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).