1
(low GC) (high GC)
Warm-blooded vertebrates
- Chromatin structure - Time of replication - Gene types - Gene concentration - Retroviruses
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Chromosomal bands
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(Mb)
GC, %
Isochores of human chromosome 21
(Macaya et al., 1976) Costantini et al., 2006
GC, %
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B. DNA gels
1. RFLPs
2. PCRs
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Gel Electrophoresis
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PCR: Polymerase Chain Reaction
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Fred Sanger 1918-
C. Sanger Sequencing
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Genomics: DNA sequencing
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Reconciling the c-value paradox
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Isochores at the sequence level
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D. Microarrays
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D. New generation sequencing
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Pyrosequencing
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Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils
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Genome 10K
David Haussler UCSC
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Comparative genomics • comparing complete genomes of two or more species allows us to identify:
1. Non-coding regions that are highly conserved
• ultra-conserved regions have been identified Haussler’s group at UCSC.
2. Genes that are highly conserved
• identifies genes under strong selective constraint.
3. Rapidly evolving genes
• candidate genes have been identified for uniquely human traits (e.g., language).