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Whole genome duplication and plant genome diversity
Simon Renny-ByfieldDepartment of Ecology, Evolution and Organismal Biology
Iowa State University May 12th 2014
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
Introduction
• What is polyploidy (whole genome duplication; WGD)?
• More than a diploid set of chromosomes
• Allo vs auto• How to identify
polyploids?
Divergence time (mya)
Introduction
• Chromosome counts • Age estimates of
duplicated genes• Syntenty analysis
Jiao et al., 2011 ScienceSchnable et al., 2011 PNAS
• The greatest realization of the plant genomics era?
IntroductionStebbins (1950) – 35%Grant (1963,1981) – 47%Goldblatt (1980) – 70-80%Lewis (1980) – 70-80%
Current view – 100% of seed plants are polyploid
• Are polyploids just “happy accidents”?
OR
• Does WGD help explain Darwin’s “abominable mystery” - the “rapid rise and early diversification” of the angiosperms
Introduction
Three brief stories...
①Diversification of polyploid genomes
②Diversification of duplicated genes following ancient WGD.
③How polyploids become more diploid-like again, and again.
1. Diversification of polyploid genomes
• Polyploid genomes are highly dynamic– How do they vary?– Over what time scale?– Do different sub-genomes behave differently?
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
• 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
N. tom
S4 synthetic tobacco
tobacco
N. tom
Renny-Byfield et al., 2012 PLoS One
1. Diversification of polyploid genomes
WGDs and genome diversity
The paternal (N. tomentosiformis) genome appears to be underrepresented in tobacco
Renny-Byfield et al., 2012 MBE
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
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
2. Diversification of duplicated genes following ancient WGD
2. Diversification of duplicated genes following ancient WGD
leaf rootste
mcotyledon
bractpetal
stamen
carpelovule 10 d
ovule 20 d
genomic DNA
Dt 64 37 45 37 65 100 100 0 100 64 51At 36 63 55 63 35 0 0 100 0 36 49
Reciprocal silencing of alternative homoeologs
Adams et al., 2003
2. Diversification of duplicated genes following ancient WGD
Renny-Byfield et al., 2014 GBE
2. Diversification of duplicated genes following ancient WGD
2. Diversification of duplicated genes following ancient WGD
Almost complete divergence in expression after ca. 60 my
Renny-Byfield et al., 2014 GBE
2. Diversification of duplicated genes following ancient WGD
Gene (G) effect Tissue (T) effect G x T interaction
Renny-Byfield et al., 2014 GBE
3. Bias fractionation following WGD
• What happens to most genes following WGD..
Woodhouse et al., 2010 PloS Biology
3. Bias fractionation following WGD
• CoGe SynMap tool
• Examine CDS for colinearity with reference genome
• Allows identification of duplicated regions
3. Bias fractionation following WGD
3. Bias fractionation following WGD
• Ten chromosome level comparisons
• Significant bias in gene loss in all comparisons
3. Bias fractionation following WGD
Over expression of genes on LF chromosomes
3. Bias fractionation following WGD
Most Fractionated
Least Fractionated
24 sRNAs preferentially locate to the MF genome
“...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...”
Current project
• Two independent domestication events.
• One polyploid and one diploid
• 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
• 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
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
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