Whole genome duplication and plant genome diversity.spare
1. Whole genome duplication and
plant genome diversity
Simon Renny-Byfield
Department of Ecology, Evolution and Organismal
Biology
Iowa State University
May 12th 2014
2. Outline
• Brief Introduction
• The controversy of polyploidy..
• Repetitive DNA evolution in polyploids
• Evolution of gene duplicates in paleopolyploids
• Genome diploidisation and fractionation in
paleopolyploids
• Cotton fiber transcriptomics and domestication
3. Introduction
• What is polyploidy
(whole genome
duplication; WGD)?
• More than a diploid set
of chromosomes
• Allo vs auto
• How to identify
polyploids?
4. Divergence time (mya)
Introduction
• Chromosome counts
• Age estimates of
duplicated genes
• Syntenty analysis
Jiao et al., 2011 Science
Schnable et al., 2011 PNAS
5. • The greatest
realization of the
plant genomics
era?
Introduction
Stebbins (1950) – 35%
Grant (1963,1981) – 47%
Goldblatt (1980) – 70-80%
Lewis (1980) – 70-80%
Current view – 100% of
seed plants are polyploid
6. • Are polyploids just “happy
accidents”?
OR
• Does WGD help explain Darwin’s
“abominable mystery” - the
“rapid rise and early
diversification” of the
angiosperms
Introduction
7. Three brief stories...
①Diversification of polyploid genomes
②Diversification of duplicated genes following
ancient WGD.
③How polyploids become more diploid-like
again, and again.
8. 1. Diversification of polyploid genomes
• Polyploid genomes are highly dynamic
– How do they vary?
– Over what time scale?
– Do different sub-genomes behave differently?
9. 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. Diversification of polyploid genomes
10. • Estimate repeat content of
progenitors and allopolyploid
– RepeatExplorer pipeline
– Assess divergence of the
allopolyploid from the diploids
Novak et al., 2010 BMC GenomicsRenny-Byfield et al., 2011 MBE
1. Diversification of polyploid genomes
12. WGDs and genome diversity
The paternal (N. tomentosiformis) genome
appears to be underrepresented in tobacco
Renny-Byfield et al., 2012 MBE
13. 2. Diversification of duplicated genes
following ancient WGD
“If as a consequence of polyploidy a large
number of genes become duplicated, and the
characters governed by such genes are of
importance to the species, one of the
members may mutate, leaving the character
unimpaired, with the further possibility that
the mutation may be of benefit to the
species”
S. C Harland, 1936
14. 2. Diversification of duplicated genes
following ancient WGD
• Neofunctionalization (Ohno, 1970)
• Sub-functionalisation (Force, Lynch and others)
http://www.personal.psu.edu/rua15/Stage3.jpg
18. Renny-Byfield et al., 2014 GBE
2. Diversification of duplicated genes
following ancient WGD
19. 2. Diversification of duplicated genes
following ancient WGD
Almost complete divergence in expression after ca. 60 my
Renny-Byfield et al., 2014 GBE
20. 2. Diversification of duplicated genes
following ancient WGD
Gene (G) effect Tissue (T) effect G x T interaction
Renny-Byfield et al., 2014 GBE
21. 3. Bias fractionation following
WGD
• What happens to most genes following WGD..
Woodhouse et al., 2010 PloS Biology
22. 3. Bias fractionation following
WGD
• CoGe SynMap tool
• Examine CDS for
colinearity with
reference genome
• Allows identification
of duplicated regions
26. 3. Bias fractionation following
WGD
Most Fractionated
Least Fractionated
24 sRNAs preferentially locate to the MF genome
27. “...it seemed to me probable that a
careful study … of cultivated plants
would offer the best chance of making
out this obscure problem…I may
venture to express my conviction of
the high value of such studies….”
“…If it profit a plant to have its seeds
more and more widely disseminated
by the wind, I can see no greater
difficulty in this being effected through
natural selection, than in the cotton-
planter increasing and improving by
selection the down in the pods on his
cotton-trees...”
28. Current project
• Two independent domestication events.
• One polyploid and one diploid
29. • RNAseq at Four development stages:
– 5 , 10, 15, and 20 DPA
• Wild and domesticated lines:
– Three in each group
• Polyploid and diploid groups:
– Wild A1, domesticated A1
– Wild AD1, domesticated AD1
Current project
30. • Gene Expression architecture
– How do transcriptional networks
alter (i.e. similar to Swanson-
Wagner et al.,2011)
– connectivity, edge weight,
movement of nodes.
– Superimposition of graph
structure to compare networks in
wild and domesticated (Lelandias al.,
2006, Bionformatics)
– Are there parallel changes in
diploid vs polyploid groups
Current project
http://www.georgebassellab.com/wp-
content/uploads/2012/01/seedNet.jpg
31. Conclusions
• WGD is ubiquitous in angiosperms
• Polyploid genomes are highly dynamic
• Parental sub-genomes can behave differently
• Gene duplication (via WGD) can result in biological
novelty
• Processes of genome turnover and fractionation
result in diploidization
• Bias fractionation linked to expression and local TE
coverage
