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
1. Diversifica0on of polyploid genomes
• 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
N. tom
S4 synthe0c tobacco
tobacco
N. tom
Renny-‐Byfield et al., 2012 PLoS One
1. Diversifica0on 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. Diversifica0on of duplicated genes following ancient WGD
• Neofunc0onaliza0on (Ohno, 1970) • Subfunc0onaliza0on (Force, Lynch and others)
hMp://www.personal.psu.edu/rua15/Stage3.jpg
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
2. Diversifica0on of duplicated genes following ancient WGD
Almost complete divergence in expression aier ca. 60 my
Renny-‐Byfield et al., 2014 GBE
2. Diversifica0on of duplicated genes following ancient WGD
Gene (G) effect Tissue (T) effect G x T interac0on
Renny-‐Byfield et al., 2014 GBE
3. Biased frac0ona0on following WGD
• What happens to most genes following WGD..
Woodhouse et al., 2010 PloS Biology
3. Biased frac0ona0on following WGD
• CoGe SynMap tool
• Examine CDS for colinearity with reference genome
• Allows iden0fica0on of duplicated regions
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
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
!"#$%#$%&'(%()*+#,)-%.$%*'*+/%0"(%/),1*"%0"#%$2%
3. Biased frac0ona0on following WGD
leaf petal seed
0
200
400
600
coun
t (nu
mbe
r of w
ins)
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
M L
F)
0.02
0.04
0.06
density
3. Biased frac0ona0on following WGD
0
2
4
6
−1000 −500 0 500 1000distance from transcription start/stop site (bp)
mea
n nu
mbe
r of m
appe
d re
ads Most Frac0onated
Least Frac0onated
24nt siRNAs preferen0ally locate to the MF genome
• 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
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