Whole genome duplication and diversification of plant genomes

Whole genome duplica0on and plant genome diversity

Simon Renny-‐Byfield Department of Ecology, Evolu0on and Organismal

Biology Iowa State University

May 12th 2014

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

Introduc0on

•  What is polyploidy (whole genome duplica0on; WGD)?

•  More than a diploid set of chromosomes

•  Allo vs auto •  How to iden0fy polyploids?

Divergence 0me (mya)

Introduc0on

•  Chromosome counts •  Age es0mates of duplicated genes

•  Syntenty analysis

Jiao et al., 2011 Science Schnable et al., 2011 PNAS

•  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

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.

1. Diversifica0on of polyploid genomes

•  Polyploid genomes are highly dynamic – How do they vary? – Over what 0me 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


•  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


N. tom

S4 synthe0c tobacco

tobacco

N. tom

Renny-‐Byfield et al., 2012 PLoS One


WGDs and genome diversity

The paternal (N. tomentosiformis) genome appears to be underrepresented in tobacco

Renny-‐Byfield et al., 2012 MBE

2. Diversifica0on of duplicated genes following ancient WGD

S. C Harland, 1936


•  Neofunc0onaliza0on (Ohno, 1970) •  Subfunc0onaliza0on (Force, Lynch and others)

hMp://www.personal.psu.edu/rua15/Stage3.jpg



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


Renny-‐Byfield et al., 2014 GBE



Almost complete divergence in expression aier ca. 60 my



Gene (G) effect Tissue (T) effect G x T interac0on


3. Biased frac0ona0on following WGD

•  What happens to most genes following WGD..

Woodhouse et al., 2010 PloS Biology


•  CoGe SynMap tool

•  Examine CDS for colinearity with reference genome

•  Allows iden0fica0on of duplicated regions



•  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

9 (190) 580 2637 10 (33,34,36) 227 2637

133.4951 <1x10-15

7 2 (88,86,89) 420 1873 13 (76,75) 225 1873

49.7891 1.7x10-12

8 5 (133,132) 236 2040 9 (191) 608 2040

135.7528 <1x10-15

9 4 (113,114,130) 343 3599 9 (188,189) 981 3599

260.1665 <1x10-15

9 (188,189) 981 3599 13 (79,80,81,82) 400 3599

205.1855 <1x10-15

4 (113,114,130) 343 3599 13 (79,80,81,82) 400 3599

5.0709 0.0243

10 9 (195) 397 1873 11 (44) 170 1873

78.3511 <1x10-15

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leaf petal seed

0

200

400

600

coun

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mbe

r of w

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LFMF

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 5log(RPKM MF)

log(

RPK

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0.02

0.04

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density


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−1000 −500 0 500 1000distance from transcription start/stop site (bp)

mea

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ads Most Frac0onated

Least Frac0onated

24nt siRNAs preferen0ally locate to the MF genome

Current project

•  Two independent domes0ca0on events.

•  One polyploid and one diploid

•  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

•  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

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