Whole genome duplication and plant genome diversity.spare

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