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Jeffrey Ross-Ibarra
@jrossibarra • www.rilab.org
Plant Sciences • Center for Population Biology • Genome Center
University of California Davis
Bigger is different: the role of plant genome
size in adaptation
Brandon Gaut
log haploid genome size
Zea maysA. thaliana
#species
Brandon Gaut
log haploid genome size
Zea maysA. thaliana
#species
Springer et al. (2016) Plant Cell
1 Megabase DNA
maize
Arabidopsis
Lloyd et al. 2017 bioRxiv
A .thaliana functional prediction
Lloyd et al. 2017 bioRxiv
A .thaliana functional prediction
Lloyd et al. 2017 bioRxiv
A .thaliana functional prediction
Rodgers-Melnick et al. 2016 PNAS
b Ames Diversity Panel
Intergenic Open
Chromatin (33%)
Coding
(41%)
UTR, proximal
% VA explained in maize
(height, flowering, etc.)
● ●
●
●
0
5
10
15
20
25
200 400 600 800 1000
Genome Size (Mb)
OpenChromatinSize(Mb)
Genome_feature
●
Exon
Intergenic
Proximal
Total_open_chromatin
A
75%
80%
85%
90%
95%
%Non−exonicOpenChromatin
B
Maher et al. 2017 bioRxiv
Mei et al. 2017 bioRxiv
Rodgers-Melnick et al. 2016 PNAS
b Ames Diversity Panel
Intergenic Open
Chromatin (33%)
Coding
(41%)
UTR, proximal
% VA explained in maize
(height, flowering, etc.)
25%
75%
78%
22%
0%
25%
50%
75%
100%
Arabidopsis Maize
Species
Percentage
Genic Non−genic
a
0.0
0.2
0.4
0.6
0.8
100
101
102
103
104
105
106
Arabidopsis non−genic GWAS hits
distance to nearest gene (bp, log scale)
Density
b
0.0
0.2
0.4
0.6
0.8
100
101
102
103
104
105
106
Maize non−genic GWAS hits
distance to nearest gene (bp, log scale)
Density
c
Mei et al. 2017 bioRxiv
GWAS hits
25%
75%
78%
22%
0%
25%
50%
75%
100%
Arabidopsis Maize
Species
Percentage
Genic Non−genic
a
0.0
0.2
0.4
0.6
0.8
100
101
102
103
104
105
106
Arabidopsis non−genic GWAS hits
distance to nearest gene (bp, log scale)
Density
b
0.0
0.2
0.4
0.6
0.8
100
101
102
103
104
105
106
Maize non−genic GWAS hits
distance to nearest gene (bp, log scale)
Density
c
Mei et al. 2017 bioRxiv
GWAS hits
Doebley 2004, Studer et al. 2011
tb1
Hopscotch
ZmCCT
CACTA
Yang et al. 2013
plant architecture flowering time
Pyhäjärvi et al. 2013 GBEFigure S4 LD in chromosome 9 among mexicana populations based on SNPs with minor
allele frequency >0.1.
Inv9d
Inv9e
Inv4n
macrohairs,
anthocyanin
Hufford et al. 2013 PLoS Genetics
Pyhäjärvi et al. 2013 GBEFigure S4 LD in chromosome 9 among mexicana populations based on SNPs with minor
allele frequency >0.1.
Inv9d
Inv9e
Pyhäjärvi et al. 2013 GBE
4% of B73 absent
~8% absent
30% of the low copy sequence
absent from reference genome
%readsunmappedreads
Gore et al. 2009 Science
Chia et al 2012 Nat Gen
✓⇡
n 1X
i=1
1
i
= S
θπ	~	8%	pairwise	diff	
1-S%	pan-genome	in	ref
4% of B73 absent
~8% absent
30% of the low copy sequence
absent from reference genome
%readsunmappedreads
Gore et al. 2009 Science
Chia et al 2012 Nat Gen
✓⇡
n 1X
i=1
1
i
= S
θπ	~	8%	pairwise	diff	
1-S%	pan-genome	in	ref
0%#
20%#
40%#
60%#
80%#
100%#
Angle# Length# NLB# SLB# Width#
10kb%RDV% Gene%RDV% HapMap2%genic%
HapMap2%Intergenic% HapMap1%genic% HapMap1%Intergenic%
0#
2#
4#
6#
8#
10#
12#
14#
16#
18#
20#
Angle# Length# NLB# SLB# Width# 0#
25#
30#
35#
Intergenic# Intronic#SNPs#
UTR# UP/Down#Stream#
Syn#SNP# Splice#Site#
NonSyn#SNP# 10Kb#RDV#
A.# B.# C.#
D.#
0%#
20%#
40%#
60%#
80%#
100%#
Angle# Length# NLB# SLB# Width#
10kb%RDV% Gene%RDV%
HapMap2%Intergenic% HapMap1%genic%
20#
25#
30#
35#
lue#(Hlog10)#
Intergenic# Intronic#SNPs#
UTR# UP/Down#Stream#
Syn#SNP# Splice#Site#
NonSyn#SNP# 10Kb#RDV#
Gene#RDV#
A.# B.
D.#
0%#
20%#
40%#
60%#
80%#
100%#
Angle# Length# NLB# SLB# Width#
10kb%RDV% Gene%RDV% HapMap2%genic%
HapMap2%Intergenic% HapMap1%genic% HapMap1%Interge
0#
2#
4#
6#
8#
10#
12#
14#
16#
18#
20#
Angle# Length# NLB#
25#
30#
35#
g10)#
Intergenic# Intronic#SNPs#
UTR# UP/Down#Stream#
Syn#SNP# Splice#Site#
NonSyn#SNP# 10Kb#RDV#
Gene#RDV#
A.# B.#
D.#
0%#
20%#
40%#
60%#
80%#
100%#
Angle# Length# NLB# SLB# Width#
10kb%RDV% Gene%RDV% HapMap2%genic%
HapMap2%Intergenic% HapMap1%genic% HapMap1%Intergenic%
0#
2#
4#
6#
8#
10#
12#
14#
16#
18#
20#
Angle# Length# NLB# SLB# Width#
Intergenic
0# 0.5#
10#
15#
20#
25#
30#
35#
pHvalue#(Hlog10)#
Intergenic# Intronic#SNPs#
UTR# UP/Down#Stream#
Syn#SNP# Splice#Site#
NonSyn#SNP# 10Kb#RDV#
Gene#RDV#
A.# B.# C.#
D.#
foldenrichment
hard
sweep
Hermisson & Pennings 2017 Meth Ecol Evol
hard
sweep
Hermisson & Pennings 2017 Meth Ecol Evol
hard
sweep
Hermisson & Pennings 2017 Meth Ecol Evol
hard
sweep
multiple
mutations
“soft” sweeps
Hermisson & Pennings 2017 Meth Ecol Evol
hard
sweep
multiple
mutations
standing
variation
“soft” sweeps
Hermisson & Pennings 2017 Meth Ecol Evol
hard
sweep
multiple
mutations
standing
variation
“soft” sweeps
Θb=4ΝeμbL
beneficial
mutation rate
genome
size
effective
population
size
Hermisson & Pennings 2017 Meth Ecol Evol
hard
sweep
multiple
mutations
standing
variation
“soft” sweeps
Θb=4ΝeμbL
beneficial
mutation rate
genome
size
effective
population
size
Hermisson & Pennings 2017 Meth Ecol Evol
Θb<1 Θb>1
Beissinger et al. 2016 Nature Plants
nucleotidediversity
distance to nearest substitution (cM)
prediction: bigger genomes have few hard sweeps
Beissinger et al. 2016 Nature Plants
nucleotidediversity
distance to nearest substitution (cM)
prediction: bigger genomes have few hard sweeps
Sattah et al. 2011 PLoS Gen.
Williamson et al. 2014 PLoS Gen
Hernandez et al. 2011 Science
Beissinger et al. 2016 Nature Plants
L = 2,500 Mbp
Sattah et al. 2011 PLoS Gen.
Williamson et al. 2014 PLoS Gen
Hernandez et al. 2011 Science
Beissinger et al. 2016 Nature Plants
L = 2,500 Mbp
diversity
L = 220 Mbp
Sattah et al. 2011 PLoS Gen.
Williamson et al. 2014 PLoS Gen
Hernandez et al. 2011 Science
Beissinger et al. 2016 Nature Plants
L = 2,500 Mbp
distance from substitution
L = 3,100 Mbp
L = 130 Mbp
diversity
L = 220 Mbp
M T G P H R L
GGTCGAC ATG ACT GGT CCA CAT CGA CTG TAG
M T G P H R L
GGTCGAC ATG ACT GGT CCA CAT CGA CTG TAG
M T N P H R L
GGTCGAC ATG ACT GAT CCA CAT CGA CTG TAG
structural
change to protein
M T G P H R L
GGTAAAC ATG ACT GGT CCA CAT CGA CTG TAG
GG—-AC ATG ACT GGT CCA CAT CGA CTG TAG
regulatory change to
expression
Hufford et al. 2012 Nat. Gen.
Chia et al. 2012 Nat. Gen
maizeteosinte
prediction: bigger genomes have more intergenic (regulatory?) adaptation
Hufford et al. 2012 Nat. Gen.
Chia et al. 2012 Nat. Gen
maizeteosinte
prediction: bigger genomes have more intergenic (regulatory?) adaptation
Hufford et al. 2012 Nat. Gen.
Chia et al. 2012 Nat. Gen
maizeteosinte
prediction: bigger genomes have more intergenic (regulatory?) adaptation
5-10% selected regions
do not include genes
Takuno et al. 2015 Genetics
Low High
common garden
Takuno et al. 2015 Genetics
39%
61%
Intergenic
Genic
19%
81%
Standing Variation
New mutation
Low High
common garden adaptive variants
Pyhäjärvi et al. GBE 2013
enrichment
intergenic<——>coding
Hancock et al 2011 Science
environmental
association
allele freq.
differentiation
Pyhäjärvi et al. GBE 2013
enrichment
intergenic<——>coding
Hancock et al 2011 Science
enrichment
no<———>yes
intergenic
synonymous
nonsynonymous
environmental
association
allele freq.
differentiation
Mei et al. 2017 bioRxiv
%adaptivenonsynonymous
substitutions
p=0.0075
prediction: big genomes have fewer adaptive nonsynonymous substitutions
● ●
●
●
0
5
10
15
20
25
200 400 600 800 1000
Genome Size (Mb)
OpenChromatinSize(Mb)
Genome_feature
●
Exon
Intergenic
Proximal
Total_open_chromatin
A
●
●
75%
80%
85%
90%
95%
500 1000 1500 2000 2500
Genome Size (Mb)
%Non−exonicOpenChromatin
Species
●
●
●
●
●
●
●
●
●
Arabidopsis
Brachypodium
Cotton
Maize
Medicago
Millet
Rice
Sorghum
Tomato
Tissue
●
●
Callus
Fiber
Fruit
Leaf
Root
Seedling
Shoot
B
Genome
Functional
Space
● ●
●
●
0
5
10
15
20
25
200 400 600 800 1000
Genome Size (Mb)
OpenChromatinSize(Mb)
Genome_feature
●
Exon
Intergenic
Proximal
Total_open_chromatin
A
●
●
75%
80%
85%
90%
95%
500 1000 1500 2000 2500
Genome Size (Mb)
%Non−exonicOpenChromatin
Species
●
●
●
●
●
●
●
●
●
Arabidopsis
Brachypodium
Cotton
Maize
Medicago
Millet
Rice
Sorghum
Tomato
Tissue
●
●
Callus
Fiber
Fruit
Leaf
Root
Seedling
Shoot
B
Genome
Functional
Space
Functional
Space
Hard sweeps
● ●
●
●
0
5
10
15
20
25
200 400 600 800 1000
Genome Size (Mb)
OpenChromatinSize(Mb)
Genome_feature
●
Exon
Intergenic
Proximal
Total_open_chromatin
A
●
●
75%
80%
85%
90%
95%
500 1000 1500 2000 2500
Genome Size (Mb)
%Non−exonicOpenChromatin
Species
●
●
●
●
●
●
●
●
●
Arabidopsis
Brachypodium
Cotton
Maize
Medicago
Millet
Rice
Sorghum
Tomato
Tissue
●
●
Callus
Fiber
Fruit
Leaf
Root
Seedling
Shoot
B
Genome
Functional
Space
Functional
Space
Soft Sweeps
Intergenic
Adaptation
Functional
Space
Hard sweeps
Acknowledgements
UC Davis
Graham Coop
Wenbin Mei
Dan Gates
Markus Stetter
Michelle Stitzer
Plant Genome
Research Program
HiLo
Lab Alumni
Matt Hufford (Iowa State)
Tanja Pyhäjärvi (Oulu)
Shohei Takuno (Sokendai)
● ●
●
●
0
5
10
15
20
25
200 400 600 800 1000
Genome Size (Mb)
OpenChromatinSize(Mb)
Genome_feature
●
Exon
Intergenic
Proximal
Total_open_chromatin
A
●
●
75%
80%
85%
90%
95%
500 1000 1500 2000 2500
Genome Size (Mb)
%Non−exonicOpenChromatin
Species
●
●
●
●
●
●
●
●
●
Arabidopsis
Brachypodium
Cotton
Maize
Medicago
Millet
Rice
Sorghum
Tomato
Tissue
●
●
Callus
Fiber
Fruit
Leaf
Root
Seedling
Shoot
B
Genome
Functional
Space
● ●
●
●
0
5
10
15
20
25
200 400 600 800 1000
Genome Size (Mb)
OpenChromatinSize(Mb)
Genome_feature
●
Exon
Intergenic
Proximal
Total_open_chromatin
A
●
●
75%
80%
85%
90%
95%
500 1000 1500 2000 2500
Genome Size (Mb)
%Non−exonicOpenChromatin
Species
●
●
●
●
●
●
●
●
●
Arabidopsis
Brachypodium
Cotton
Maize
Medicago
Millet
Rice
Sorghum
Tomato
Tissue
●
●
Callus
Fiber
Fruit
Leaf
Root
Seedling
Shoot
B
Genome
Functional
Space
Functional
Space
Hard sweeps
● ●
●
●
0
5
10
15
20
25
200 400 600 800 1000
Genome Size (Mb)
OpenChromatinSize(Mb)
Genome_feature
●
Exon
Intergenic
Proximal
Total_open_chromatin
A
●
●
75%
80%
85%
90%
95%
500 1000 1500 2000 2500
Genome Size (Mb)
%Non−exonicOpenChromatin
Species
●
●
●
●
●
●
●
●
●
Arabidopsis
Brachypodium
Cotton
Maize
Medicago
Millet
Rice
Sorghum
Tomato
Tissue
●
●
Callus
Fiber
Fruit
Leaf
Root
Seedling
Shoot
B
Genome
Functional
Space
Functional
Space
Soft Sweeps
Intergenic
Adaptation
Functional
Space
Hard sweeps

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Adaptation in plant genomes: bigger is different

  • 1. Jeffrey Ross-Ibarra @jrossibarra • www.rilab.org Plant Sciences • Center for Population Biology • Genome Center University of California Davis Bigger is different: the role of plant genome size in adaptation
  • 2.
  • 3. Brandon Gaut log haploid genome size Zea maysA. thaliana #species
  • 4. Brandon Gaut log haploid genome size Zea maysA. thaliana #species Springer et al. (2016) Plant Cell 1 Megabase DNA maize Arabidopsis
  • 5. Lloyd et al. 2017 bioRxiv A .thaliana functional prediction
  • 6. Lloyd et al. 2017 bioRxiv A .thaliana functional prediction
  • 7. Lloyd et al. 2017 bioRxiv A .thaliana functional prediction Rodgers-Melnick et al. 2016 PNAS b Ames Diversity Panel Intergenic Open Chromatin (33%) Coding (41%) UTR, proximal % VA explained in maize (height, flowering, etc.)
  • 8. ● ● ● ● 0 5 10 15 20 25 200 400 600 800 1000 Genome Size (Mb) OpenChromatinSize(Mb) Genome_feature ● Exon Intergenic Proximal Total_open_chromatin A 75% 80% 85% 90% 95% %Non−exonicOpenChromatin B Maher et al. 2017 bioRxiv Mei et al. 2017 bioRxiv Rodgers-Melnick et al. 2016 PNAS b Ames Diversity Panel Intergenic Open Chromatin (33%) Coding (41%) UTR, proximal % VA explained in maize (height, flowering, etc.)
  • 9. 25% 75% 78% 22% 0% 25% 50% 75% 100% Arabidopsis Maize Species Percentage Genic Non−genic a 0.0 0.2 0.4 0.6 0.8 100 101 102 103 104 105 106 Arabidopsis non−genic GWAS hits distance to nearest gene (bp, log scale) Density b 0.0 0.2 0.4 0.6 0.8 100 101 102 103 104 105 106 Maize non−genic GWAS hits distance to nearest gene (bp, log scale) Density c Mei et al. 2017 bioRxiv GWAS hits
  • 10. 25% 75% 78% 22% 0% 25% 50% 75% 100% Arabidopsis Maize Species Percentage Genic Non−genic a 0.0 0.2 0.4 0.6 0.8 100 101 102 103 104 105 106 Arabidopsis non−genic GWAS hits distance to nearest gene (bp, log scale) Density b 0.0 0.2 0.4 0.6 0.8 100 101 102 103 104 105 106 Maize non−genic GWAS hits distance to nearest gene (bp, log scale) Density c Mei et al. 2017 bioRxiv GWAS hits
  • 11. Doebley 2004, Studer et al. 2011 tb1 Hopscotch ZmCCT CACTA Yang et al. 2013 plant architecture flowering time
  • 12. Pyhäjärvi et al. 2013 GBEFigure S4 LD in chromosome 9 among mexicana populations based on SNPs with minor allele frequency >0.1. Inv9d Inv9e
  • 13. Inv4n macrohairs, anthocyanin Hufford et al. 2013 PLoS Genetics Pyhäjärvi et al. 2013 GBEFigure S4 LD in chromosome 9 among mexicana populations based on SNPs with minor allele frequency >0.1. Inv9d Inv9e Pyhäjärvi et al. 2013 GBE
  • 14. 4% of B73 absent ~8% absent 30% of the low copy sequence absent from reference genome %readsunmappedreads Gore et al. 2009 Science Chia et al 2012 Nat Gen ✓⇡ n 1X i=1 1 i = S θπ ~ 8% pairwise diff 1-S% pan-genome in ref
  • 15. 4% of B73 absent ~8% absent 30% of the low copy sequence absent from reference genome %readsunmappedreads Gore et al. 2009 Science Chia et al 2012 Nat Gen ✓⇡ n 1X i=1 1 i = S θπ ~ 8% pairwise diff 1-S% pan-genome in ref 0%# 20%# 40%# 60%# 80%# 100%# Angle# Length# NLB# SLB# Width# 10kb%RDV% Gene%RDV% HapMap2%genic% HapMap2%Intergenic% HapMap1%genic% HapMap1%Intergenic% 0# 2# 4# 6# 8# 10# 12# 14# 16# 18# 20# Angle# Length# NLB# SLB# Width# 0# 25# 30# 35# Intergenic# Intronic#SNPs# UTR# UP/Down#Stream# Syn#SNP# Splice#Site# NonSyn#SNP# 10Kb#RDV# A.# B.# C.# D.# 0%# 20%# 40%# 60%# 80%# 100%# Angle# Length# NLB# SLB# Width# 10kb%RDV% Gene%RDV% HapMap2%Intergenic% HapMap1%genic% 20# 25# 30# 35# lue#(Hlog10)# Intergenic# Intronic#SNPs# UTR# UP/Down#Stream# Syn#SNP# Splice#Site# NonSyn#SNP# 10Kb#RDV# Gene#RDV# A.# B. D.# 0%# 20%# 40%# 60%# 80%# 100%# Angle# Length# NLB# SLB# Width# 10kb%RDV% Gene%RDV% HapMap2%genic% HapMap2%Intergenic% HapMap1%genic% HapMap1%Interge 0# 2# 4# 6# 8# 10# 12# 14# 16# 18# 20# Angle# Length# NLB# 25# 30# 35# g10)# Intergenic# Intronic#SNPs# UTR# UP/Down#Stream# Syn#SNP# Splice#Site# NonSyn#SNP# 10Kb#RDV# Gene#RDV# A.# B.# D.# 0%# 20%# 40%# 60%# 80%# 100%# Angle# Length# NLB# SLB# Width# 10kb%RDV% Gene%RDV% HapMap2%genic% HapMap2%Intergenic% HapMap1%genic% HapMap1%Intergenic% 0# 2# 4# 6# 8# 10# 12# 14# 16# 18# 20# Angle# Length# NLB# SLB# Width# Intergenic 0# 0.5# 10# 15# 20# 25# 30# 35# pHvalue#(Hlog10)# Intergenic# Intronic#SNPs# UTR# UP/Down#Stream# Syn#SNP# Splice#Site# NonSyn#SNP# 10Kb#RDV# Gene#RDV# A.# B.# C.# D.# foldenrichment
  • 16. hard sweep Hermisson & Pennings 2017 Meth Ecol Evol
  • 17. hard sweep Hermisson & Pennings 2017 Meth Ecol Evol
  • 18. hard sweep Hermisson & Pennings 2017 Meth Ecol Evol
  • 23. Beissinger et al. 2016 Nature Plants nucleotidediversity distance to nearest substitution (cM) prediction: bigger genomes have few hard sweeps
  • 24. Beissinger et al. 2016 Nature Plants nucleotidediversity distance to nearest substitution (cM) prediction: bigger genomes have few hard sweeps
  • 25. Sattah et al. 2011 PLoS Gen. Williamson et al. 2014 PLoS Gen Hernandez et al. 2011 Science Beissinger et al. 2016 Nature Plants L = 2,500 Mbp
  • 26. Sattah et al. 2011 PLoS Gen. Williamson et al. 2014 PLoS Gen Hernandez et al. 2011 Science Beissinger et al. 2016 Nature Plants L = 2,500 Mbp diversity L = 220 Mbp
  • 27. Sattah et al. 2011 PLoS Gen. Williamson et al. 2014 PLoS Gen Hernandez et al. 2011 Science Beissinger et al. 2016 Nature Plants L = 2,500 Mbp distance from substitution L = 3,100 Mbp L = 130 Mbp diversity L = 220 Mbp
  • 28. M T G P H R L GGTCGAC ATG ACT GGT CCA CAT CGA CTG TAG
  • 29. M T G P H R L GGTCGAC ATG ACT GGT CCA CAT CGA CTG TAG M T N P H R L GGTCGAC ATG ACT GAT CCA CAT CGA CTG TAG structural change to protein
  • 30. M T G P H R L GGTAAAC ATG ACT GGT CCA CAT CGA CTG TAG GG—-AC ATG ACT GGT CCA CAT CGA CTG TAG regulatory change to expression
  • 31. Hufford et al. 2012 Nat. Gen. Chia et al. 2012 Nat. Gen maizeteosinte prediction: bigger genomes have more intergenic (regulatory?) adaptation
  • 32. Hufford et al. 2012 Nat. Gen. Chia et al. 2012 Nat. Gen maizeteosinte prediction: bigger genomes have more intergenic (regulatory?) adaptation
  • 33. Hufford et al. 2012 Nat. Gen. Chia et al. 2012 Nat. Gen maizeteosinte prediction: bigger genomes have more intergenic (regulatory?) adaptation 5-10% selected regions do not include genes
  • 34. Takuno et al. 2015 Genetics Low High common garden
  • 35. Takuno et al. 2015 Genetics 39% 61% Intergenic Genic 19% 81% Standing Variation New mutation Low High common garden adaptive variants
  • 36. Pyhäjärvi et al. GBE 2013 enrichment intergenic<——>coding Hancock et al 2011 Science environmental association allele freq. differentiation
  • 37. Pyhäjärvi et al. GBE 2013 enrichment intergenic<——>coding Hancock et al 2011 Science enrichment no<———>yes intergenic synonymous nonsynonymous environmental association allele freq. differentiation
  • 38. Mei et al. 2017 bioRxiv %adaptivenonsynonymous substitutions p=0.0075 prediction: big genomes have fewer adaptive nonsynonymous substitutions
  • 39. ● ● ● ● 0 5 10 15 20 25 200 400 600 800 1000 Genome Size (Mb) OpenChromatinSize(Mb) Genome_feature ● Exon Intergenic Proximal Total_open_chromatin A ● ● 75% 80% 85% 90% 95% 500 1000 1500 2000 2500 Genome Size (Mb) %Non−exonicOpenChromatin Species ● ● ● ● ● ● ● ● ● Arabidopsis Brachypodium Cotton Maize Medicago Millet Rice Sorghum Tomato Tissue ● ● Callus Fiber Fruit Leaf Root Seedling Shoot B Genome Functional Space
  • 40. ● ● ● ● 0 5 10 15 20 25 200 400 600 800 1000 Genome Size (Mb) OpenChromatinSize(Mb) Genome_feature ● Exon Intergenic Proximal Total_open_chromatin A ● ● 75% 80% 85% 90% 95% 500 1000 1500 2000 2500 Genome Size (Mb) %Non−exonicOpenChromatin Species ● ● ● ● ● ● ● ● ● Arabidopsis Brachypodium Cotton Maize Medicago Millet Rice Sorghum Tomato Tissue ● ● Callus Fiber Fruit Leaf Root Seedling Shoot B Genome Functional Space Functional Space Hard sweeps
  • 41. ● ● ● ● 0 5 10 15 20 25 200 400 600 800 1000 Genome Size (Mb) OpenChromatinSize(Mb) Genome_feature ● Exon Intergenic Proximal Total_open_chromatin A ● ● 75% 80% 85% 90% 95% 500 1000 1500 2000 2500 Genome Size (Mb) %Non−exonicOpenChromatin Species ● ● ● ● ● ● ● ● ● Arabidopsis Brachypodium Cotton Maize Medicago Millet Rice Sorghum Tomato Tissue ● ● Callus Fiber Fruit Leaf Root Seedling Shoot B Genome Functional Space Functional Space Soft Sweeps Intergenic Adaptation Functional Space Hard sweeps
  • 42. Acknowledgements UC Davis Graham Coop Wenbin Mei Dan Gates Markus Stetter Michelle Stitzer Plant Genome Research Program HiLo Lab Alumni Matt Hufford (Iowa State) Tanja Pyhäjärvi (Oulu) Shohei Takuno (Sokendai)
  • 43. ● ● ● ● 0 5 10 15 20 25 200 400 600 800 1000 Genome Size (Mb) OpenChromatinSize(Mb) Genome_feature ● Exon Intergenic Proximal Total_open_chromatin A ● ● 75% 80% 85% 90% 95% 500 1000 1500 2000 2500 Genome Size (Mb) %Non−exonicOpenChromatin Species ● ● ● ● ● ● ● ● ● Arabidopsis Brachypodium Cotton Maize Medicago Millet Rice Sorghum Tomato Tissue ● ● Callus Fiber Fruit Leaf Root Seedling Shoot B Genome Functional Space
  • 44. ● ● ● ● 0 5 10 15 20 25 200 400 600 800 1000 Genome Size (Mb) OpenChromatinSize(Mb) Genome_feature ● Exon Intergenic Proximal Total_open_chromatin A ● ● 75% 80% 85% 90% 95% 500 1000 1500 2000 2500 Genome Size (Mb) %Non−exonicOpenChromatin Species ● ● ● ● ● ● ● ● ● Arabidopsis Brachypodium Cotton Maize Medicago Millet Rice Sorghum Tomato Tissue ● ● Callus Fiber Fruit Leaf Root Seedling Shoot B Genome Functional Space Functional Space Hard sweeps
  • 45. ● ● ● ● 0 5 10 15 20 25 200 400 600 800 1000 Genome Size (Mb) OpenChromatinSize(Mb) Genome_feature ● Exon Intergenic Proximal Total_open_chromatin A ● ● 75% 80% 85% 90% 95% 500 1000 1500 2000 2500 Genome Size (Mb) %Non−exonicOpenChromatin Species ● ● ● ● ● ● ● ● ● Arabidopsis Brachypodium Cotton Maize Medicago Millet Rice Sorghum Tomato Tissue ● ● Callus Fiber Fruit Leaf Root Seedling Shoot B Genome Functional Space Functional Space Soft Sweeps Intergenic Adaptation Functional Space Hard sweeps