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Genomes and their Evolution
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?
New approaches have accelerated the pace
of genome sequencing
1 Cut the DNA
into overlapping
fragments short enough
for sequencing
Whole-Genome
Shotgun Approach
to
Genome
Sequencingdeveloped by Craig 2
Venter
Clone the fragments
in plasmid or phage
vectors.
3 Sequence each
fragment.
4 Order the
sequences into
one overall
sequence
with computer
software.
Scientists use bioinformatics to analyze
genomes and their functions
Bioinformatics resources are provided by a number of sources
Comparison of sequences of “new” genes with those of
known genes in other species may help identify new genes
Genome comparisons of closely related species
help us understand recent evolutionary events
Bacteria
Most recent
common
ancestor
of all living
things
Eukarya
Archaea
4
3
2
Billions of years ago
1
0
Chimpanzee
Human
Mouse
70
60
50
40
30
20
Millions of years ago
10
0
Understanding Genes and
Gene Expression at the
Systems Level
Translation and
ribosomal functions
Glutamate
biosynthesis
Mitochondrial
functions
Vesicle
fusion
RNA processing
Transcription
and chromatinrelated functions
Nuclearcytoplasmic
transport
Nuclear migration
and protein
degradation
Mitosis
DNA replication
and repair
Peroxisomal
functions
Serinerelated
biosynthesis
Amino acid
permease pathway
Metabolism
and amino acid
biosynthesis
Secretion
and vesicle
transport
Protein folding,
glycosylation, and
cell
wall biosynthesis
Cell polarity and
Danny
morphogenesis
Hillis Ted Talk
Start at 8 minutes
By summer of 2007, the
sequencing of more than 600
genomes had
been completed.
Fig. 21-7
•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.
L1
sequences
(17%)
Alu elements
(10%)
Exons (regions of genes coding for protein
or giving rise to rRNA or tRNA) (1.5%)
Repetitive
DNA that
includes
transposable
elements
and related
sequences
(44%)
Introns and
regulatory
sequences
(24%)
Unique
noncoding
DNA (15%)
Repetitive
DNA
unrelated to
transposable
elements
(15%)
Simple sequence
DNA (3%)
Large-segment
duplications (5–6%)
Transposable Elements
• The first
evidence for
wandering DNA
segments
– Came from
geneticist
Barbara
McClintock’s
breeding
experiments
with Indian corn
Nobel Prize 1983
Transposons, move
by means of a
DNA intermediate
Retrotransposons
move by means of
an RNA
intermediate
Transposon
DNA of
genome
Transposon
is copied
New copy of
transposon
Insertion
Mobile transposon
(a) Transposon movement (“copy-and-paste” mechanism)
Retrotransposon
New copy of
retrotransposon
RNA
Insertion
Reverse
transcriptase
(b) Retrotransposon movement
The transposable element can alter the expression of a
gene at the new location
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
Alu inserts as markers of primate evolution
(retrotransposon)
Salem, et al. 2003. PNAS 100:12787-12791
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.
Fig. 21-10a
DNA
RNA transcripts
Nontranscribed
spacer
Transcription unit
DNA
18S
5.8S
28S
rRNA
28S
18S
(a) Part of the ribosomal RNA gene family
5.8S
α-globins and β-globins are examples of
multigene families of nonidentical genes
Heme
-Globin
Hemoglobin
-Globin
-Globin gene family
-Globin gene family
Chromosome 16
2
Embryo
1
Chromosome 11
2
G
1
Fetus
and adult
Embryo
A
Fetus
Adult
Figure 21.14
Ancestral globin gene
Evolutionary time
Duplication of
ancestral gene

Mutation in
both copies
Transposition to
different chromosomes


Further duplications

and mutations



   2 1 
2
1
-Globin gene family
on chromosome 16



G

A


-Globin gene family
on chromosome 11
ICE FISH GENE DUPLICATION EVOLUTIONARY HISTORY
CLIP

Alterations of Chromosome Structure
Human
chromosome 2
Chimpanzee
chromosomes
Telomere
sequences
Centromere
sequences
Telomere-like
sequences
12
Human
chromosome 16
Centromere-like
sequences
13
(a) Human and chimpanzee chromosomes
Mouse
chromosomes
7
8
16
17
(b) Human and mouse chromosomes
Humans have 23 pairs of chromosomes, while chimpanzees have 24 pairs
Chromosomal rearrangements are thought to contribute to the generation of new species
The accumulation of changes in the genome
provides a record of evolutionary history
Bacteria
Most recent
common
ancestor
of all living
things
Eukarya
Archaea
4
3
2
Billions of years ago
1
0
Chimpanzee
Human
Mouse
70
60
50
40
30
20
Millions of years ago
10
0
Comparing Genomes Within a Species
• As a species, humans have only
been around about 200,000
years and have low withinspecies 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
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 in
forensic science.
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
Abstract
The 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.
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
Hox genes
Molecular analysis of the
homeotic genes in
Drosophila has shown
that they all include a
sequence called a
homeobox
Neil Shubin and Sean Carroll
Discuss homeobox genes
Adult
fruit fly
Fruit fly embryo
(10 hours)
Fly
chromosome
Mouse
chromosomes
Mouse embryo
(12 days)
Adult mouse
GHOSTS
Fig. 21-3-1
1 Cut the DNA
into overlapping
fragments short enough
for sequencing
2 Clone the fragments
in plasmid or phage
vectors.
Whole-Genome Shotgun Approach to
Genome Sequencing- developed by Craig Venter
Fig. 21-3-2
1 Cut the DNA
into overlapping
fragments short enough
for sequencing
2 Clone the fragments
in plasmid or phage
vectors.
3 Sequence each
fragment.
Fig. 21-2-1
Chromosome
bands
Cytogenetic map
Genes located
by FISH
Three-Stage Approach to Genome Sequencing
Fig. 21-2-2
Chromosome
bands
Cytogenetic map
Genes located
by FISH
1
Linkage mapping
Genetic
markers
Fig. 21-2-3
Chromosome
bands
Cytogenetic map
Genes located
by FISH
1
Linkage mapping
Genetic
markers
2
Physical mapping
Overlapping
fragments
Fig. 21-2-4
Chromosome
bands
Cytogenetic map
Genes located
by FISH
1
Linkage mapping
Genetic
markers
2
Physical mapping
Overlapping
fragments
3
DNA sequencing
Metagenomics
Genetic diversity is explored without isolating intact organisms.
From: National Academy of Science, 2009