Genome Sizes in Eukaryotes from Table 8'4

1
Genome Sizes in Eukaryotes (from Table 8.4)
Yeast 12,000 kb Rice 590,000 kb Chicken
1,200,000 kb
Dog 2,900,000 kb Humans 3,600,000 kb Pine
tree 68,000,000 kb
1 kb 1000 base pairs
2
Grass Species picograms DNA per diploid nucleus
1 pg 500,000 kb
Source Bennetzen and Kellogg, 1997
3
The C-value paradox
Genomes from organisms of similar complexity
that encode similar amounts of genetic
information can vary substantially in size
4
What contributes to differences in C-value?

• Gene duplication
• Transposable elements

5
How does gene duplication occur?

• whole genome duplication (polyploidy)
• whole chromosome duplication (aneuploidy)
• duplication of chromosomal segments
• (segmental duplication)
• gene duplication

6
Whole genome (polyploidy) or whole chromosome
(aneuploidy) duplication
Normal
Polyploidy
Aneuploidy
7
Gene duplication by unequal crossing over
deletion
addition
8
Importance of gene duplication
Arabidopsis genome initiative
9
Duplication in A. thaliana
Arabidopsis genome initiative
10
The Maize Genome

• 60 to 80 duplicated
• Up to 30 triplicated

11
Time (million years)

10
20
30
group
orp
1

orp
2
A
ant
1

ant
2
ohp
1

ohp
2
r

b
cpn
a
cpn
b
cdc
2
a

cdc
2
b
whp
1

c
2
fer
1

fer
2
B
c
1

pl
1
ibp
1

ibp
2
tbp
1

tbp
2
vpl
4
a
vpl
4
b
obf
1

obf
2
pgpa
1

pgpa
2
maizesorghum
maizepennisetum
0.40
0.00
0.10
0.20
0.30
substitutions per synonymous site
12
The origin of the maize genome an hypothesis
maize
Sorghum
Pennisetum
0.0
11.4
16.5
20.5
28.8
Time (million years before present)
13
Phylogenetic placement of the tetraploid event
Hordeum vulgare, 10.9
Aegilops spp., 11.8
Triticum monococcum, 11.3
Festuca/Lolium spp., 5.6
Oryza sativa, 0.9
Zea luxurians, 8.8
Zea mays, 5.7
Tripsacum dactyloides, 7.7
Sorghum bicolor, 1.6
Pennisetum spp., 4.8
segmental allotetraploid event
14
Is duplication alone enough to explain variation
in genome sizes?
Transposable elements and their roles in genome
evolution
15
Barbara McClintock Discovered Transposable
Elements 1948 Nobel Prize - 1983
16
Transposable Elements

• Two types
• Class I RNA intermediate using reverse
  transcriptase (replicative)
• DNA-RNA-DNA
• Class II DNA elements (conservative)
• Excision and Jump

17

• Estimates of the repetitive fraction of the maize
  genome vary from 50 to 80.

What is this repetitive DNA and when did
it arise?
18
Retrotransposons in the Adh1 region
Retrotransposon families defined by LTR
19
Nested retrotransposons in an intergenic region
of the maize genome

• The retrotransposon families in the adh region
  comprise 50 of the maize genome.
• May be a representative region 85 of repetitive
  DNAs found in other genomic regions were also
  found in the adh1 region

20
When did the retrotransposons insert?

• Divergence between LTR sequences can provide an
  estimate of the insertion date of a
  retrotransposon.
• San Miguel et al. (1998) sequenced 17 pairs of
  LTRs, estimated sequence divergence between
  LTRs, and calculated insertion times for each
  retrotransposon.

21
Millions of Years
Estimated
Ago
substitutions/kb
Kake
-1
0
0
Grande-Zm
-1
Opie
-2
Cinful
-1
Opie
-3
10
Huck
-2
1
Ji
-1
Opie
-1
Ji-
4
Milt
20
Ji-
3
Fourf
2
Reina
30
Huck
-1
Victim
3
40
50
4
60
Ji-
6
5
Tekay
70
6
u22
adh1
-F
22
Summary dating the insertion of retrotransposons

• Insertion time estimates correspond with the
  stratigraphic layering of retrotransposons
• Oldest insertion roughly 5 to 5.5 million years
  ago
• Most insertions were within the last 3 million
  years.
• If the adh1 region is representative of the
  genome, these results imply that the maize genome
  size could have doubled in size in the last 5.5
  million years due to retrotransposons alone.

23
Phylogenetic placement of retrotransposon invasion
Hordeum vulgare, 10.9
Aegilops spp., 11.8
Triticum monococcum, 11.3
Festuca/Lolium spp., 5.6
Oryza sativa, 0.9
Zea luxurians, 8.8
Zea mays, 5.7
Tripsacum dactyloides, 7.7
Sorghum bicolor, 1.6
Pennisetum spp., 4.8
retrotransposon invasion
segmental allotetraploid event
24
Where do transposable elements come from?

• - retrotransposons may have viral origins
• horizontal transfer

25
Horizontal transfer the voyage of mariner
1300 bp
Transposase gene
28 bp repeat
mariner is a DNA element first identified in
fruit flies
26
Isolating mariner from other species with PCR
Transposase gene
27
Phylogeny of mariner sequences from insects
Horizontal (lateral) transfer
28
Detecting Horizontal Transfer(a made-up example)
Organismal Phylogeny
29
Phylogeny of mariner sequences from insects
Horizontal (lateral) transfer
30
What are the effects of Transposable Elements?

• Increase/decrease genome size
• Gene interruption
• Can carry genes and benefit an organism
• e.g., bacteria and chloramphenicol resistance
• Alter gene expression?
• Can cause genome rearrangement e.g.
• Charcot-Marie-Tooth Disease indels due to
  TE-mediated
• recombination
• Contribute to new genes?