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Whole genome duplica0on and plant genome diversity Simon RennyByfield Department of Ecology, Evolu0on and Organismal Biology Iowa State University May 12 th 2014

Whole genome duplication and diversification of plant genomes

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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  

S.  C  Harland,  1936  

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  

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  

Renny-­‐Byfield  et  al.,  2014  GBE  

2.  Diversifica0on  of  duplicated  genes  following  ancient  WGD  

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  

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  

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