Supplemental Figure 1. Overview of synteny conservation ... · Criteria to score collinearity conservation were: 1) ... AT4G36920 FLO2,AP2,FL1 (1714) AT3G44460 ATBZIP67,DPBF2

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Supplemental Figure 1. Overview of synteny conservation between Arabidopsis and other dicot

species. This figure shows the percentage of orthologous genes for each Arabidopsis gene for which the flanking genes were conserved by collinearity. Criteria to score collinearity conservation were: 1) whether the genes upstream and/or downstream of the ortholog in the comparator species were orthologous to the genes upstream and/or downstream of the Arabidopsis test gene and 2) whether these orthologs maintained the same relative orientation. In the figure complete (both upstream and downstream)(white box), upstream (grey box) and downstream (black box) conservation is shown. Asterisks indicate species included for phylogenetic footprinting (Arabidopsis lyrata was excluded due to a non-saturated substitution pattern).

Supplemental Data. Van de Velde et al. Plant Cell (2014) 10.1105/tpc.114.127001

Supplemental Figure 2. Distribution of genes that have orthologs in the dicot comparator species for each orthology detection method.The number of Arabidopsis genes with orthologs in different comparator dicot species is depicted for the

integrative orthology (purple boxes) and BHIF method (blue boxes), respectively (left y-axis). A cumulative

overview is also shown for both methods (purple and blue line, respectively) showing the total percentage

of genes for which orthologs could be delineated (right y-axis).

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Supplemental Figure 3. Recovery of experimental AtProbe elements using different phylogenetic footprinting approaches.A) For the different phylogenetic footprinting approaches developed in this study, the recovery of AtProbe elements was determined. Black boxes show the percentage of recovered elements while white boxes show the percentage of uniquely recovered elements. The black line shows the cumulative recovery over all methods. B) A venn diagram was constructed for the four methods that recovered AtProbe elements. The number of recovered elements for Sigma are displayed in black, for ACANA in green, for Seaweeds 60 in yellow and for CMM in purple.

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Supplemental Figure 4. Recovery of AtProbe elements for the CNSs described in this paper (A)

and by Haudry et al. (2013)(B). Black lines denote upstream sequences, colored boxes depict AtProbe elements, and black boxes show significant CNSs.


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sites flower

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Supplemental Figure 5. Enrichment and overlap of in vivo functional regions with CNSs.Grey boxes show the fold enrichment of different histone marks and DH sites. Black diamonds show

the percentages of CNSs that overlap with each in vivo functional region dataset.


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Supplemental Figure 6. Comparison of fold enrichment for in vivo functional binding site regions.Fold enrichment for in vivo functional binding sites is shown for our CNSs dataset (white boxes),

simple motif mapping (grey boxes) and motif mapping within DH sites (black boxes).


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AT1G22640 MYB3 (48)AT5G02030 HB-6,LSN,RPL,BLH9,PNY (437)AT2G41070 EEL,BZIP12,DPBF4 (4)AT3G09230 MYB1 (64)AT5G12870 MYB46 (902)AT4G38620 MYB4 (752)AT3G08500 MYB83 (659)AT5G62380 ANAC101,VND6 (462)AT1G71930 ANAC030,VND7 (449)AT3G61910 ANAC066,NST2 (449)AT1G32770 ANAC012,SND1,NST3 (449)AT2G46770 ANAC043,NST1 (449)AT1G28300 LEC2 (42)AT4G18960 AG (25)AT2G45660 AGL20,SOC1 (158)AT3G54340 AP3,ATAP3 (2041)AT1G20980 SPL14,SPL1R2,FBR6 (31)AT4G37750 CKC,DRG,CKC1,ANT (30)AT5G15800 AGL2,SEP1 (35)AT2G03710 AGL3,SEP4 (15) AT5G61850 LFY3,LFY (1483)AT3G26790 FUS3 (1298)AT4G36990 HSF4,HSFB1 (931)AT3G23240 ERF1 (231)AT5G20240 PI (1382)AT4G36920 FLO2,AP2,FL1 (1714)AT3G44460 ATBZIP67,DPBF2 (812)AT3G45150 TCP16 (85)AT5G39610 ANAC092,ORE1 (281)AT3G24650 SIS10,ABI3 (226)AT1G32640 MYC2,JIN1,JAI1,ZBF1 (650)AT5G13790 AGL15 (4543)AT1G59750 ARF1 (783)AT5G08790 ANAC081,ATAF2 (859)AT1G13260 EDF4,RAV1 (1130)AT5G22220 E2FB,E2F1 (13)AT1G47870 E2FC,ATE2F2 (59)AT5G14960 E2FD,E2L1,DEL2 (59)AT2G36010 E2FA,E2F3 (146)AT3G01330 E2FF,E2L2,DEL3 (133)AT2G47190 MYB2 (129)AT4G31800 WRKY18 (45)AT3G62420 BZIP53 (218)AT2G18160 BZIP2,GBF5 (218)AT4G34590 GBF6,BZIP11,ATB2 (218)AT1G75390 BZIP44 (218)AT5G65210 TGA1 (222)AT1G45249 ABF2,AREB1(264)AT5G11260 TED 5,HY5 (114)AT4G25470 FTQ4,CBF2,DREB1C (114)AT4G36730 GBF1 (106)AT4G01120 GBF2,ATBZIP54 (106)AT2G46270 GBF3 (106)AT2G36270 ABI5,GIA1 (53)AT1G69490 ANAC029,NAP (2)AT3G27920 MYB0,GL1 (39)AT1G51600 GATA28,TIFY2A,ZML2 (50)AT3G24520 HSFC1 (47)AT5G10140 FLC,FLF,AGL25 (153)AT2G20570 GLK1,ATGLK1,GPRI1 (461)AT1G09530 POC1,PAP3,PIF3 (704)AT5G24470 PRR5 (851)AT3G19290 ABF4,AREB2 (368)AT1G49720 ABF1 (573)AT2G43010 PIF4,SRL2 (1643)AT1G19350 BES1,BZR2 (2121)AT3G59060 PIL6,PIF5 (1155)AT3G22170 FHY3 (1841)AT1G69120 AGL7,AP1 (801)AT5G56110 MYB103,MS188,MYB80 (23)AT4G25480 CBF3,DREB1A (12)AT5G05410 DREB2A,DREB2 (10)AT1G68840 TEM2,RAV2,EDF2,RAP2.8 (142)AT3G50060 MYB77 (17)AT2G04880 WRKY1,ZAP1 (18)AT2G22300 SR1,CAMTA3 (20)AT3G56400 WRKY70 (165)AT4G35040 BZIP19 (8)AT2G16770 BZIP23 (8)AT5G07100 WRKY26 (21)AT2G46130 WRKY43 (20)AT5G22570 WRKY38 (20)AT3G10500 ANAC053 (85)AT1G32870 ANAC013 (85)AT1G34180 ANAC016 (85)AT1G34190 ANAC017 (85)AT5G04410 ANAC078 (85)AT5G65310 HB5,ATHB5 (41)AT4G31550 WRKY11 (7)AT3G01470 HAT5,HD-ZIP-1,HB-1 (21)AT5G11590 TINY2 (6)AT3G54320 WRI1,ASML1,WRI (22)AT1G16490 MYB58 (181)AT1G79180 MYB63 (181)AT3G23250 MYB15,ATY19 (45)AT3G49690 MYB84,RAX3 (103)AT1G73805 SARD1 (9)AT5G26920 CBP60G (9)AT2G46830 CCA1 (213)

1e-701 p-value

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Supplemental Figure 7. GO enrichment for all TF-targets in the predicted GRN.

A heatmap was generated using Genesis that displays, per TF, the enrichment of target genes towardsGO slim annotations (hypergeometric distribution + Bonferroni correction). The number of target genes for each TF is shown in parenthesis. The color gradient shows the p-values of the different enriched gene sets.


Supplemental Figure 8. Evaluation of the biological relevance of highly and moderately conserved interactions using the biological validation metrics.Comparison of the five biological metrics for the predicted sub-networks with highly

(blue boxes, >6 species) and moderately (purple boxes, 2-6 species) conserved interactions.

Fold enrichments are shown for the CORNET stress and developmental expression compendia, Gene

Ontology annotations, Mapman annotations and Functional modules. All reported fold enrichments

are significant (p-value < 0.05).

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(n=18914)

Predicted network low conservation

(n=21844)


TF and type Abiotic Biotic Stress Hormone Development Seed Flower Leaf Root Compendium 2 Whole plant

AT1G16490 MYB58 (34); predicted 0 0.5 0 0.06 0.03 0.03 0.26 0.12 0 0 0AT1G16490 MYB58 (8); experimental 0 0.5 0 0.12 0 0 0.12 0 0 0.25 0AT1G32770 ANAC012 NST3 SND1 (42); experimental 0.02 0.26 0.02 0 0.14 0.12 0.19 0.05 0.07 0.1 0.02AT1G32770 ANAC012 NST3 SND1 (92); predicted 0.11 0.15 0.07 0 0.03 0.05 0.12 0.03 0.37 0.03 0.03AT1G71930 ANAC030 VND7 (146); predicted 0.03 0.15 0.04 0.26 0.01 0.01 0 0.4 0.01 0.07 0.01AT1G71930 ANAC030 VND7 (36); experimental 0.03 0.28 0.06 0.36 0 0 0 0.11 0.06 0.08 0.03AT1G79180 MYB63 (15); experimental 0.13 0.2 0.2 0.2 0 0 0.07 0 0 0.2 0AT1G79180 MYB63 (73); predicted 0.19 0.21 0.23 0.16 0.01 0.01 0.03 0.01 0.01 0.12 0AT2G46770 ANAC043 NST1 (145); predicted 0.03 0.09 0.01 0.11 0.03 0.02 0.07 0.39 0.13 0.12 0AT2G46770 ANAC043 NST1 (8); experimental 0 0.25 0 0 0.12 0.12 0.25 0.12 0.12 0 0AT3G08500 MYB83 (209); predicted 0.01 0.1 0.01 0 0.12 0.15 0.11 0.38 0.11 0 0AT3G08500 MYB83 (8); experimental 0 0.12 0 0 0 0 0.25 0.38 0.12 0.12 0AT3G27920 GL1 MYB0 (7); experimental 0 0.14 0 0 0 0.14 0 0.57 0 0.14 0AT3G27920 GL1 MYB0 (7); predicted 0 0.14 0 0.14 0 0.43 0 0.14 0 0.14 0AT4G36920 AP2 FL1 FLO2 (451); predicted 0.44 0.04 0.45 0.01 0 0.01 0 0 0 0.03 0.01AT4G36920 AP2 FL1 FLO2 (50); experimental 0.44 0 0.46 0.02 0 0 0.04 0 0 0.04 0AT5G11260 HY5 TED 5 (35); experimental 0.23 0.11 0.37 0.17 0 0.03 0 0 0 0.03 0.06AT5G11260 HY5 TED 5 (41); predicted 0.15 0.1 0.44 0.29 0 0 0 0.02 0 0 0AT5G12870 MYB46 (22); experimental 0 0.32 0 0.32 0 0 0.09 0.05 0.05 0.18 0AT5G12870 MYB46 (250); predicted 0.01 0.26 0.01 0.24 0 0.02 0.15 0.22 0 0.07 0.02AT5G13790 AGL15 (9); experimental 0 0.11 0 0.11 0.33 0 0 0.11 0 0.22 0.11AT5G13790 AGL15 (910); predicted 0 0.12 0 0.2 0.07 0.01 0 0.55 0 0.01 0.02AT5G56110 MS188 MYB103 MYB80 (5); predicted 0 0.4 0 0 0.2 0 0 0.2 0 0 0.2AT5G56110 MS188 MYB103 MYB80 (7); experimental 0 0.57 0 0 0.14 0 0 0.14 0 0.14 0AT5G61850 LFY LFY3 (385); predicted 0.01 0 0.01 0.02 0.02 0.48 0.04 0.09 0.22 0.01 0.11AT5G61850 LFY LFY3 (8); experimental 0.12 0 0.25 0 0.12 0 0 0 0.5 0 0AT5G62380 ANAC101 VND6 (161); predicted 0.01 0.19 0 0.19 0.01 0.02 0.11 0.39 0.01 0.06 0.02AT5G62380 ANAC101 VND6 (6); experimental 0 0.67 0 0.17 0 0 0 0.17 0 0 0

Supplemental Figure 9. Comparison between experimental and predicted GRN of

co-expressed target genes in different conditions.

The fraction of target genes showing specific co-expression in each condition is displayed.The color gradient shows the fractions of the target genes. The total number of target genes showing specific co-expression for each TF is shown in parenthesis.


DAN1

QRT3 AGL30

LCB2

MYB101

AP3

VAMP726

NPG1

ANAC055 MYB94

ARAC1

CKX5

TRP1

MPK9

NDL1

MYB32

GA2OX1

AGL11

AGO9

INO

PGP10

SEP1

ATHB9

SEP2

AT4G36600

MAP1A

SLK2

EXO70C2DGK4

AT2G24320

IGI1

AT1G75160

NTT

AT2G40990

GAUT13

GLS2

CPK24AT3G10470

AT5G24940

CDC2C

AT2G22180PERK5

PI

PRK2

DES-1-LIKE

SPL10

EB1B

BP1

FAF2

SPL11

MYB3

EMS1

SPL AMS

NST1

AG

RGL1ARF5

UBP15

ARF8

AT4G33040

WOX3

Hormone ChIP Binding

DE down DE up

Pollen development

Pollen tube development

Meristem development

Hormone response

Anther development

Flower development

Stamen development

Carpel development

Petal development

Transcriptionfactor

Supplemental Figure 10. A condition-specific GRN for PI and AP3 based on hormone-specific TF-target co-expression edges. Genes that have GO annotations related to flower development are displayed. ChIP-bound regions associated with the target gene are shown as dashed lines while differentially expressed genes are shown by an arrowhead for up-regulation and by a vertical line for down-regulation, respectively. Red diamonds are the source TFs, grey diamonds are target genes that are TFs and rounded rectangles are other targetgenes. Rounded boxes depict different GO biological processes.


Documents

Supplemental Figure 1. Overview of synteny conservation ... · Criteria to score collinearity conservation were: 1) ... AT4G36920 FLO2,AP2,FL1 (1714) AT3G44460 ATBZIP67,DPBF2