Lecture 20 Evolutionary genomics - Division of Physical &...
Transcript of Lecture 20 Evolutionary genomics - Division of Physical &...
Lecture 20 Evolutionary genomics
A. Genomic approaches
B. DNA gels
C. Sanger sequencing
D. Microarrays
E. New Generation Sequencing
A. Genomic approaches
1. Cot, melting, renaturation
2. Cesium Chloride gradients
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”
Genome sizes are also highly variable within groups
Cot, and melting curves
Isochores
(low GC)
L Cold-blooded vertebrates
L L L H3 H2 H1
(low GC) (high GC)
Warm-blooded vertebrates
Isochores
L L L H3 H2 H1
(low GC) (high GC)
Warm-blooded vertebrates
- Chromatin structure - Time of replication - Gene types - Gene concentration - Retroviruses
Chromosomal bands
(Mb)
GC, %
Isochores of human chromosome 21
(Macaya et al., 1976) Costantini et al., 2006
GC, %
B. DNA gels
1. RFLPs
2. PCRs
Gel Electrophoresis
PCR: Polymerase Chain Reaction
Fred Sanger 1918-
C. Sanger Sequencing
Genomics: DNA sequencing
Reconciling the c-value paradox
Isochores at the sequence level
D. Microarrays
D. New generation sequencing
Pyrosequencing
Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils
Genome 10K
David Haussler UCSC
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).