1. Whole
genome
duplica0on
and
plant
genome
diversity
Simon
Renny-­‐Byfield
Department
of
Ecology,
Evolu0on
and
Organismal
Biology
Iowa
State
University
May
12th
2014

2. Outline
• Brief
Introduc0on
• The
role
polyploidy
in
plant
evolu0on
• Repe00ve
DNA
evolu0on
in
polyploids
• Evolu0on
of
gene
duplicates
in
paleopolyploids
• Genome
diploidisa0on
and
frac0ona0on
in
paleopolyploids
• CoMon
fiber
transcriptomics
and
domes0ca0on

3. Introduc0on
• What
is
polyploidy
(whole
genome
duplica0on;
WGD)?
• More
than
a
diploid
set
of
chromosomes
• Allo
vs
auto
• How
to
iden0fy
polyploids?

4. Divergence
0me
(mya)
Introduc0on
• Chromosome
counts
• Age
es0mates
of
duplicated
genes
• Syntenty
analysis
Jiao
et
al.,
2011
Science
Schnable
et
al.,
2011
PNAS

5. • The
greatest
realiza0on
of
the
plant
genomics
era?
Introduc0on
Stebbins
(1950)
–
35%
Grant
(1963,1981)
–
47%
GoldblaM
(1980)
–
70-­‐80%
Lewis
(1980)
–
70-­‐80%
Current
view
–
100%
of
seed
plants
are
polyploid

6. Three
brief
stories...
① Diversifica0on
of
polyploid
genomes
② Diversifica0on
of
duplicated
genes
following
ancient
WGD.
③ How
polyploids
become
more
diploid-­‐like
again,
and
again.

7. 1.
Diversifica0on
of
polyploid
genomes
• Polyploid
genomes
are
highly
dynamic
– How
do
they
vary?
– Over
what
0me
scale?
– Do
different
sub-­‐genomes
behave
differently?

8. N.
sylvestris
x
N.
tomentosiformis
2n
=
24
2n
=
24
N.
tabacum
Genome
doubling
2n
=
48
2650 MB per 1C 2650 MB per 1C
5200 MB per 1C
1.
Diversifica0on
of
polyploid
genomes

9. • Es0mate
repeat
content
of
progenitors
and
allopolyploid
– RepeatExplorer
pipeline
– Assess
divergence
of
the
allopolyploid
from
the
diploids
Novak
et
al.,
2010
BMC
Genomics
Renny-­‐Byfield
et
al.,
2011
MBE
1.
Diversifica0on
of
polyploid
genomes

10. N.
tom
S4
synthe0c
tobacco
tobacco
N.
tom
Renny-­‐Byfield
et
al.,
2012
PLoS
One
1.
Diversifica0on
of
polyploid
genomes

11. WGDs
and
genome
diversity
The paternal (N. tomentosiformis) genome
appears to be underrepresented in tobacco
Renny-­‐Byfield
et
al.,
2012
MBE

12. 2.
Diversifica0on
of
duplicated
genes
following
ancient
WGD
S.
C
Harland,
1936

13. 2.
Diversifica0on
of
duplicated
genes
following
ancient
WGD
• Neofunc0onaliza0on
(Ohno,
1970)
• Subfunc0onaliza0on
(Force,
Lynch
and
others)
hMp://www.personal.psu.edu/rua15/Stage3.jpg

14. 2.
Diversifica0on
of
duplicated
genes
following
ancient
WGD

15. 2.
Diversifica0on
of
duplicated
genes
following
ancient
WGD
Dt
64
37
45
37
65
100
100
0
100
64
51
At
36
63
55
63
35
0
0
100
0
36
49
Adams
et
al.,
2003

16. 2.
Diversifica0on
of
duplicated
genes
following
ancient
WGD

17. Renny-­‐Byfield
et
al.,
2014
GBE
2.
Diversifica0on
of
duplicated
genes
following
ancient
WGD

18. 2.
Diversifica0on
of
duplicated
genes
following
ancient
WGD
Almost
complete
divergence
in
expression
aier
ca.
60
my
Renny-­‐Byfield
et
al.,
2014
GBE

19. 2.
Diversifica0on
of
duplicated
genes
following
ancient
WGD
Gene
(G)
effect
Tissue
(T)
effect
G
x
T
interac0on
Renny-­‐Byfield
et
al.,
2014
GBE

20. 3.
Biased
frac0ona0on
following
WGD
• What
happens
to
most
genes
following
WGD..
Woodhouse
et
al.,
2010
PloS
Biology

21. 3.
Biased
frac0ona0on
following
WGD
•
CoGe
SynMap
tool
•
Examine
CDS
for
colinearity
with
reference
genome
•
Allows
iden0fica0on
of
duplicated
regions

22. 3.
Biased
frac0ona0on
following
WGD

23. 3.
Biased
frac0ona0on
following
WGD
•
Ten
chromosome
level
comparisons
•
Significant
bias
in
gene
loss
in
all
comparisons
T. cacao
chromosome
G. raimondii
chromosome
(block numbers)
observed predicted !2
p value
2 5 (137,138,139) 929 3641
8 (179,184,185) 642 3641
42.8072 6.1x10-11
6 6 (149,150) 147 2637
9 (190) 580 2637
226.6415 <1x10-15
6 (149,150) 147 2637
10 (33,34,36) 227 2637
15.5573 8x10-5

24. 3.
Biased
frac0ona0on
following
WGD
leaf petal seed
0
200
400
600
count(numberofwins)
LF
MF
Over
expression
of
genes
on
LF
chromosomes
leaf petal seed
−2.5
0.0
2.5
5.0
7.5
−5 0 5 −5 0 5 −5 0 5
log(RPKM MF)
log(RPKMLF)
0.02
0.04
0.06
density

25. 3.
Biased
frac0ona0on
following
WGD
0
2
4
6
−1000 −500 0 500 1000
distance from transcription start/stop site (bp)
meannumberofmappedreads
Most
Frac0onated
Least
Frac0onated
24nt
siRNAs
preferen0ally
locate
to
the
MF
genome

27. Current
project
•
Two
independent
domes0ca0on
events.
•
One
polyploid
and
one
diploid

28. • RNAseq
at
Four
development
stages:
– 5
,
10,
15,
and
20
DPA
• Wild
and
domes0cated
lines:
– Three
in
each
group
• Polyploid
and
diploid
groups:
– Wild
A1,
domes0cated
A1
– Wild
AD1,
domes0cated
AD1
Current
project

29. • Gene
expression
architecture
– How
do
transcrip0onal
networks
alter
(i.e.
similar
to
Swanson-­‐Wagner
et
al.,2011)
– connec0vity,
edge
weight,
movement
of
nodes.
– Superimposi0on
of
graphs
to
compare
networks
in
wild
and
domes0cated
(Lelandias
al.,
2006,
Bioinforma0cs)
– Are
there
parallel
changes
in
diploid
vs
polyploid
groups
Current
project
hMp://www.georgebassellab.com/wp-­‐content/
uploads/2012/01/seedNet.jpg

30. Conclusions
• WGD
is
ubiquitous
in
angiosperms
• Polyploid
genomes
are
highly
dynamic
• Parental
sub-­‐genomes
can
behave
differently
• Gene
duplica0on
(via
WGD)
can
result
in
biological
novelty
• Processes
of
genome
turnover
and
frac0ona0on
result
in
diploidiza0on
• Bias
frac0ona0on
linked
to
expression
and
local
TE
coverage