Supporting Information

Vert et al. 10.1073/pnas.0803996105

Fig. S1. ARF2 interacts with BIN2 but not BES1 or BZR1. Shown is a representative example of staining for lacZ reporter expression for a variety of plasmid combinations. Staining is not detected for any of the plasmids on their own. Yeast transformed with BIN2 and ARF2 are the only tested strains to show detectable reporter activity. A–D show increasing strength of interactions for well characterized control proteins.

Vert et al. www.pnas.org/cgi/content/short/0803996105 1of28 Fig. S2. ARF2 protein accumulation is not altered by BR treatment. Western blot using anti-ARF2 antibodies on total extracts from plants without or with 1 ␮M BL. The nonspecific band indicated with an asterisk (Lower) serves as a loading control.

Vert et al. www.pnas.org/cgi/content/short/0803996105 2of28 Fig. S3. BIN2 can phosphorylate and reduce DNA binding of BES1. (A) Our preparation of BIN2 kinase can phosphorylate BES1. Upper shows Coomassie blue staining, and Lower shows Western blot using anti-MPB antibody. (B) In vitro DNA binding assays show that phosphorylation of BES1 by BIN2 greatly reduces BES1 binding to DNA, consistent with the results reported by Vert and Chory (1). Equivalent amounts of protein were incubated with DNA-coated beads. Proteins bound to the DNA were then pulled down, released by boiling, and run on an SDS/PAGE gel. Western blots using indicated antibodies are shown. Very little to no DNA is recovered when BIN2 is added to the reaction in the absence of BES1.

1. Vert G, Chory J (2006) Downstream nuclear events in brassinosteroid signalling. Nature441:96–100.

Vert et al. www.pnas.org/cgi/content/short/0803996105 3of28 Fig. S4. arf2 resistance to BRZ is temperature-sensitive. At 20°C, arf2 mutants respond normally to BRZ treatment. If plants are grown at 22°C, hypocotyl elongation in arf2 mutants is dramatically less sensitive to reduced BR levels than what is observed in wild-type plants.

Vert et al. www.pnas.org/cgi/content/short/0803996105 4of28 Table S1. in response to the following treatments: mock (m), brassinolide (b), auxin (a), or the combination of both hormones (c) cm1 cb1 ca1 cc1 cm3 cb3 ca3 cc3 cm6 cb6 ca6 cc6

At4 g08950 0.4 1.0 0.7 1.3 0.4 1.5 0.6 1.8 0.8 1.4 0.9 1.6 SE 0.0 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.2 0.1 0.1 0.4 At3 g45970 0.9 1.0 1.0 1.5 0.4 1.0 0.6 1.3 0.6 0.8 0.6 1.1 SE 0.1 0.1 0.1 0.2 0.1 0.1 0.2 0.1 0.1 0.1 0.1 0.3 At1 g62440 0.1 0.4 0.3 0.4 0.2 1.2 0.3 2.2 0.4 0.7 0.3 2.6 SE 0.1 0.1 0.0 0.1 0.0 0.1 0.1 0.1 0.2 0.3 0.0 0.5 At1 g29490 0.2 0.6 0.7 1.7 0.2 0.7 0.2 1.7 0.4 0.3 0.3 1.6 SE 0.2 0.3 0.1 0.2 0.2 0.2 0.1 0.2 0.3 0.3 0.0 0.4 At4 g30290 0.6 0.4 0.5 0.5 0.3 0.6 0.3 1.2 0.6 0.7 0.4 1.7 SE 0.0 0.1 0.1 0.0 0.0 0.0 0.0 0.1 0.1 0.1 0.0 0.3 At1 g52830 0.3 0.7 1.6 2.5 0.1 0.5 0.4 1.6 0.2 0.3 0.4 1.0 SE 0.1 0.2 0.2 0.3 0.1 0.1 0.1 0.1 0.2 0.2 0.0 0.3 At3 g55840 0.4 1.3 0.6 1.7 0.2 1.2 0.4 1.8 0.4 1.0 0.4 1.9 SE 0.0 0.2 0.1 0.2 0.1 0.1 0.2 0.1 0.2 0.2 0.1 0.4 At2 g23170 0.0 0.1 2.2 1.8 0.0 0.0 2.8 2.5 0.0 0.0 2.0 1.9 SE 0.1 0.2 0.2 0.1 0.1 0.1 0.3 0.1 0.1 0.1 0.1 0.4 At4 g32280 0.4 0.7 2.3 2.0 0.4 0.3 1.3 1.2 0.2 0.1 0.8 0.6 SE 0.2 0.3 0.3 0.2 0.2 0.2 0.2 0.1 0.2 0.3 0.1 0.3 At4 g14560 0.2 0.3 1.7 1.2 0.4 0.3 1.3 1.0 0.3 0.3 1.2 0.9 SE 0.1 0.2 0.2 0.1 0.1 0.1 0.2 0.1 0.1 0.1 0.1 0.3 At5 g02760 0.7 0.9 1.7 1.6 0.6 0.8 0.9 1.4 0.5 0.6 0.8 1.4 SE 0.1 0.1 0.2 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.0 0.3 At5 g47370 0.6 0.9 2.5 2.2 0.5 0.6 1.0 1.3 0.4 0.6 1.3 1.2 SE 0.1 0.2 0.3 0.2 0.1 0.2 0.2 0.1 0.1 0.1 0.1 0.3

Expression was analyzed by quantitative RT-PCR, and all data are normalized to the expression of At1 g13320, a gene with constant expression. Numbers refer to the number of hours seedlings were exposed to each treatment (e.g., 1 ϭ 1 h). The average expression level for three replicate treatments is shown on the first line with the standard error (SE) shown on the second line.

Vert et al. www.pnas.org/cgi/content/short/0803996105 5of28 Table S2. One hundred most significant genes differentially expressed under BRZ treatment in wild-type Col-0 plants (genes were ranked by adjusted P value). Average expression for each condition is given. A:arf2, C: Col, B: BRZ, M: mock. Ratios for arf2 on BRZ vs. arf2 on mock (AB/AM) and Col on BRZ vs. mock (CB/CM) are also shown. Adjusted log Affy AGI P value (odds) AB AM CB CM AB/AM CB/CM Annotation

262682࿝at At1 g75900 1.4E-11 16.2 130 1006 130 943 0.7 0.7 unknown 263890࿝at At2 g37030 2.1E-11 15.9 140 21 138 25 6.5 5.5 SAUR46 267101࿝at At2 g41480 1.3E-10 14.5 35 61 42 153 0.6 0.3 PER25 peroxidase 249894࿝at At5 g22580 1.3E-10 14.5 2010 233 1890 254 1.5 1.4 unknown 256145࿝at At1 g48750 2.4E-10 14.0 1224 463 1112 351 1.2 1.3 lipid transfer protein 245891࿝at At5 g09220 3.2E-10 13.7 605 380 773 147 1.1 1.4 transport protein AAP2 253627࿝at At4 g30650 4.9E-10 13.3 20 141 16 58 0.3 0.3 RCI2E low temperature and salt responsive protein 264007࿝at At2 g21140 5.9E-10 13.2 509 2426 756 4335 0.8 0.8 unknown 247162࿝at At5 g65730 6.2E-10 13.1 65 25 119 27 2.1 1.9 AtXTH6 263443࿝at At2 g28630 6.2E-10 13.1 120 550 108 278 0.7 0.7 fatty acid elongase 263098࿝at At2 g16005 6.9E-10 13.0 29 28 29 390 1.1 0.3 unknown 254809࿝at At4 g12410 7.0E-10 13.0 192 52 340 46 1.9 2.2 SAUR35 255177࿝at At4 g08040 7.3E-10 13.0 111 18 131 23 3.5 2.6 AtACS11 264217࿝at At1 g60190 7.6E-10 12.9 165 325 138 258 0.8 0.8 Plant U-box protein, AtPUB19 267457࿝at At2 g33790 7.8E-10 12.9 215 21 80 21 4.2 3.5 unknown 264968࿝at At1 g67360 1.4E-09 12.4 173 236 99 276 0.9 0.7 unknown 246250࿝at At4 g36880 1.4E-09 12.4 465 1818 206 910 0.8 0.8 cysteine proteinase 261881࿝at At1 g80760 1.5E-09 12.3 112 47 103 44 1.9 1.9 Delta tonoplast integral protein 260070࿝at At1 g73830 2.0E-09 12.1 370 137 431 129 1.2 1.3 BEE3, bHLH050 250475࿝at At5 g10180 2.0E-09 12.1 1597 425 496 82 1.2 1.4 sulfate transporter 251768࿝at At3 g55940 2.1E-09 12.0 35 98 29 121 0.6 0.4 phosphoinositide-specific C 259846࿝at At1 g72140 2.2E-09 12.0 45 56 28 103 0.9 0.5 transporter PTR2-B 263809࿝at At2 g04570 2.2E-09 12.0 330 815 349 1004 0.8 0.8 GDSL-motif / 264527࿝at At1 g30760 2.3E-09 11.9 45 121 46 141 0.6 0.6 reticuline oxidase-like protein 249037࿝at At5 g44130 2.4E-09 11.9 133 446 244 1286 0.7 0.7 unknown 259616࿝at At1 g47960 2.8E-09 11.8 128 160 101 195 0.9 0.8 unknown 245422࿝at At4 g17470 3.1E-09 11.7 77 65 66 265 1.1 0.5 PPT1-like 250646࿝at At5 g06720 3.4E-09 11.6 24 81 28 126 0.5 0.3 PER53 peroxidase 250199࿝at At5 g14180 3.6E-09 11.5 275 696 133 345 0.8 0.7 unknown 250157࿝at At5 g15180 3.9E-09 11.5 86 29 159 30 1.8 2.1 PER56 peroxidase 245506࿝at At4 g15700 5.6E-09 11.1 31 20 51 17 1.2 2.0 251072࿝at At5 g01740 6.1E-09 11.1 1741 166 1634 319 1.7 1.4 unknown 251196࿝at At3 g62950 6.3E-09 11.0 61 43 86 33 1.2 1.9 glutaredoxin 254907࿝at At4 g11190 6.8E-09 10.9 205 315 475 1704 0.9 0.8 unknown 263876࿝at At2 g21880 7.0E-09 10.9 215 332 140 351 0.9 0.8 RAS superfamily GTP-binding protein 246228࿝at At4 g36430 7.7E-09 10.8 45 177 36 252 0.5 0.4 PER49 peroxidase 252118࿝at At3 g51400 8.0E-09 10.8 216 66 199 53 1.7 2.0 unknown 257952࿝at At3 g21770 8.2E-09 10.8 432 942 349 1000 0.9 0.8 PER30 peroxidase 255549࿝at At4 g01950 1.0E-08 10.6 363 793 321 1289 0.9 0.8 mitochondrial glycerol-phosphate acyltransferase 256601࿝s࿝at At3 g28290 1.0E-08 10.6 355 306 206 41 1.2 5.0 integrin-like 259878࿝at At1 g76790 1.1E-08 10.5 256 281 226 688 1.0 0.8 catechol O-methyltransferase COMT-like8 256598࿝at At3 g30180 1.1E-08 10.5 1945 551 2143 588 1.2 1.2 BR6OX2 262427࿝s࿝at At1 g47600 1.3E-08 10.4 230 55 435 53 1.7 1.9 thioglucosidase 261327࿝at At1 g44830 1.3E-08 10.3 239 100 274 88 1.2 1.3 AP2-EREBP transcription factor 248252࿝at At5 g53250 1.5E-08 10.2 1113 2602 1105 3530 0.9 0.9 unknown 258629࿝at At3 g02850 1.6E-08 10.2 190 107 179 55 1.3 1.7 stelar Kϩ outward rectifying channel (SKOR) 245463࿝at At4 g17030 1.8E-08 10.0 89 211 102 260 0.7 0.6 AtEXLB1 254667࿝at At4 g18280 2.0E-08 9.9 139 1194 109 441 0.6 0.7 glycine-rich cell wall protein 248844࿝s࿝at At5 g46900 2.4E-08 9.8 872 1383 882 3282 0.9 0.8 extA 249719࿝at At5 g35735 2.7E-08 9.7 128 321 64 168 0.8 0.7 unknown 247723࿝at At5 g59220 2.7E-08 9.7 155 157 103 318 1.0 0.7 protein 2C 263063࿝s࿝at At2 g18140 2.7E-08 9.6 27 47 24 86 0.6 0.4 PER14 peroxidase 259328࿝at At3 g16440 2.8E-08 9.6 217 134 205 81 1.1 1.4 lectin 267590࿝at At2 g39700 2.8E-08 9.6 257 380 346 889 0.9 0.8 AtEXPA4 249482࿝at At5 g38980 2.9E-08 9.6 513 95 175 65 1.5 1.4 unknown 250231࿝at At5 g13910 2.9E-08 9.6 189 69 165 66 1.6 1.7 AP2-EREBP transcription factor LEAFY PETIOLE 246550࿝at At5 g14920 3.3E-08 9.5 3202 1680 3397 1240 1.1 1.1 unknown 247477࿝at At5 g62340 3.5E-08 9.4 137 27 88 23 3.3 2.7 unknown 264404࿝at At2 g25160 3.6E-08 9.4 43 27 91 169 1.4 0.7 CYP82F1 253957࿝at At4 g26320 3.6E-08 9.4 133 227 135 446 0.8 0.6 unknown 245392࿝at At4 g15680 4.3E-08 9.2 29 28 82 25 1.0 2.1 glutaredoxin

Vert et al. www.pnas.org/cgi/content/short/0803996105 6of28 Adjusted log Affy AGI P value (odds) AB AM CB CM AB/AM CB/CM Annotation

259445࿝at At1 g02400 4.4E-08 9.2 244 396 184 423 0.9 0.8 dioxygenase 254042࿝at At4 g25810 4.7E-08 9.1 216 643 227 564 0.8 0.8 At-XTH23 251509࿝at At3 g59010 4.8E-08 9.1 124 74 70 218 1.2 0.7 pectinesterase 254926࿝at At4 g11280 4.8E-08 9.1 85 156 67 133 0.8 0.7 ACC synthase (AtACS-6) 246415࿝at At5 g17160 4.8E-08 9.1 59 103 46 104 0.8 0.6 unknown 265194࿝at At1 g05010 5.2E-08 9.0 4933 1870 5840 2551 1.1 1.1 1-aminocyclopropane-1-carboxylate oxidase, ACO4 264774࿝at At1 g22890 5.3E-08 9.0 214 168 248 84 1.0 1.3 unknown 253177࿝s࿝at At4 g35150 5.8E-08 8.9 80 43 137 49 1.3 1.4 O-methyltransferase 251245࿝at At3 g62090 5.8E-08 8.9 118 64 93 38 1.2 1.6 PIF6, bHLH132 266209࿝at At2 g27550 6.0E-08 8.9 176 152 118 48 1.1 1.8 similar to Terminal Flower 260957࿝at At1 g06080 6.4E-08 8.8 775 208 1362 424 1.3 1.2 delta 9 desaturase 260748࿝at At1 g49210 6.6E-08 8.8 87 33 86 32 1.6 1.5 RING-H2 finger protein RHA3a 255265࿝at At4 g05190 6.9E-08 8.7 73 85 59 106 0.8 0.7 kinesin 263734࿝at At1 g60030 8.0E-08 8.6 31 42 34 71 0.8 0.6 nucleobase ascorbate transporter AtNAT7 267618࿝at At2 g26760 8.2E-08 8.6 78 145 69 184 0.8 0.7 cyclin CYCB1;4 256725࿝at At2 g34070 8.2E-08 8.6 373 1058 358 1011 0.8 0.8 unknown 258897࿝at At3 g05730 9.7E-08 8.4 289 273 550 71 1.0 1.5 unknown 267075࿝at At2 g41070 1.0E-07 8.4 197 140 152 76 1.1 1.3 bZIP12 267305࿝at At2 g30070 1.2E-07 8.2 133 50 187 67 1.4 1.3 high affinity Kϩ transporter (AtKUP1/AtKT1p) 246481࿝s࿝at At5 g15960 1.3E-07 8.1 141 1016 103 605 0.7 0.7 cold and ABA inducible protein KIN1 247377࿝at At5 g63180 1.4E-07 8.0 714 422 594 188 1.1 1.2 pectate 249527࿝at At5 g38710 1.5E-07 8.0 34 99 26 76 0.5 0.5 proline oxidase 252612࿝at At3 g45160 1.6E-07 7.9 82 22 78 24 2.2 2.0 unknown 257203࿝at At3 g23730 1.7E-07 7.9 444 133 806 235 1.3 1.2 At-XTH16 267233࿝s࿝at At2 g43920 2.0E-07 7.7 2469 1101 2333 1057 1.1 1.1 unknown 264529࿝at At1 g30820 2.3E-07 7.5 255 384 222 419 0.9 0.8 CTP synthase 266828࿝at At2 g22930 2.5E-07 7.5 20 27 21 35 0.7 0.6 flavonol 3-O-glucosyltransferase 252571࿝at At3 g45280 2.6E-07 7.4 22 20 36 16 1.3 2.0 syntaxin SYP72 263632࿝at At2 g04795 4.5E-07 6.9 167 128 157 94 1.1 1.3 unknown 257197࿝at At3 g23800 4.6E-07 6.9 287 242 302 79 1.0 1.5 selenium binding protein 259962࿝at At1 g53690 7.0E-07 6.4 14 27 21 35 0.6 0.7 RNA polymerase II 251565࿝at At3 g58190 7.2E-07 6.4 18 21 21 41 0.8 0.5 ASL16 255860࿝at At5 g34940 1.0E-06 6.1 295 182 242 74 1.1 1.3 heparanase 266967࿝at At2 g39530 1.1E-06 6.0 115 87 104 41 1.1 1.5 unknown 264909࿝at At2 g17300 1.5E-06 5.7 33 39 34 51 0.7 0.6 unknown 267460࿝at At2 g33810 3.5E-06 4.8 54 27 43 21 1.3 1.6 AtSPL3 247282࿝at At5 g64240 3.9E-06 4.7 248 163 262 101 1.2 1.3 unknown 255795࿝at At2 g33380 1.7E-05 3.2 50 156 26 53 0.6 0.5 -binding EF-hand protein, Clo3 248611࿝at At5 g49520 2.4E-04 0.5 50 130 38 58 0.6 0.6 AtWRKY48

Vert et al. www.pnas.org/cgi/content/short/0803996105 7of28 Table S3. One hundred most significant genes differentially expressed under BRZ treatment in arf2 mutant plants (genes were ranked by adjusted P value). Average expression for each condition is given. A, arf2; C, Col; B, BRZ; M, mock. Ratios for arf2 on BRZ vs. arf2 on mock (AB/AM) and Col on BRZ vs. mock (CB/CM) are also shown. Adjusted log Affy AGI P value (odds) AB AM CB CM AB/AM CB/CM Annotation

260406࿝at At1 g69920 1.9E-08 17.8 29 221 31 33 0.1 0.9 glutathione , AtGSTU12 263890࿝at At2 g37030 1.6E-07 15.3 140 21 138 25 6.5 5.5 SAUR46 261021࿝at At1 g26380 1.6E-07 15.5 42 486 39 32 0.1 1.2 reticuline oxidase 267457࿝at At2 g33790 1.6E-07 15.2 215 21 80 21 10.3 3.7 unknown 262682࿝at At1 g75900 1.6E-07 15.1 130 1006 130 943 0.1 0.1 unknown 245041࿝at At2 g26530 1.6E-07 15.1 53 153 44 44 0.3 1.0 unknown 247882࿝at At5 g57785 1.6E-07 15.5 583 92 844 431 6.3 2.0 unknown 263443࿝at At2 g28630 2.0E-07 14.8 120 550 108 278 0.2 0.4 fatty acid elongase 265411࿝at At2 g16630 2.4E-07 14.5 97 628 115 108 0.2 1.1 unknown protein 249894࿝at At5 g22580 2.6E-07 14.4 2010 233 1890 254 8.6 7.4 unknown 251072࿝at At5 g01740 2.7E-07 14.2 1741 166 1634 319 10.5 5.1 unknown 253627࿝at At4 g30650 2.7E-07 14.3 20 141 16 58 0.1 0.3 RCI2E low temperature and salt responsive protein 253073࿝at At4 g37410 3.1E-07 14.1 164 54 141 222 3.0 0.6 CYP81F4 267565࿝at At2 g30750 5.0E-07 13.6 17 100 16 18 0.2 0.9 CYP71A12 249482࿝at At5 g38980 1.3E-06 12.8 513 95 175 65 5.4 2.7 unknown 246099࿝at At5 g20230 1.7E-06 12.5 54 697 45 102 0.1 0.4 blue copper binding protein 255177࿝at At4 g08040 2.0E-06 12.3 111 18 131 23 6.1 5.6 AtACS11 265670࿝s࿝at At2 g32210 2.0E-06 12.2 39 190 34 70 0.2 0.5 unknown 261881࿝at At1 g80760 2.0E-06 12.2 112 47 103 44 2.4 2.4 Delta tonoplast integral protein 254667࿝at At4 g18280 2.0E-06 12.1 139 1194 109 441 0.1 0.2 glycine-rich cell wall protein 258277࿝at At3 g26830 3.0E-06 11.7 21 84 19 17 0.3 1.1 CYP71B15, PAD3 247293࿝at At5 g64510 3.0E-06 11.7 23 54 22 27 0.4 0.8 unknown 267595࿝at At2 g32990 4.2E-06 11.3 460 66 376 90 6.9 4.2 glucanse 264007࿝at At2 g21140 4.2E-06 11.3 509 2426 756 4335 0.2 0.2 unknown 245353࿝at At4 g16000 4.5E-06 11.2 123 337 256 286 0.4 0.9 unknown 247477࿝at At5 g62340 5.3E-06 11.0 137 27 88 23 5.1 3.9 unknown 251977࿝at At3 g53250 5.3E-06 11.0 111 36 149 71 3.1 2.1 SAUR57 260957࿝at At1 g06080 5.3E-06 10.9 775 208 1362 424 3.7 3.2 delta 9 desaturase 267261࿝at At2 g23120 5.5E-06 10.9 763 2440 661 1103 0.3 0.6 unknown 261474࿝at At1 g14540 5.9E-06 10.8 58 340 49 43 0.2 1.1 PER4 peroxidase 267411࿝at At2 g34930 6.4E-06 10.7 33 203 34 39 0.2 0.9 unknown 256145࿝at At1 g48750 6.7E-06 10.6 1224 463 1112 351 2.6 3.2 lipid transfer protein 264527࿝at At1 g30760 1.1E-05 10.1 45 121 46 141 0.4 0.3 reticuline oxidase-like protein 259426࿝at At1 g01470 1.4E-05 9.9 1391 3767 1248 1768 0.4 0.7 1-phosphatidylinositol-4-phosphate 5-kinase 252827࿝at At4 g39950 1.4E-05 9.8 82 515 100 153 0.2 0.7 CYP79B2 265194࿝at At1 g05010 1.4E-05 9.8 4933 1870 5840 2551 2.6 2.3 1-aminocyclopropane-1-carboxylate oxidase, ACO4 256598࿝at At3 g30180 1.6E-05 9.7 1945 551 2143 588 3.5 3.6 BR6OX2 259705࿝at At1 g77450 1.6E-05 9.6 286 768 215 303 0.4 0.7 NAC transcription factor 263402࿝at At2 g04050 1.9E-05 9.4 21 57 19 24 0.4 0.8 unknown 249459࿝at At5 g39580 2.0E-05 9.3 288 933 354 368 0.3 1.0 PER62 peroxidase 246250࿝at At4 g36880 2.0E-05 9.3 465 1818 206 910 0.3 0.2 cysteine proteinase 249037࿝at At5 g44130 2.5E-05 9.0 133 446 244 1286 0.3 0.2 unknown 247215࿝at At5 g64905 2.6E-05 9.0 26 98 23 22 0.3 1.0 unknown 261247࿝at At1 g20070 2.6E-05 8.9 108 451 106 176 0.2 0.6 unknown 252118࿝at At3 g51400 2.6E-05 8.9 216 66 199 53 3.3 3.8 unknown 257203࿝at At3 g23730 2.9E-05 8.8 444 133 806 235 3.3 3.4 At-XTH16 259516࿝at At1 g20450 3.3E-05 8.7 974 2445 633 1362 0.4 0.5 unknown 254809࿝at At4 g12410 3.6E-05 8.5 192 52 340 46 3.7 7.4 SAUR35 262911࿝s࿝at At1 g59860 4.0E-05 8.4 49 126 25 52 0.4 0.5 HSP17.6A 252214࿝at At3 g50260 4.0E-05 8.4 268 661 202 228 0.4 0.9 AP2-EREBP transcription factor, Rap2.1 262119࿝s࿝at At1 g02930 4.0E-05 8.3 2191 6334 2213 1718 0.3 1.3 glutathione S-transferase 251847࿝at At3 g54640 4.0E-05 8.4 150 547 140 120 0.3 1.2 tryptophan synthase alpha chain 254042࿝at At4 g25810 4.0E-05 8.3 216 643 227 564 0.3 0.4 At-XTH23 264217࿝at At1 g60190 4.0E-05 8.4 165 325 138 258 0.5 0.5 Plant U-box protein, AtPUB19 264787࿝at At2 g17840 4.2E-05 8.3 581 1415 517 814 0.4 0.6 unknown 250351࿝at At5 g12030 4.2E-05 8.2 39 175 18 40 0.2 0.4 HSP17.6A 261020࿝at At1 g26390 4.4E-05 8.2 21 168 19 21 0.1 0.9 reticuline oxidase 267305࿝at At2 g30070 4.6E-05 8.1 133 50 187 67 2.7 2.8 high affinity Kϩ transporter (AtKUP1/AtKT1p) 246481࿝s࿝at At5 g15960 4.6E-05 8.1 141 1016 103 605 0.1 0.2 cold and ABA inducible protein KIN1 256548࿝at At3 g14770 4.6E-05 8.1 182 545 204 663 0.3 0.3 unknown 258746࿝at At3 g05950 4.9E-05 8.0 91 350 43 81 0.3 0.5 germin

Vert et al. www.pnas.org/cgi/content/short/0803996105 8of28 Adjusted log Affy AGI P value (odds) AB AM CB CM AB/AM CB/CM Annotation

252870࿝at At4 g39940 5.0E-05 7.9 40 173 51 81 0.2 0.6 adenosine-5-phosphosulfate-kinase 264052࿝at At2 g22330 5.0E-05 8.0 122 342 146 260 0.4 0.6 putative cytochrome P450 263403࿝at At2 g04040 5.0E-05 7.9 25 113 28 29 0.2 0.9 unknown 245193࿝at At1 g67810 5.1E-05 7.9 512 1613 453 674 0.3 0.7 unknown 267233࿝s࿝at At2 g43920 5.6E-05 7.8 2469 1101 2333 1057 2.2 2.2 unknown 265674࿝at At2 g32190 5.8E-05 7.7 48 258 29 75 0.2 0.4 unknown 253100࿝at At4 g37400 5.8E-05 7.7 27 54 22 33 0.5 0.7 CYP81F3 255538࿝at At4 g01680 5.9E-05 7.6 567 207 494 227 2.7 2.2 AtMYB55 251025࿝at At5 g02190 5.9E-05 7.6 123 69 120 83 1.8 1.4 chloroplast nucleoid DNA binding protein CND41 252482࿝at At3 g46670 6.0E-05 7.6 27 69 25 38 0.4 0.7 UDP-glucose glucosyltransferase 250199࿝at At5 g14180 6.6E-05 7.4 275 696 133 345 0.4 0.4 unknown 247095࿝at At5 g66400 6.6E-05 7.4 1034 3448 389 514 0.3 0.8 dehydrin 266743࿝at At2 g02990 7.4E-05 7.3 47 86 75 95 0.5 0.8 , RNS1 245352࿝at At4 g15490 8.4E-05 7.1 23 75 22 29 0.3 0.8 indole-3-acetate beta-glucosyltransferase 249942࿝at At5 g22300 8.6E-05 7.0 32 77 35 41 0.4 0.9 Nitrilase 4 250475࿝at At5 g10180 8.8E-05 7.0 1597 425 496 82 3.8 6.0 sulfate transporter 254321࿝at At4 g22590 8.9E-05 7.0 63 174 50 121 0.4 0.4 trehalose-6-phosphate phosphatase 245463࿝at At4 g17030 8.9E-05 6.9 89 211 102 260 0.4 0.4 AtEXLB1 252011࿝at At3 g52720 9.2E-05 6.9 176 68 160 79 2.6 2.0 carbonic anhydrase (CAH1) 252612࿝at At3 g45160 9.7E-05 6.8 82 22 78 24 3.7 3.2 unknown 259962࿝at At1 g53690 9.7E-05 6.8 14 27 21 35 0.5 0.6 RNA polymerase II 264846࿝at At2 g17850 1.1E-04 6.6 61 33 89 60 1.9 1.5 rhodanese protein AtStr17 260748࿝at At1 g49210 1.1E-04 6.5 87 33 86 32 2.6 2.7 RING-H2 finger protein RHA3a 256017࿝at At1 g19180 1.1E-04 6.5 276 705 241 297 0.4 0.8 unknown 250157࿝at At5 g15180 1.3E-04 6.3 86 29 159 30 3.0 5.2 PER56 peroxidase 261327࿝at At1 g44830 1.3E-04 6.3 239 100 274 88 2.4 3.1 AP2-EREBP transcription factor 253799࿝at At4 g28140 1.3E-04 6.2 30 76 30 47 0.4 0.7 AP2-EREBP transcription factor, Rap2.4 247634࿝at At5 g60520 1.6E-04 6.0 47 22 26 21 2.1 1.2 unknown 263002࿝at At1 g54200 1.7E-04 5.9 97 37 87 52 2.6 1.7 unknown 252529࿝at At3 g46490 1.9E-04 5.8 193 67 109 55 2.9 2.0 gibberellin 20-oxidase-like 251282࿝at At3 g61630 2.3E-04 5.5 119 310 104 126 0.4 0.8 AP2-EREBP transcription factor 247212࿝at At5 g65040 2.4E-04 5.5 83 184 83 122 0.5 0.7 unknown 252908࿝at At4 g39670 2.5E-04 5.4 83 233 56 66 0.4 0.9 unknown 252131࿝at At3 g50930 3.7E-04 4.9 50 123 45 77 0.4 0.6 ubiquinol-cytochrome c reductase 258873࿝at At3 g03240 4.4E-04 4.7 26 53 31 50 0.5 0.6 unknown 255795࿝at At2 g33380 5.8E-04 4.3 50 156 26 53 0.3 0.5 calcium-binding EF-hand protein, Clo3 248611࿝at At5 g49520 1.4E-03 3.0 50 130 38 58 0.4 0.7 AtWRKY48 245696࿝at At5 g04190 1.8E-03 2.7 241 106 171 95 2.3 1.8 Phytochrome Kinase 4 259371࿝at At1 g69080 7.1E-03 0.7 278 127 211 109 2.2 1.9 unknown

Vert et al. www.pnas.org/cgi/content/short/0803996105 9of28 Table S4. Complete list of differentially regulated genes. Comparisons are between wild-type (Col) on BRZ vs. mock (BRZ࿝Col), arf2 mutants on BRZ vs. mock (BRZ࿝arf2), and arf2 mutants vs. wild-type under mock treatment conditions (arf2࿝Col). Up or down refers to relative expression difference in the first condition compared to the second (e.g. BRZ versus mock, arf2 versus Col). Up Down

BRZ࿝Col BRZ࿝arf2 arf2࿝Col BRZ࿝Col BRZ࿝arf2 arf2࿝Col

At5 g22580 At5 g01740 At1 g26380 At2 g16005 At1 g26380 At5 g62010 At5 g09220 At2 g33790 At5 g57220 At4 g36430 At5 g57220 At5 g47990 At1 g47600 At5 g22580 At3 g13610 At1 g75900 At5 g15960 At1 g55240 At2 g37030 At5 g57785 At1 g66690 At2 g21140 At4 g18280 At2 g16005 At4 g12410 At2 g37030 At2 g23270 At5 g06720 At3 g46230 At2 g25160 At5 g01740 At2 g32990 At4 g14630 At3 g55940 At4 g39950 At1 g43800 At5 g10180 At5 g38980 At1 g14540 At5 g44130 At1 g69920 At5 g53870 At3 g05730 At4 g08040 At3 g28290 At4 g36880 At5 g20230 At5 g57785 At4 g08040 At4 g12410 At5 g66400 At2 g41480 At3 g13610 At1 g65310 At3 g28290 At5 g62340 At5 g12030 At3 g14770 At1 g75900 At4 g11190 At3 g53980 At3 g29410 At2 g30750 At4 g01950 At2 g30750 At4 g17470 At4 g15680 At5 g10180 At1 g26390 At1 g72140 At4 g30650 At3 g29970 At5 g15180 At1 g06080 At5 g43520 At5 g04120 At5 g12030 At4 g18550 At5 g65730 At3 g51400 At4 g22710 At5 g15960 At2 g16630 At5 g22460 At2 g05070 At3 g30180 At2 g26560 At4 g17470 At4 g39940 At1 g02800 At2 g33790 At3 g53980 At2 g16630 At4 g30650 At3 g09350 At5 g02760 At4 g15690 At3 g45160 At1 g69920 At4 g11190 At1 g14540 At5 g20740 At1 g21460 At5 g57780 At5 g26920 At1 g30760 At2 g32190 At4 g37800 At3 g02850 At2 g36870 At5 g64905 At2 g18140 At2 g04040 At2 g41480 At3 g23730 At5 g15180 At1 g74590 At5 g46900 At5 g52640 At4 g37410 At1 g06080 At3 g53250 At3 g54640 At4 g18280 At1 g26390 At3 g22120 At5 g55620 At2 g44910 At1 g15010 At1 g03820 At2 g32210 At2 g34490 At2 g32990 At5 g13910 At1 g67980 At1 g76790 At2 g34930 At5 g44130 At3 g45160 At1 g43800 At3 g26830 At3 g59010 At4 g36880 At3 g04290 At3 g23800 At3 g23730 At3 g30720 At4 g26320 At1 g20070 At2 g16060 At2 g41230 At1 g47600 At2 g38860 At5 g47990 At2 g29500 At1 g72610 At3 g01450 At4 g37410 At1 g56300 At2 g26760 At5 g64905 At2 g02100 At2 g27550 At4 g33550 At5 g10180 At3 g46230 At2 g28630 At1 g03820 At5 g62340 At1 g80760 At3 g05950 At1 g67360 At2 g26560 At3 g59010 At3 g30180 At5 g67020 At5 g42830 At2 g32190 At3 g54640 At5 g24780 At1 g21050 At4 g01680 At5 g48430 At3 g21770 At3 g26830 At2 g39700 At5 g38980 At5 g53830 At2 g04040 At2 g04570 At2 g21140 At5 g44580 At1 g48750 At1 g73830 At2 g35980 At3 g12580 At5 g26920 At3 g42570 At1 g79360 At1 g49210 At4 g39950 At5 g52480 At5 g12020 At2 g23170 At1 g77640 At3 g52720 At2 g15120 At5 g14180 At1 g59860 At4 g38660 At5 g05880 At1 g48750 At3 g09350 At2 g32210 At5 g42830 At1 g62180 At3 g46490 At5 g54510 At2 g43000 At5 g53250 At2 g38860 At1 g09200 At2 g30070 At4 g39800 At4 g24150 At4 g25810 At5 g44130 At5 g10770 At5 g34940 At3 g46490 At2 g44370 At1 g52830 At1 g67810 At2 g18140 At3 g15370 At1 g11210 At2 g02930 At1 g30690 At1 g66690 At5 g59870 At3 g62090 At5 g07030 At2 g29500 At5 g25610 At4 g22710 At4 g39800 At2 g41050 At4 g03340 At1 g30370 At1 g60030 At3 g12580 At5 g02890 At1 g44830 At5 g10770 At3 g59930 At5 g38710 At2 g33380 At4 g28250 At2 g39530 At4 g14560 At2 g41730 At3 g18200 At3 g04630 At4 g33550 At4 g35150 At1 g69080 At1 g52690 At2 g34070 At2 g46650 At1 g76790 At5 g63180 At5 g65730 At1 g02930 At5 g35735 At4 g15490 At5 g60760 At5 g43520 At2 g16060 At1 g27730 At2 g28630 At3 g16530 At5 g62000 At2 g29670 At4 g22160 At2 g03760 At2 g39700 At4 g33666 At5 g57780 At1 g73830 At5 g66590 At3 g46230 At5 g41900 At3 g05950 At4 g16985 At4 g07820 At5 g53980 At5 g20230 At2 g21880 At4 g37370 At1 g70850 At5 g53830 At5 g04190 At2 g38870 At1 g53540 At1 g15010 At3 g62820 At1 g67050 At2 g17230 At2 g27550 At5 g59220 At2 g43000 At4 g18425 At5 g13910 At5 g16030 At4 g37290 At1 g68290 At1 g67980 At3 g05400 At3 g16440 At1 g05010 At2 g34930 At1 g34750 At3 g10450 At1 g33811 At3 g62950 At1 g62770 At3 g05730 At4 g22590 At2 g26530 At5 g42580 At2 g39350 At2 g30070 At5 g05730 At3 g25980 At2 g41730 At1 g70470 At1 g22890 At1 g67100 At2 g39510 At1 g02400 At5 g38710 At3 g20210 At2 g21560 At4 g03210 At5 g09220 At5 g65800 At2 g38870 At5 g48850 At3 g51400 At3 g50660 At2 g26530 At5 g52640 At5 g58070 At3 g53250 At5 g14920 At2 g25810 At4 g37370 At2 g48130 At1 g61340 At5 g26150 At3 g21870 At5 g66080 At1 g73480 At4 g15920 At2 g22330 At1 g55210

Vert et al. www.pnas.org/cgi/content/short/0803996105 10 of 28 Up Down

BRZ࿝Col BRZ࿝arf2 arf2࿝Col BRZ࿝Col BRZ࿝arf2 arf2࿝Col

At4 g36670 At1 g06120 At2 g45220 At5 g42580 At5 g66400 At4 g10240 At3 g16800 At3 g01450 At1 g19610 At5 g66390 At5 g05730 At4 g29270 At4 g22160 At4 g35150 At3 g05640 At5 g23820 At3 g46670 At4 g22490 At5 g12050 At1 g54200 At1 g77640 At1 g73220 At5 g51440 At5 g55620 At3 g15620 At2 g28470 At1 g18970 At1 g23800 At3 g61630 At5 g57760 At1 g49210 At1 g76210 At3 g22800 At3 g12700 At5 g39580 At1 g72140 At2 g44910 At4 g37300 At5 g37670 At5 g11110 At3 g22370 At4 g24780 At2 g41070 At2 g21560 At4 g15490 At4 g20320 At1 g77450 At2 g21140 At5 g64240 At1 g27670 At2 g33380 At5 g17160 At5 g49520 At5 g47370 At5 g14090 At5 g02200 At4 g39670 At5 g53590 At5 g13360 At4 g25780 At1 g52140 At4 g37470 At1 g05560 At4 g33260 At3 g24500 At4 g26320 At4 g24050 At5 g05880 At5 g39670 At5 g26150 At2 g34070 At4 g30140 At1 g49470 At1 g65310 At2 g38470 At1 g48480 At5 g06720 At4 g10270 At5 g24030 At1 g65370 At1 g78460 At1 g02800 At4 g16000 At1 g67100 At4 g02330 At1 g21050 At3 g18250 At4 g17030 At4 g20320 At4 g31840 At2 g33810 At5 g49630 At4 g35985 At5 g44610 At2 g04050 At3 g43190 At2 g30510 At3 g48970 At4 g39940 At3 g05490 At2 g28210 At5 g48000 At1 g64590 At5 g66110 At1 g55450 At3 g61160 At4 g39670 At3 g08860 At3 g01670 At3 g05400 At3 g61630 At3 g17420 At1 g26420 At1 g77120 At2 g34430 At2 g43920 At1 g16030 At5 g50200 At3 g05640 At5 g51210 At5 g05960 At3 g01190 At1 g59860 At5 g43780 At4 g14365 At5 g10400 At2 g18290 At2 g41050 At5 g52640 At3 g24500 At1 g02930 At4 g19420 At2 g21910 At5 g55620 At5 g57890 At4 g01430 At3 g54050 At5 g48485 At5 g02540 At1 g44830 At1 g20070 At5 g64310 At5 g52310 At1 g72970 At4 g00238 At5 g47800 At5 g12020 At3 g50930 At2 g21330 At5 g46240 At1 g17180 At5 g51670 At1 g33790 At4 g36110 At4 g31500 At5 g46900 At3 g23810 At5 g14920 At2 g32190 At1 g07720 At2 g23120 At4 g21990 At4 g22570 At3 g01680 At5 g59820 At3 g16470 At1 g10960 At3 g49750 At1 g80840 At1 g64460 At5 g07460 At2 g18210 At4 g14690 At4 g04830 At1 g21400 At1 g52140 At4 g18280 At2 g39430 At1 g01470 At4 g28530 At2 g43920 At1 g20190 At2 g18690 At3 g54050 At1 g30370 At5 g53190 At2 g25810 At5 g01210 At1 g19020 At5 g23400 At5 g64310 At5 g06720 At4 g15700 At3 g01670 At2 g35930 At1 g20450 At5 g37670 At1 g52100 At5 g19530 At3 g29030 At3 g10450 At2 g22470 At4 g28140 At1 g28400 At3 g25930 At5 g38970 At4 g34138 At1 g70470 At5 g14180 At1 g05760 At4 g18510 At3 g20210 At3 g23800 At2 g39450 At2 g36790 At1 g60030 At1 g80760 At4 g12880 At1 g14550 At5 g24780 At1 g14550 At2 g37630 At2 g34620 At5 g15740 At1 g62280 At5 g23860 At1 g05560 At1 g68290 At5 g54980 At5 g42680 At1 g51890 At3 g04290 At4 g24150 At1 g52830 At3 g59930 At5 g37790 At1 g77450 At3 g23090 At4 g26260 At5 g23820 At3 g25190 At1 g03170 At3 g50260 At1 g74310 At4 g23890 At5 g66390 rps12.1 At5 g02190 At5 g05220 At2 g02820 At1 g30760 At5 g20630 At3 g46900 At1 g75500 At4 g17490 At1 g47960 At3 g55940 At5 g55730 At3 g14560 At5 g17490 At1 g62510 At2 g23110 At4 g22590 At3 g17420 At4 g18590 At1 g31290 At3 g05170 At4 g28530 At2 g18690 At1 g29520 At4 g10310 At1 g11190 At1 g32940 At3 g43720 At5 g05410 At4 g22460 At5 g23060 At3 g18850 At1 g05680 At4 g00360 At4 g23060 At3 g01450 At4 g27520 At5 g22860 At1 g26250 At2 g30930 At5 g52570 At5 g01740 At4 g14560 At5 g04530 At3 g02850 At1 g30820 At2 g22860 At1 g11670 At4 g31310 At5 g12940 At3 g49840 At1 g76540 At1 g54040 At1 g78860 At5 g05140 At5 g03760 At4 g04990 At5 g25140 At2 g17660 At5 g59220 At1 g23720 At1 g28290 At3 g50970 At1 g74660 At4 g34138 At5 g53370 At2 g36870 At4 g19380 At1 g12010 At2 g27140 At4 g36430 At5 g44440 At1 g05010 At2 g21185 At1 g56060 At3 g59690 At5 g04120 At3 g07420 At1 g36060 At2 g33810 At5 g28630 At4 g33666 At5 g02020 At3 g23090 At2 g46660 At1 g63260 At4 g29780 At2 g43050 At5 g05220 At4 g35060 At4 g01250 At1 g75590 At2 g36790 At5 g20230 At4 g29780 At3 g23730 At2 g29310 At5 g02760 At5 g27420 At2 g30860 At3 g23920 At2 g29620 At3 g45280 At1 g36060 At1 g67810 At3 g12110 At2 g23110 At1 g15820 At1 g54740 At1 g36940 At5 g17990 At3 g12620 At2 g35930 At3 g06840 At1 g10060 At1 g74500 At1 g10340 At1 g71040 At5 g47330 At2 g21220 At4 g36540 At1 g47210 At5 g09530 At1 g80240 At3 g06500 At4 g11610 At1 g33440 At1 g68110 At3 g62150 At4 g28250 At1 g73480 At2 g27360 At1 g33811 At3 g50750 At2 g42060 At4 g22460 At5 g59820 At4 g25420

Vert et al. www.pnas.org/cgi/content/short/0803996105 11 of 28 Up Down

BRZ࿝Col BRZ࿝arf2 arf2࿝Col BRZ࿝Col BRZ࿝arf2 arf2࿝Col

At2 g02950 At3 g62090 At1 g63560 At3 g26170 At3 g14770 At3 g58190 At4 g35720 At1 g14700 At5 g46050 At5 g01075 At5 g38900 At2 g02300 At4 g37300 At5 g60520 At3 g54040 At3 g25290 At4 g32950 At1 g44760 At5 g14410 At3 g63130 At1 g74360 At2 g41380 At5 g12420 At3 g51600 At1 g62500 At5 g03960 At3 g12580 At5 g02020 At4 g37290 At2 g17850 At2 g33840 At2 g41090 At3 g20470 At5 g63800 At4 g01140 At5 g67020 At2 g44570 At1 g33811 At3 g19920 At1 g55210 At2 g44370 At1 g44575 At5 g18600 At1 g64390 At1 g05575 At4 g31500 At1 g19180 At2 g39430 At2 g40940 At1 g72610 At1 g16850 At3 g48020 At1 g56300 At5 g10100 At2 g29130 At5 g51810 At1 g66880 At5 g17980 At3 g53230 At5 g62920 At3 g48720 At4 g36530 At4 g36880 At5 g52310 At5 g01600 At1 g13130 At1 g17700 At3 g25830 At5 g39580 At1 g64700 At1 g19020 At1 g22590 At1 g67710 At1 g64470 At4 g36500 At3 g15540 At2 g15120 At4 g08950 At1 g25320 At3 g15620 At3 g04630 At3 g51670 At2 g04570 At1 g30750 At3 g61640 At2 g41800 At2 g17660 At3 g58190 At1 g74310 At5 g01075 At4 g22756 At1 g76500 At5 g38900 At3 g13650 At3 g50260 At3 g51670 At1 g63260 At2 g42990 At2 g39530 At3 g02640 At5 g46050 At2 g36100 At1 g28290 At3 g10080 At1 g64780 At1 g44800 At1 g55490 At5 g04200 At1 g62770 At4 g31820 At1 g18980 At1 g64610 At2 g46790 At5 g26270 At5 g57785 At4 g24780 At1 g21310 At2 g30210 At5 g65040 At1 g06080 At4 g30460 At4 g36360 At1 g18570 At4 g39030 At1 g15230 At5 g08000 At2 g34300 At2 g05070 At5 g51440 At5 g63450 At1 g21100 At3 g25290 At5 g02200 At4 g38660 At4 g01026 At2 g38620 At1 g53690 At3 g10910 At1 g63720 At1 g10640 At5 g34940 At2 g34490 At1 g71400 At5 g15350 At4 g31820 At1 g62510 At1 g70170 At1 g71380 At5 g42900 At1 g72200 At2 g30010 At1 g22650 At5 g04970 At2 g34500 At4 g37400 At1 g67910 At1 g75820 At1 g17700 At1 g26420 At3 g22600 At4 g25810 At2 g30210 At4 g36530 At2 g05790 At4 g39640 At1 g73120 At3 g19920 At3 g56200 At2 g44160 At3 g19620 At1 g61360 At3 g11410 At2 g17840 At5 g60200 At5 g26731 At1 g17180 At2 g43610 At3 g03000 At4 g37220 At5 g24580 At1 g14700 At2 g42910 At5 g14570 At5 g64770 At5 g35735 At1 g15260 At4 g36780 At4 g02380 At3 g54150 At4 g21850 At2 g28400 At1 g17190 At1 g21500 At4 g33960 At2 g28400 At2 g15970 At2 g28000 At1 g30380 At1 g76210 At1 g68560 At4 g14365 At1 g14350 At1 g20450 At4 g11310 At2 g14100 At3 g06840 At5 g01670 At1 g10370 At2 g35980 At5 g46700 At1 g62280 At5 g63180 At2 g35820 At5 g11650 At3 g54150 At4 g18970 At1 g56430 At3 g51600 At5 g13360 At3 g16850 At1 g74590 At5 g13140 At2 g29980 At2 g07671 At2 g15480 At3 g61820 At2 g25200 At4 g25100 At3 g54590 At3 g51895 At4 g28460 At3 g22370 At3 g50930 At4 g34160 At5 g18240 At1 g06980 At4 g33666 At1 g04140 At2 g35820 At1 g80240 At3 g15820 At5 g51210 At1 g19180 At2 g33380 At1 g19610 At5 g61130 At5 g48800 At3 g50890 At1 g02360 At4 g23690 At4 g15920 At2 g28790 At4 g01680 At3 g62630 At4 g33050 At1 g65310 At3 g08970 At1 g75500 At3 g15850 At2 g19660 At2 g40010 At5 g12030 At1 g10370 At1 g78000 At5 g66310 At3 g27690 At5 g03030 At4 g11280 At1 g72060 At5 g65360 At3 g48550 At4 g17460 At5 g47070 At3 g55840 At5 g62520 At5 g16030 At1 g31330 At2 g34620 At5 g52450 At1 g35180 At4 g27070 At1 g27480 At5 g14500 At2 g13610 At1 g19380 At5 g26270 At4 g01026 At3 g18200 At4 g08310 At3 g18050 At4 g23890 At4 g05190 At5 g17990 At2 g27140 At5 g03150 At3 g14940 At1 g22890 At5 g61340 At5 g28430 At3 g48100 At3 g22880 At1 g76620 At5 g05410 At4 g32870 At5 g64510 At3 g01500 At3 g52720 At1 g19900 At1 g70810 At1 g16060 At3 g50350 At1 g22885 At5 g38970 At2 g35470 At2 g29340 At1 g59860 At1 g07440 At2 g17500 At3 g62680 At3 g61640 At1 g17180 At2 g36100 At2 g27080 At4 g37445 At5 g59520 At4 g36540 At1 g01470 At1 g25400 At3 g03640 At1 g76220 At3 g54890 At3 g14560 At5 g52310 At2 g25160 At5 g27420 At1 g70670 At5 g16440 At5 g35670 At5 g63180 At3 g03240 At1 g74360 At5 g61340 At3 g53250 At5 g24030 At5 g48540 At5 g17850 At4 g01950 At5 g14120 At4 g39720 At5 g14450 At4 g36610 At1 g72970 At2 g22470 At2 g17230 At5 g51670 At2 g29980 At1 g64590 At3 g48460 At5 g59080 At1 g64700 At4 g33810 At3 g03270 At4 g30650 At4 g31910 At3 g23250 At5 g19970 At1 g76100 At4 g28220 At4 g27070 At1 g29195 At5 g39110 At4 g21850 At3 g62160 At5 g60950 At2 g38390 At2 g32240 At5 g17850 At4 g18570 At3 g59480 At5 g44440 At5 g43450 At5 g54160 At4 g36110 At1 g28670

Vert et al. www.pnas.org/cgi/content/short/0803996105 12 of 28 Up Down

BRZ࿝Col BRZ࿝arf2 arf2࿝Col BRZ࿝Col BRZ࿝arf2 arf2࿝Col

At1 g49660 At5 g14780 At2 g04050 At2 g47500 At4 g01310 At1 g52230 At3 g06840 At5 g53370 At5 g41740 At3 g47670 At2 g33430 At2 g42990 At1 g64470 At5 g07010 At3 g22370 At2 g22330 At2 g38340 At3 g63140 At1 g64460 At2 g37640 At2 g28210 At4 g37790 At4 g17490 At3 g27690 At5 g54490 At5 g48485 At3 g53230 At3 g16450 At1 g12010 At2 g18210 At2 g31670 At2 g17850 At4 g02330 At5 g53190 At5 g19240 At3 g18280 At5 g49960 At1 g49200 At5 g02150 At5 g64190 At4 g31240 At1 g14730 At5 g51460 At5 g10400 At1 g78070 At4 g35060 At1 g56060 At2 g42840 At5 g01210 At5 g51500 At4 g38440 At3 g22400 At2 g26440 At5 g23400 At2 g30600 At2 g28790 At3 g46670 At1 g02850 At5 g53250 At5 g17980 At1 g06120 At4 g24340 At1 g71400 At3 g48520 At4 g20000 At3 g52370 At1 g02900 At3 g53540 At4 g12550 At4 g34710 At3 g28210 At1 g77690 At3 g50640 At3 g16570 At1 g51920 At3 g20370 At1 g78070 At1 g65840 At5 g52370 At1 g56430 At2 g23110 At3 g08040 At1 g24100 At2 g47260 At2 g04795 At3 g02850 At2 g46650 At1 g22530 At5 g38700 At5 g42180 At1 g18880 At2 g18300 At1 g61560 At2 g43535 At3 g18250 At4 g01950 At4 g21400 At3 g26610 At4 g23920 At1 g22550 At3 g56400 At5 g53590 At4 g12550 At1 g77690 At2 g29130 At1 g29980 At4 g21860 At5 g52510 At2 g18300 At3 g45780 At3 g14620 At2 g17120 At5 g11920 At3 g03270 At3 g61470 At1 g05020 At2 g23120 At2 g37710 At1 g55450 At1 g08990 At1 g51940 At1 g52100 At3 g09940 At1 g65840 At1 g51890 At5 g18970 At1 g78460 At1 g75820 At4 g37400 At4 g01140 At1 g79680 At2 g37330 At4 g37550 At4 g24480 At5 g14190 At5 g16250 At1 g61260 At4 g23670 At3 g63200 At4 g35720 At2 g39920 At5 g40690 At1 g56150 At3 g14067 At4 g15390 At1 g07420 At1 g75860 At3 g10340 At5 g16970 At2 g46680 At5 g66110 At4 g08950 At4 g30660 At1 g76090 At3 g09940 At3 g09160 At2 g29340 At1 g11350 At3 g01970 At3 g22620 At5 g04340 At1 g79520 At2 g47930 orf111d At3 g03640 At5 g58070 At5 g55180 At1 g56580 At1 g13670 At2 g24280 At3 g06500 At1 g64670 At2 g40140 At3 g12110 At3 g10525 At2 g40230 At4 g17215 At1 g60190 At5 g14190 At3 g54400 At1 g68110 At2 g17880 At4 g13180 At5 g62550 At1 g60190 At3 g52540 At2 g26070 At2 g25160 At3 g56400 At4 g28290 At1 g56660 At1 g29490 At5 g43700 At1 g68570 At1 g23830 At1 g13930 At5 g52450 At4 g37470 At5 g04860 At2 g18290 At4 g25200 At1 g20070 At4 g28085 At3 g16770 At1 g53520 At4 g04830 At5 g58070 At2 g25625 At1 g55265 At1 g71740 At4 g16770 At1 g23080 At1 g24140 At1 g68880 At5 g43520 At1 g55670 At3 g16770 At3 g60700 At4 g20000 At3 g19553 At5 g02490 At1 g04800 At2 g38540 At3 g02980 At2 g15490 At3 g42570 At5 g44610 At2 g33210 At3 g61390 At4 g10955 At2 g46750 At2 g36220 At5 g20150 At4 g08300 At1 g31050 At1 g52190 At5 g39110 At5 g03380 At1 g25400 At3 g17790 At5 g14470 At1 g62380 At5 g19240 At1 g10360 At4 g32870 At5 g48500 At3 g24670 At4 g37800 At2 g38340 At3 g23920 At4 g14430 At1 g18870 At1 g74500 At2 g21050 At1 g58340 At2 g41870 At2 g01610 At2 g44940 At5 g15310 At4 g38530 At2 g28630 At3 g02880 At5 g41740 At5 g20885 At2 g40313 At3 g46200 At3 g55980 At1 g54120 At4 g11280 At5 g04530 At2 g47270 At1 g72180 At1 g61340 At3 g52360 At2 g04400 At1 g19330 At5 g59540 At1 g49750 At2 g36630 At5 g11540 At1 g71040 At1 g04770 At5 g05690 At4 g22570 At2 g04400 At1 g78290 At1 g51920 At5 g54270 At2 g31750 At1 g44760 At5 g01600 At3 g56800 At4 g35985 At4 g37300 At3 g11620 At2 g29390 At3 g16530 At4 g23450 At2 g45220 At1 g32540 At3 g60290 At5 g60530 At3 g16120 At5 g18970 At2 g40350 At5 g01820 At3 g20790 At1 g60630 At2 g32120 At2 g18010 At3 g10340 At2 g01420 At5 g14780 At4 g32280 At2 g19970 At1 g70370 At1 g09950 At3 g03840 At5 g23840 At1 g50110 At2 g41070 At2 g01610 At4 g01430 At5 g02440 At1 g70100 At2 g40900 At3 g62410 At4 g37220 At1 g23710 At5 g22860 At1 g68550 At1 g62180 At3 g19990 At2 g27360 At3 g21770 At5 g65640 At5 g15530 At5 g03230 At4 g17370 At5 g45670 At4 g39830 At5 g10210 At1 g54200 At2 g46660 At1 g72450 At1 g79270 At5 g16010 At3 g19030 At5 g58960 At3 g28860 At3 g62260 At2 g39050 At3 g49840 At2 g37620 At1 g52190 At3 g15410 At1 g36640 At1 g50490 At4 g28460 At1 g68400 At5 g60720 At3 g50440 At2 g32210 At1 g28400 At5 g28630 At1 g73370 At2 g17880 At3 g01810 At4 g00910 At2 g42840 At1 g16850 At5 g60670 At2 g02170 At5 g48500 At4 g14430 At1 g20440 At3 g03240 At2 g02130 At2 g28470 At1 g26920 At3 g47540 At4 g18970 At1 g33110 At4 g33960

Vert et al. www.pnas.org/cgi/content/short/0803996105 13 of 28 Up Down

BRZ࿝Col BRZ࿝arf2 arf2࿝Col BRZ࿝Col BRZ࿝arf2 arf2࿝Col

At4 g29080 At2 g46225 At5 g49520 At2 g43290 At2 g47180 At2 g02820 At2 g30520 At5 g38140 At2 g27660 At4 g38860 At4 g17030 At3 g16470 At1 g29660 At2 g30510 At5 g62490 At4 g28085 At1 g21680 At2 g41300 At4 g02380 At5 g59520 At5 g44480 At5 g62200 At3 g09440 At4 g02090 At2 g35270 At1 g25320 At1 g80840 At1 g70270 At2 g41380 At5 g35740 At4 g12880 At1 g50710 At1 g55110 At5 g05410 At5 g25260 At1 g08380 At4 g16780 At2 g37585 At2 g38500 At4 g19960 At1 g62570 At1 g17200 At1 g75590 At4 g27520 At4 g15550 At5 g10210 At5 g47450 At2 g32430 At3 g15440 At2 g47930 At5 g11070 At5 g06760 At2 g32120 At2 g46950 At1 g60960 At3 g56240 At3 g26470 At4 g33040 At1 g10340 At3 g56370 At2 g39930 At3 g15020 At3 g04520 At1 g64380 At1 g55530 At3 g45780 At5 g63510 At2 g20390 At1 g23710 At1 g72230 At4 g33050 At4 g09030 At3 g49920 At2 g20930 At2 g29330 At2 g37940 At4 g18430 At1 g77700 At3 g05520 At2 g01420 At1 g51360 At5 g27350 At2 g02990 At5 g60890 At2 g19970 At4 g22490 At5 g06860 At3 g54950 At4 g25100 At5 g42100 At5 g53980 At3 g15820 At4 g12470 At3 g14440 At5 g14570 At2 g27370 At5 g65300 At2 g39900 At4 g33540 At1 g17060 At4 g28290 At2 g22860 At5 g59890 At4 g34160 At3 g61190 At5 g49520 At1 g07690 At5 g62940 At5 g35670 At3 g59010 At4 g17840 At5 g46700 At1 g57990 At4 g14130 At4 g23650 At5 g60760 At3 g51000 At1 g62570 At2 g46750 At5 g37300 At4 g28190 At1 g78000 At3 g24500 At5 g15350 At4 g36500 At1 g07420 At2 g32440 At5 g45940 At5 g05960 At1 g54030 At3 g47430 At4 g34220 At2 g13610 At4 g17260 At3 g48920 At5 g60660 At1 g68880 At5 g01790 At3 g50560 At5 g63660 At1 g15230 At3 g19580 At1 g77950 At2 g18980 At5 g37790 At3 g54080 At1 g18390 At1 g05760 At2 g29460 At2 g20080 At1 g17810 At5 g62890 At3 g16440 At1 g67750 At1 g13340 At3 g52780 At1 g04310 At5 g60670 At1 g74310 At4 g11820 At1 g02400 At4 g28720 At2 g39980 At4 g36380 At3 g11580 At5 g20885 At4 g12470 At1 g55260 At5 g07090 At2 g41760 At5 g59720 At5 g04340 At2 g02930 At5 g63970 At5 g60530 At1 g69690 At4 g27830 At2 g22930 At5 g41080 At1 g78060 At4 g05200 At5 g26200 At1 g64400 At3 g54000 At3 g04000 At4 g29720 At3 g28550 At3 g54260 At3 g28930 At3 g48350 At1 g17170 At5 g40890 At4 g10060 At4 g38690 At2 g40140 At1 g73390 At3 g09410 At3 g46700 At1 g59740 At5 g44110 At1 g07350 At3 g56480 At3 g56090 At5 g05290 At4 g02200 At5 g48940 At2 g36930 At2 g23120 At3 g61190 At3 g10610 At1 g15910 At1 g65570 At1 g72680 At3 g15950 At2 g26760 At4 g09740 At4 g04830 At4 g10310 At2 g17840 At2 g35710 At5 g03380 At1 g20020 At5 g19890 At1 g70890 At2 g07140 At3 g09350 At3 g09020 At3 g28040 At5 g22700 At1 g62360 At3 g09410 At1 g30360 At5 g65800 At1 g49200 At1 g67870 At1 g68130 At1 g29660 At5 g14190 At3 g62150 At5 g63140 At2 g23170 At3 g53400 At1 g55530 At2 g31945 At1 g11960 At4 g39350 At2 g40540 At5 g02540 At4 g01870 At1 g31710 At1 g66880 At1 g48000 At3 g07350 At1 g06930 At2 g39200 At3 g05950 At5 g19440 At1 g19670 At3 g53720 At5 g54370 At4 g20830 At5 g57800 At5 g07460 At1 g60440 At5 g08415 At4 g14130 At3 g28210 At5 g22740 At5 g22300 At3 g18130 At2 g14920 At5 g09220 At5 g54860 At3 g27890 At1 g78290 At4 g12600 At3 g18940 At1 g79620 At1 g51790 At1 g53690 At5 g67600 At2 g33570 At3 g03040 At5 g03190 At5 g63210 At3 g63470 At3 g22800 At2 g22930 At5 g44260 At2 g26070 At4 g31500 At3 g55950 At1 g30720 At5 g48360 At1 g27670 At5 g51200 At3 g47430 At5 g14640 At1 g18740 At5 g37260 At5 g13280 At5 g65280 At2 g29490 At5 g62350 At2 g36770 At5 g51200 At1 g12330 At2 g25880 At4 g16660 At2 g02300 At1 g61820 At5 g40630 At2 g36890 At2 g28760 At2 g07698 At2 g47260 At1 g08920 At3 g27960 At1 g53000 At4 g00730 At1 g14870 At5 g13840 At1 g66160 At2 g29570 At1 g51830 At1 g31950 At3 g09270 At2 g02680 At1 g23800 At5 g01090 At3 g19960 At1 g73650 At5 g11210 At1 g71740 At3 g62260 At3 g23930 At2 g18400 At4 g16060 At5 g44920 At4 g37400 At2 g46600 At1 g02730 At5 g18470 At2 g17650 At3 g04000 At4 g25250 At3 g12700 At1 g62990 At3 g23190 At1 g47340 At5 g10300 At1 g48260 At5 g50200 At2 g19880 At5 g59090 At4 g17770 At5 g02810 At1 g55265 At2 g47600 At4 g22570 At5 g49230 At5 g66700 At5 g61190 At2 g35650 At3 g46130 At3 g21370 At4 g19530 At4 g13950 At5 g57300 At1 g06520 At2 g20610 At4 g01430 At4 g22930 At2 g02130 At1 g53540 At4 g17280 At3 g26170 At3 g55130 At5 g03960 At3 g50240 At4 g05200 At1 g29050 At3 g14620 At1 g53300

Vert et al. www.pnas.org/cgi/content/short/0803996105 14 of 28 Up Down

BRZ࿝Col BRZ࿝arf2 arf2࿝Col BRZ࿝Col BRZ࿝arf2 arf2࿝Col

At4 g28150 At1 g22060 At5 g15130 At1 g08560 At5 g45340 At4 g39320 At3 g50660 At3 g28050 At2 g30260 At4 g00370 At5 g58570 At1 g02950 At1 g80830 At1 g75980 At5 g16630 At3 g18280 At2 g37130 At3 g11690 At1 g58370 At1 g12330 At4 g38080 At3 g52370 At5 g19855 At1 g19440 At4 g25620 At1 g25560 At2 g29740 At3 g09490 At2 g02680 At5 g16000 At3 g55050 At3 g23170 At3 g50950 At3 g20670 At4 g20830 At1 g69770 At1 g03660 At3 g07350 At3 g62090 At4 g16515 At4 g30530 At2 g30070 At3 g23880 At1 g49660 At3 g23920 At5 g08370 At1 g72430 At1 g48630 At5 g49630 At3 g06130 At3 g49620 At3 g05990 At1 g22570 At3 g54750 At2 g21185 At4 g31890 At2 g46440 At5 g60200 At1 g14870 At2 g21050 At1 g69690 At2 g33370 At2 g38400 At3 g03840 At3 g10300 At3 g53190 At2 g41090 At4 g12600 At5 g62520 At3 g51860 At5 g16250 At1 g53140 At1 g23850 At5 g04820 At4 g21320 At4 g21830 At5 g25610 At5 g50720 At3 g06460 At4 g37110 At5 g62910 At1 g62430 At2 g41480 At2 g25790 At5 g11260 At2 g39510 At5 g05480 At4 g05520 At1 g76990 At2 g18290 At4 g23700 At3 g55005 At1 g71730 At1 g12845 At4 g23920 At1 g49750 At3 g59900 At5 g08100 At5 g57090 At4 g30170 At1 g02850 At3 g54080 At1 g50110 At2 g04850 At1 g17170 At3 g26720 At1 g64160 At5 g45940 At5 g02160 At1 g28395 At1 g31100 At1 g63440 At3 g50950 At1 g55190 At1 g77670 At3 g06680 At1 g49570 At4 g00330 At1 g61360 At5 g65630 At1 g24530 At5 g27360 At1 g56320 At5 g49890 At4 g23190 At1 g64200 At3 g51600 At3 g13510 At5 g24030 At1 g15210 At3 g01970 At5 g02190 At5 g60400 At5 g49960 At1 g48130 At1 g70900 At5 g22060 At3 g62110 At2 g30610 At3 g46900 At4 g08850 At3 g03170 At3 g58710 At5 g03760 At1 g68560 At1 g53300 At1 g79680 At1 g77450 At3 g19580 At3 g57165 At3 g09800 At1 g33750 At5 g39050 At1 g53700 At5 g26655 At3 g60550 At4 g19030 At3 g44720 At4 g31800 At1 g09380 At3 g54090 At3 g49500 At1 g33110 At2 g30550 At3 g19390 At5 g54510 At5 g37660 At1 g20450 At1 g08500 At3 g26720 At1 g12240 At4 g16780 At1 g01140 At5 g37300 At4 g00330 At2 g40230 At5 g22440 At1 g21680 At3 g14190 At3 g01290 At5 g44110 At1 g69700 At3 g50560 At4 g09030 At1 g19380 At1 g05310 At2 g29530 At3 g05800 At2 g01180 At3 g46690 At1 g44760 At5 g11550 At4 g27300 At2 g20750 At2 g30860 At5 g23050 At3 g24150 At5 g48410 At5 g23220 At1 g69890 At3 g56240 At4 g33810 At4 g35090 At1 g27950 At3 g45450 At2 g29330 At4 g15790 At5 g03490 At3 g13430 At2 g30140 At1 g30570 At4 g21326 At4 g31420 At5 g24290 At1 g01120 At4 g18400 At5 g40610 At5 g58570 At5 g49900 At2 g20920 At2 g36630 At5 g15160 At5 g14180 At4 g02280 At3 g22600 At1 g60710 At3 g10610 At1 g02850 At4 g32950 At3 g50650 At1 g08340 At4 g35210 At5 g61010 At3 g52470 At5 g49640 At5 g48490 At2 g46950 At1 g66160 At1 g54010 At4 g11190 At5 g47800 At1 g21710 At5 g38980 At3 g48940 At5 g62360 At1 g26920 At3 g10940 At5 g06320 At1 g08325 At3 g22890 At3 g15300 At1 g08380 At4 g19960 At5 g66230 At5 g54160 At1 g10550 At5 g16000 At4 g02410 At3 g60840 At2 g16900 At1 g76410 At2 g40640 At3 g25190 At1 g09460 At2 g39700 At1 g73650 At2 g25980 At1 g69930 At5 g20150 At3 g55970 At3 g50440 At1 g67040 At5 g55180 At4 g28210 At4 g25200 At5 g07030 At5 g66800 At3 g26690 At3 g46700 At3 g43720 At2 g36570 At5 g15310 At5 g66440 At1 g01470 At1 g73390 At2 g01940 At1 g04290 At1 g52200 At2 g17840 At4 g02410 At4 g16670 At4 g25120 At3 g51330 At2 g36310 At5 g59490 At2 g07711 At5 g05890 At2 g29470 At3 g04060 At3 g19553 At1 g07280 At5 g24300 At1 g22985 At3 g53620 At5 g61190 At3 g25860 At1 g80190 At5 g25930 At2 g27970 At3 g48520 At1 g04290 At4 g14770 At5 g03310 At5 g66260 At1 g78310 At1 g61360 At3 g29375 At4 g28140 At4 g37410 At2 g41110 At2 g22980 At1 g12740 At4 g22610 At4 g05100 At4 g17090 At5 g18790 At4 g25870 At1 g75240 At1 g74410 At3 g48020 At2 g41310 At5 g64940 At3 g14690 At2 g37870 At2 g18140 At1 g52230 At2 g47140 At4 g23180 At5 g47910 At3 g63010 At5 g22500 At5 g27740 At3 g28740 At4 g12510 At3 g44720

Vert et al. www.pnas.org/cgi/content/short/0803996105 15 of 28 Up Down

BRZ࿝Col BRZ࿝arf2 arf2࿝Col BRZ࿝Col BRZ࿝arf2 arf2࿝Col

At1 g72180 At4 g34610 At5 g67600 At5 g41800 At1 g28380 At5 g56360 At3 g51470 At5 g15120 At4 g20070 At5 g47910 At4 g02840 At1 g53520 At5 g02260 At4 g27860 At4 g38420 At5 g44210 At2 g29310 At5 g24800 At5 g06200 At1 g14810 At3 g18850 At5 g13960 At2 g40000 At4 g14380 At4 g17840 At5 g60950 At1 g11960 At1 g78070 At1 g70610 At3 g25560 At5 g59090 At5 g41400 At1 g12200 At3 g25210 At4 g35380 At1 g61260 At3 g54950 At4 g28410 At2 g32020 At5 g65040 At2 g31945 At2 g17230 At1 g74450 At3 g09440 At4 g39640 At4 g19410 At2 g43590 At2 g41300 At3 g46700 At1 g24340 At1 g44130 At5 g13700 At5 g27350 At3 g13845 At4 g23190 At2 g48030 At2 g01180 At3 g16660 At1 g64970 At1 g06640 At3 g48350 At2 g41610 At2 g18680 At5 g57610 At5 g25440 At2 g37280 At1 g01480 At4 g23410 At2 g30490 At3 g48740 At5 g13200 At5 g60890 At3 g25980 At5 g03190 At3 g21790 At3 g49840 At1 g74450 At1 g06210 At1 g13750 At5 g02220 At3 g17770 At5 g18670 At4 g16830 At1 g69530 At5 g60660 At4 g12330 At1 g24340 At2 g19880 At5 g16960 At3 g28860 At5 g25440 At5 g20270 At2 g21880 NULL At4 g26260 At5 g63590 At3 g07650 At5 g57850 At5 g13310 At3 g10320 At3 g20340 At1 g14890 At3 g59080 At1 g18140 At5 g45670 At5 g15740 At5 g67340 At4 g24900 At2 g35710 At5 g27410 At5 g05300 At2 g05940 At5 g09970 At1 g64660 At3 g08590 At2 g22860 At4 g16260 At5 g22440 At2 g46240 At1 g17620 At1 g55920 At3 g50240 At3 g61390 At3 g56370 At5 g10210 At1 g26210 At3 g23790 At4 g37730 At1 g64380 At4 g13950 At4 g37180 At1 g64200 At4 g26320 At3 g18960 At5 g25260 At1 g53140 At3 g54000 At4 g14130 At4 g17230 At5 g57070 At4 g31800 At4 g13640 At4 g29140 At2 g31110 At5 g12010 At3 g62630 At5 g24470 At1 g78060 At1 g64200 At1 g25560 At4 g01850 At1 g30080 At5 g13200 At2 g31085 At1 g77950 At2 g17300 At3 g04060 At1 g31060 At2 g16900 At1 g02730 At4 g10960 At5 g11160 At1 g18380 At3 g23790 At1 g48330 At4 g01590 At2 g47180 At5 g01520 At2 g40270 At5 g03180 At3 g14660 At5 g45340 At1 g63440 At4 g34610 At2 g46600 At2 g41880 At4 g26120 At2 g05160 At4 g38580 At5 g02560 At3 g48460 At1 g70500 At1 g77480 At1 g08990 At5 g62550 At1 g72490 At2 g32440 At2 g23450 At1 g69930 At3 g11210 At4 g22590 At5 g01820 At4 g39660 At1 g11240 At3 g20340 At1 g14370 At5 g53590 At1 g61180 At4 g10910 At5 g51680 At1 g57630 At2 g40670 At5 g22060 At4 g24180 At1 g01480 At4 g24430 At3 g51890 At1 g67940 At4 g27830 At3 g18050 At5 g19440 At1 g73080 At3 g27210 At1 g69700 At4 g24160 At3 g23870 At2 g28780 At1 g26450 At1 g19530 At1 g59660 At5 g39550 At1 g10120 At5 g51810 At5 g10190 At1 g13210 At5 g24840 At1 g13990 At5 g08000 At2 g27660 At2 g17630 At5 g62150 At5 g41080 At1 g46768 At1 g70950 At3 g08970 At2 g27370 At2 g17300 At3 g23520 At4 g23700 At1 g18740 At3 g09710 At1 g23460 At4 g10070 At3 g15210 At4 g24380 At3 g01320 At5 g12420 At3 g08880 At2 g02820 At2 g02450 At5 g58220 At5 g25270 At4 g39230 At4 g26150 At1 g30070 At4 g25640 At3 g60120 At5 g51840 At5 g63200 At5 g63660 At4 g05190

Vert et al. www.pnas.org/cgi/content/short/0803996105 16 of 28 Up Down

BRZ࿝Col BRZ࿝arf2 arf2࿝Col BRZ࿝Col BRZ࿝arf2 arf2࿝Col

At2 g32540 At2 g41010 At1 g29520 At5 g11600 At4 g38550 At5 g44060 At5 g50720 At1 g11210 At2 g41730 At3 g45210 At5 g23080 At3 g58710 At1 g56020 At2 g47730 At1 g72800 At2 g32860 At3 g46690 At2 g25200 At1 g51110 At4 g10250 At1 g03370 At4 g15660 At1 g48750 At5 g48450 At5 g18800 At5 g59490 At5 g47640 At1 g12260 At5 g58120 At3 g57630 At4 g11290 At3 g07600 At2 g01150 At2 g07674 At2 g04795 At5 g12010 At4 g30993 At4 g05020 At1 g62180 At1 g65000 At2 g38820 At3 g16340 At1 g26290 At1 g22570 At1 g08920 At3 g07410 At5 g54080 At2 g32280 At3 g55720 At2 g44380 At3 g02210 At3 g21690 At1 g08460 At5 g63970 At1 g66980 At1 g68880 At2 g45190 At2 g41970 At1 g60170 At5 g24580 At5 g14570 At4 g30530 At1 g73750 At5 g52450 At2 g29990 At3 g22570 At2 g24330 At2 g22880 At5 g12840 At4 g01026 At1 g43160 At4 g13510 At2 g31260 At3 g06660 At1 g30070 At3 g52780 At3 g50900 At3 g11750 At1 g08800 At4 g18950 At1 g78310 At5 g22300 At1 g24150 At5 g61510 At3 g21720 At1 g54890 At5 g59590 At1 g03660 At3 g01290 At1 g27510 At1 g68620 At1 g69890 At2 g35730 At1 g32450 At1 g68690 At5 g40420 At1 g73980 At2 g18300 At1 g64160 At3 g20720 At1 g71695 At2 g30990 At5 g12120 At2 g02390 At2 g01180 At1 g08630 At3 g12490 At3 g54420 At4 g37900 At3 g22480 At4 g31800 At1 g22510 At5 g64180 At1 g01340 At2 g37980 At5 g65650 At5 g60950 At1 g16730

Vert et al. www.pnas.org/cgi/content/short/0803996105 17 of 28 Up Down

BRZ࿝Col BRZ࿝arf2 arf2࿝Col BRZ࿝Col BRZ࿝arf2 arf2࿝Col

At1 g56600 At4 g02880 At5 g64510 At3 g02860 At3 g10300 At5 g06570 At1 g19130 At3 g27170 At4 g39660 At5 g19890 At3 g60120 At1 g76410 At1 g53520 At3 g20500 At5 g40590 At1 g27760 At2 g25940 At3 g59700 At2 g41710 At4 g26120 At5 g03180 At2 g36770 At2 g47550 At2 g38180 At5 g48480 At4 g15700 At1 g07690 At1 g47980 At3 g60840 At3 g22570 At3 g07410 At2 g25060 At4 g01700 At5 g56720 At1 g75820 At1 g68230 At2 g39290 At4 g27520 At5 g42500 At1 g28470 At3 g16340 At4 g21310 At1 g28010 At1 g73750

Vert et al. www.pnas.org/cgi/content/short/0803996105 18 of 28 Table S5. One hundred most significant genes differentially expressed in arf2 mutant plants compared to wild-type Col plants (genes were ranked by adjusted P value). Average expression for each condition is given. A, arf2; C, Col; B, BRZ; M, mock. Ratios for arf2 on BRZ vs. arf2 on mock (AB/AM) and arf2 mock vs. Col mock (AM/CM) are also shown. Affy AGI Adjusted P value log (odds) AB AM CB CM AB/AM AM/CM Annotation

247468࿝at At5 g62010 2.3E-12 22.3 30 27 1290 1249 1.1 0.0 ARF2 260406࿝at At1 g69920 2.4E-09 19.1 29 221 31 33 0.1 6.6 glutathione transferase, AtGSTU12 261021࿝at At1 g26380 8.4E-09 17.8 42 486 39 32 0.1 15.3 reticuline oxidase 264404࿝at At2 g25160 8.4E-09 17.8 43 27 91 169 1.6 0.2 CYP82F1 245041࿝at At2 g26530 8.4E-09 17.9 53 153 44 44 0.3 3.5 unknown 253073࿝at At4 g37410 1.9E-08 17.1 164 54 141 222 3.0 0.2 CYP81F4 247882࿝at At5 g57785 7.8E-08 15.9 583 92 844 431 6.3 0.2 unknown 267565࿝at At2 g30750 9.6E-08 15.6 17 100 16 18 0.2 5.6 CYP71A12 256940࿝at At3 g30720 2.0E-07 14.9 391 277 43 43 1.4 6.5 unknown 258277࿝at At3 g26830 2.0E-07 14.8 21 84 19 17 0.3 5.0 CYP71B15, PAD3 259352࿝at At3 g05170 2.2E-07 14.7 67 61 20 21 1.1 2.9 unknown protein 265411࿝at At2 g16630 2.3E-07 14.6 97 628 115 108 0.2 5.8 unknown protein 261474࿝at At1 g14540 2.7E-07 14.3 58 340 49 43 0.2 7.9 PER4 peroxidase 253040࿝at At4 g37800 2.7E-07 14.3 48 26 112 84 1.8 0.3 At-XTH7 259653࿝at At1 g55240 3.0E-07 14.2 61 55 402 622 1.1 0.1 unknown protein 254907࿝at At4 g11190 3.1E-07 14.1 205 315 475 1704 0.7 0.2 unknown 247095࿝at At5 g66400 3.9E-07 13.8 1034 3448 389 514 0.3 6.7 dehydrin 266209࿝at At2 g27550 1.0E-06 12.9 176 152 118 48 1.2 3.2 similar to Terminal Flower 264157࿝at At1 g65310 1.0E-06 12.9 344 184 433 822 1.9 0.2 At-XTH17 263098࿝at At2 g16005 1.0E-06 12.8 29 28 29 390 1.0 0.1 unknown 248727࿝at At5 g47990 1.1E-06 12.7 77 93 304 837 0.8 0.1 CYP705A5 264745࿝at At1 g62180 1.2E-06 12.6 155 94 205 232 1.6 0.4 5 -adenylylphosphosulfate reductase 256601࿝s࿝at At3 g28290 1.5E-06 12.3 355 306 206 41 1.2 7.4 integrin-like 267101࿝at At2 g41480 1.5E-06 12.3 35 61 42 153 0.6 0.4 PER25 peroxidase 266996࿝at At2 g34490 1.5E-06 12.3 57 87 144 327 0.7 0.3 CYP710A2, C22-sterol desaturase 245422࿝at At4 g17470 2.3E-06 11.8 77 65 66 265 1.2 0.2 PPT1-like thioesterase 251248࿝at At3 g62150 2.3E-06 11.8 77 137 70 55 0.6 2.5 PGP21 250475࿝at At5 g10180 2.3E-06 11.8 1597 425 496 82 3.8 5.2 sulfate transporter 260015࿝at At1 g67980 2.4E-06 11.7 95 370 60 53 0.3 7.1 CCoAOMT6 262119࿝s࿝at At1 g02930 3.7E-06 11.3 2191 6334 2213 1718 0.3 3.7 glutathione S-transferase, AtGSTF6 254119࿝at At4 g24780 3.7E-06 11.3 156 88 210 211 1.8 0.4 pectate lyase 247215࿝at At5 g64905 4.2E-06 11.1 26 98 23 22 0.3 4.4 unknown 247949࿝at At5 g57220 4.3E-06 11.0 80 606 79 50 0.1 12.0 CYP81F2 252214࿝at At3 g50260 4.4E-06 11.0 268 661 202 228 0.4 2.9 AP2-EREBP transcription factor, Rap2.1 254648࿝at At4 g18550 4.4E-06 10.9 67 61 163 231 1.1 0.3 lipase 254188࿝at At4 g23920 4.4E-06 11.0 46 74 34 40 0.6 1.8 UDPglucose 4-epimerase 245148࿝at At2 g45220 5.5E-06 10.7 372 918 242 220 0.4 4.2 pectinesterase 249097࿝at At5 g43520 5.6E-06 10.7 104 190 118 49 0.5 3.9 unknown 247293࿝at At5 g64510 5.9E-06 10.6 23 54 22 27 0.4 2.0 unknown 253113࿝at At4 g35985 6.0E-06 10.5 89 192 53 59 0.5 3.3 unknown 267411࿝at At2 g34930 6.0E-06 10.5 33 203 34 39 0.2 5.2 unknown 257130࿝at At3 g20210 6.3E-06 10.5 317 160 455 412 2.0 0.4 asparaginyl endopeptidase 256647࿝at At3 g13610 6.3E-06 10.4 77 539 81 48 0.1 11.2 unknown 245076࿝at At2 g23170 7.0E-06 10.3 133 141 687 361 0.9 0.4 unknown protein 259705࿝at At1 g77450 7.2E-06 10.3 286 768 215 303 0.4 2.5 NAC transcription factor 258746࿝at At3 g05950 7.9E-06 10.1 91 350 43 81 0.3 4.3 germin 267263࿝at At2 g23110 7.9E-06 10.2 66 170 37 66 0.4 2.6 unknown 253046࿝at At4 g37370 9.2E-06 10.0 43 132 36 37 0.3 3.6 CYP81D8 262121࿝at At1 g02800 9.7E-06 9.9 84 61 90 207 1.4 0.3 endo-1,4-beta-glucanase 248236࿝at At5 g53870 9.7E-06 9.9 28 48 163 347 0.6 0.1 phytocyanin-like 264846࿝at At2 g17850 1.0E-05 9.8 61 33 89 60 1.9 0.5 rhodanese protein AtStr17 246099࿝at At5 g20230 1.0E-05 9.8 54 697 45 102 0.1 6.8 blue copper binding protein 261020࿝at At1 g26390 1.0E-05 9.7 21 168 19 21 0.1 8.0 reticuline oxidase 263096࿝at At2 g16060 1.0E-05 9.7 1020 467 1451 1265 2.2 0.4 class 1 non-symbiotic hemoglobin (AHB1) 263402࿝at At2 g04050 1.0E-05 9.7 21 57 19 24 0.4 2.3 unknown 251509࿝at At3 g59010 1.0E-05 9.7 124 74 70 218 1.7 0.3 pectinesterase 251847࿝at At3 g54640 1.1E-05 9.6 150 547 140 120 0.3 4.6 tryptophan synthase alpha chain 263948࿝at At2 g35980 1.2E-05 9.5 35 115 28 21 0.3 5.5 unknown 263403࿝at At2 g04040 1.4E-05 9.3 25 113 28 29 0.2 3.9 unknown 262001࿝at At1 g33790 1.6E-05 9.2 316 460 239 146 0.7 3.2 EF-hand 251884࿝at At3 g54150 1.7E-05 9.1 23 47 27 24 0.5 1.9 unknown 250351࿝at At5 g12030 1.7E-05 9.1 39 175 18 40 0.2 4.3 HSP17.6A

Vert et al. www.pnas.org/cgi/content/short/0803996105 19 of 28 Affy AGI Adjusted P value log (odds) AB AM CB CM AB/AM AM/CM Annotation

266746࿝s࿝at At2 g02930 1.8E-05 9.0 818 1671 719 400 0.5 4.2 glutathione S-transferase, AtGSTF3 248728࿝at At5 g48000 1.9E-05 8.9 35 38 103 96 0.9 0.4 cytochrome P450-like protein 260225࿝at At1 g74590 1.9E-05 8.8 63 127 41 27 0.5 4.7 glutathione S-transferase, AtGSTU10 248703࿝at At5 g48430 2.1E-05 8.8 248 382 150 93 0.6 4.1 glycoprotein 256376࿝s࿝at At1 g66690 2.1E-05 8.7 415 1533 305 173 0.3 8.9 unknown 264757࿝at At1 g61360 2.1E-05 8.7 91 127 97 63 0.7 2.0 receptor kinase IRK1 267384࿝at At2 g44370 2.2E-05 8.6 66 126 58 36 0.5 3.5 unknown 249481࿝at At5 g38900 2.4E-05 8.5 28 77 27 31 0.4 2.5 unknown 250446࿝at At5 g10770 2.4E-05 8.5 121 37 108 107 3.3 0.3 nucleoid DNA-binding protein cnd41 259729࿝at At1 g77640 2.5E-05 8.4 210 140 140 58 1.5 2.4 unknown 251017࿝at At5 g02760 2.5E-05 8.4 309 140 878 417 2.2 0.3 protein 2C 256306࿝at At1 g30370 2.6E-05 8.4 54 126 44 39 0.4 3.2 lipase 252908࿝at At4 g39670 2.6E-05 8.3 83 233 56 66 0.4 3.5 sphingosine transfer protein 261005࿝at At1 g26420 2.6E-05 8.3 23 51 19 23 0.5 2.2 reticuline oxidase 266168࿝at At2 g38870 2.6E-05 8.3 413 1262 248 290 0.3 4.4 protease inhibitor 251438࿝s࿝at At3 g59930 2.6E-05 8.3 1068 668 447 162 1.6 4.1 unknown 259479࿝at At1 g19020 2.6E-05 8.3 397 888 288 334 0.4 2.7 unknown 246943࿝at At5 g25440 2.6E-05 8.3 105 157 86 90 0.7 1.7 serine/threonine protein kinase APK1 260744࿝at At1 g15010 3.0E-05 8.1 148 402 80 96 0.4 4.2 unknown 249575࿝at At5 g37670 4.0E-05 7.7 52 115 40 43 0.4 2.7 HSP17.5 249010࿝at At5 g44580 4.3E-05 7.6 73 43 168 132 1.7 0.3 unknown 245352࿝at At4 g15490 4.5E-05 7.6 23 75 22 29 0.3 2.6 indole-3-acetate beta-glucosyltransferase 254331࿝s࿝at At4 g22710 4.9E-05 7.5 136 559 74 70 0.2 8.0 CYP706A2 253100࿝at At4 g37400 4.9E-05 7.5 27 54 22 33 0.5 1.6 CYP81F3 246368࿝at At1 g51890 5.2E-05 7.4 36 60 28 26 0.6 2.3 receptor kinase 259892࿝at At1 g72610 5.7E-05 7.3 472 232 900 613 2.0 0.4 germin 258589࿝at At3 g04290 5.9E-05 7.2 166 128 182 268 1.3 0.5 GDSL-motif lipase/acylhydrolase 250826࿝at At5 g05220 6.3E-05 7.1 17 38 20 23 0.4 1.7 unknown 265920࿝s࿝at At2 g15120 7.4E-05 6.9 116 268 92 72 0.4 3.7 unknown 245734࿝at At1 g73480 7.4E-05 6.9 188 396 105 111 0.5 3.6 247582࿝at At5 g60760 7.5E-05 6.8 165 80 163 187 2.1 0.4 unknown 263935࿝at At2 g35930 9.1E-05 6.6 82 193 69 82 0.4 2.4 plant U-box protein, AtPUB23 251565࿝at At3 g58190 1.9E-04 5.6 18 21 21 41 0.9 0.5 ASL16 254828࿝at At4 g12550 2.1E-04 5.5 429 488 405 219 0.9 2.2 CLCT protein (AIR1A) 250467࿝at At5 g10100 2.6E-04 5.2 35 23 47 43 1.5 0.5 trehalose-6-phosphate phosphatase 252004࿝at At3 g52780 6.6E-04 3.8 42 44 54 59 1.0 0.7 purple 256366࿝at At1 g66880 8.1E-04 3.6 47 82 44 49 0.6 1.7 protein kinase 251181࿝at At3 g62820 3.6E-03 1.4 74 37 164 81 2.0 0.5 pectinesterase

Vert et al. www.pnas.org/cgi/content/short/0803996105 20 of 28 Table S6. Genes differentially expressed in wild-type Col vs. arf2 mutants known to be regulated by or associated with auxin signaling. Average expression for each condition is given. A, arf2; C, Col; B, BRZ; M, mock. Ratios for arf2 mock vs. Col mock (AM/CM) are also shown. Affy AGI Adj p-value log (odds) AB AM CB CM AM/CM Annotation

264404࿝at At2 g25160 8.4E-09 17.8 43 27 91 169 0.2 CYP82F1 245041࿝at At2 g26530 8.4E-09 17.9 53 153 44 44 3.5 unknown 247095࿝at At5 g66400 3.9E-07 13.8 1034 3448 389 514 6.7 dehydrin 264157࿝at At1 g65310 1.0E-06 12.9 344 184 433 822 0.2 At-XTH17 248727࿝at At5 g47990 1.1E-06 12.7 77 93 304 837 0.1 CYP705A5 266996࿝at At2 g34490 1.5E-06 12.3 57 87 144 327 0.3 CYP710A2, C22-sterol desaturase 247215࿝at At5 g64905 4.2E-06 11.1 26 98 23 22 4.4 unknown 252214࿝at At3 g50260 4.4E-06 11.0 268 661 202 228 2.9 AP2-EREBP transcription factor, Rap2.1 245076࿝at At2 g23170 7.0E-06 10.3 133 141 687 361 0.4 GH3–3 253046࿝at At4 g37370 9.2E-06 10.0 43 132 36 37 3.6 CYP81D8 251977࿝at At3 g53250 1.7E-05 9.0 111 36 149 71 0.5 SAUR57 253643࿝at At4 g29780 2.4E-05 8.5 91 183 84 87 2.1 unknown 251017࿝at At5 g02760 2.5E-05 8.4 309 140 878 417 0.3 protein protein phosphatase 2C 256306࿝at At1 g30370 2.6E-05 8.4 54 126 44 39 3.2 lipase 252908࿝at At4 g39670 2.6E-05 8.3 83 233 56 66 3.5 sphingosine transfer protein 259479࿝at At1 g19020 2.6E-05 8.3 397 888 288 334 2.7 unknown 245250࿝at At4 g17490 2.6E-05 8.2 59 112 47 42 2.6 AP2-EREBP transcription factor ERF6 265670࿝s࿝at At2 g32210 2.9E-05 8.2 39 190 34 70 2.7 unknown 260744࿝at At1 g15010 3.0E-05 8.1 148 402 80 96 4.2 unknown 247655࿝at At5 g59820 3.6E-05 7.8 227 510 180 193 2.6 C2H2 Zn finger ZAT12 265499࿝at At2 g15480 4.0E-05 7.7 132 174 88 92 1.9 glycosyltransferase 260522࿝x࿝at At2 g41730 4.0E-05 7.7 95 269 47 87 3.1 unknown 263935࿝at At2 g35930 9.1E-05 6.6 82 193 69 82 2.4 plant U-box protein, AtPUB23 249459࿝at At5 g39580 9.8E-05 6.5 288 933 354 368 2.5 peroxidase, PER62 252827࿝at At4 g39950 1.0E-04 6.4 82 515 100 153 3.4 CYP79B2 251565࿝at At3 g58190 1.9E-04 5.6 18 21 21 41 0.5 ASL16 259443࿝at At1 g02360 2.0E-04 5.6 323 478 326 242 2.0 chitinase 254828࿝at At4 g12550 2.1E-04 5.5 429 488 405 219 2.2 AIR1 265501࿝at At2 g15490 2.3E-04 5.3 180 192 130 109 1.8 glycosyltransferase 245193࿝at At1 g67810 2.6E-04 5.1 512 1613 453 674 2.4 unknown 256576࿝at At3 g28210 2.7E-04 5.1 23 56 21 27 2.1 C2H2 Zn finger transcription factor PMZ 265674࿝at At2 g32190 2.8E-04 5.0 48 258 29 75 3.4 unknown 262045࿝at At1 g80240 3.3E-04 4.8 239 256 214 412 0.6 unknown 261719࿝at At1 g18380 3.4E-04 4.7 49 63 45 35 1.8 unknown 246270࿝at At4 g36500 3.7E-04 4.6 204 366 169 176 2.1 unknown 259331࿝at At3 g03840 4.2E-04 4.4 104 80 93 122 0.7 SAUR27 250670࿝at At5 g06860 4.3E-04 4.4 510 622 401 266 2.3 polygalacturonase inhibiting protein PGIP1 254759࿝at At4 g13180 4.5E-04 4.4 934 1124 763 649 1.7 short-chain alcohol dehydrogenas 246777࿝at At5 g27420 4.6E-04 4.3 101 225 82 98 2.3 RING-H2 zinc finger protein ATL6 256877࿝at At3 g26470 4.9E-04 4.2 282 354 295 180 2.0 unknown 248801࿝at At5 g47370 6.2E-04 3.9 781 531 1111 954 0.6 HAT2 253044࿝at At4 g37290 6.4E-04 3.9 27 55 24 22 2.5 unknown 265668࿝at At2 g32020 7.8E-04 3.6 50 79 41 46 1.7 alanine acetyl transferase 250293࿝s࿝at At5 g13360 7.8E-04 3.6 218 486 191 227 2.1 GH3–14 265276࿝at At2 g28400 8.1E-04 3.5 167 314 129 140 2.2 unknown 256024࿝at At1 g58340 9.0E-04 3.4 76 87 59 42 2.1 unknown 266017࿝at At2 g18690 9.1E-04 3.4 345 910 461 411 2.2 unknown 250940࿝at At5 g03310 9.9E-04 3.2 44 53 41 29 1.8 SAUR44 259786࿝at At1 g29660 9.9E-04 3.2 660 496 494 265 1.9 lipase/hydrolase 247406࿝at At5 g62920 1.0E-03 3.2 81 69 123 108 0.6 ARR6 266300࿝at At2 g01420 1.0E-03 3.2 649 363 752 598 0.6 AtPIN4 263379࿝at At2 g40140 1.2E-03 3.0 390 687 364 378 1.8 C3H Zn finger transcription factor CZF1 254609࿝at At4 g18970 1.3E-03 2.9 1410 1471 1445 2296 0.6 unknown 251507࿝at At3 g59080 1.3E-03 2.8 53 73 48 42 1.7 aspartyl protease 264758࿝at At1 g61340 1.3E-03 2.8 27 74 21 35 2.1 unknown 260405࿝at At1 g69930 1.4E-03 2.8 22 51 22 20 2.6 glutathione S-transferase, AtGSTU11 260152࿝at At1 g52830 1.5E-03 2.6 200 262 206 521 0.5 IAA6 256452࿝at At1 g75240 1.6E-03 2.5 980 1108 652 671 1.7 ZF-HD transcription factor AtZHD5 253957࿝at At4 g26320 1.7E-03 2.4 133 227 135 446 0.5 unknown 266663࿝at At2 g25790 2.0E-03 2.2 204 190 248 220 0.9 receptor kinase-like protein 255252࿝at At4 g04990 2.1E-03 2.2 112 193 81 70 2.8 unknown 252133࿝at At3 g50900 2.2E-03 2.1 118 158 95 96 1.6 unknown

Vert et al. www.pnas.org/cgi/content/short/0803996105 21 of 28 Affy AGI Adj p-value log (odds) AB AM CB CM AM/CM Annotation

261648࿝at At1 g27730 2.5E-03 1.9 74 150 64 65 2.3 C2H2 Zn finger ZAT10 264016࿝at At2 g21220 2.5E-03 1.9 20 20 25 31 0.7 SAUR12 264025࿝at At2 g21050 2.6E-03 1.9 154 95 144 113 0.8 AUX1-like amino acid permease LAX2 249364࿝at At5 g40590 2.7E-03 1.8 15 19 14 14 1.4 unknown 267028࿝at At2 g38470 3.8E-03 1.4 188 405 163 150 2.7 AtWRKY33 261892࿝at At1 g80840 3.9E-03 1.3 56 50 63 31 1.6 AtWRKY40 254065࿝at At4 g25420 4.2E-03 1.2 54 38 50 70 0.5 gibberellin 20-oxidase 247947࿝at At5 g57090 4.5E-03 1.1 221 193 173 121 1.6 AtPIN2 266820࿝at At2 g44940 4.5E-03 1.1 53 38 46 62 0.6 AP2-EREBP transcription factor 250676࿝at At5 g06320 5.8E-03 0.8 457 675 321 401 1.7 unknown 257761࿝at At3 g23090 7.3E-03 0.4 145 159 136 247 0.6 unknown 265327࿝at At2 g18210 8.1E-03 0.2 29 32 27 47 0.7 unknown 261938࿝at At1 g22510 9.0E-03 0.1 82 88 74 50 1.8 C3H Zn finger transcription factor

Vert et al. www.pnas.org/cgi/content/short/0803996105 22 of 28 Table S7. Auxin biosynthesis genes affected in an arf2 mutant AB AM CB CM CB/CM AM/CM AB/AM AB/CM Annotation

At4 g39950 82 515 100 153 0.7 3.4 0.2 0.5 CYP79B2 At5 g17990 173 316 175 147 1.2 2.1 0.5 1.2 anthranilate phosphoribosyltransferase At3 g54640 150 547 140 120 1.2 4.6 0.3 1.2 tryptophan synthase alpha chain (TSA1) At5 g05730 200 532 201 171 1.2 3.1 0.4 1.2 anthranilate synthase (ASA1) At4 g27070 247 527 262 251 1.0 2.1 0.5 1.0 tryptophan synthase beta-subunit (TSB2) At5 g22300 32 77 35 41 0.9 1.9 0.4 0.8 nitrilase 4 (NIT4)

Average expression for each condition is given. A, arf2; C, Col; B, BRZ; M, mock. Ratios for Col BRZ vs. mock (CB/CM), arf2 mock vs. Col mock (AM/CM), arf2 BRZ vs. arf2 mock (AB/AM), and arf2 BRZ vs. Col mock (AB/CM) are also shown.

Vert et al. www.pnas.org/cgi/content/short/0803996105 23 of 28 Table S8. All genes differentially expressed under BRZ treatment depending on genotype of treated plants (g*t genes). Average expression for each condition is given. A, arf2; C, Col; B, BRZ; M, mock. Ratios for arf2 on BRZ vs. arf2 on mock (AB/AM) and Col on BRZ vs. mock (CB/CM) are also shown. Adjusted log Affy AGI P value (odds) AB AM CB CM AB/AM CB/CM Annotation

260406࿝at At1 g69920 5.1E-07 13.7 29 221 31 33 0.1 0.9 glutathione transferase, AtGSTU12 253073࿝at At4 g37410 7.5E-07 13.1 164 54 141 222 3.0 0.6 CYP81F4 261021࿝at At1 g26380 3.2E-06 12.0 42 486 39 32 0.1 1.2 reticuline oxidase 245041࿝at At2 g26530 7.8E-06 11.3 53 153 44 44 0.3 1.0 unknown 265411࿝at At2 g16630 1.2E-05 10.8 97 628 115 108 0.2 1.1 unknown 267565࿝at At2 g30750 2.6E-05 10.1 17 100 16 18 0.2 0.9 PPT1-like thioesterase 258277࿝at At3 g26830 4.7E-05 9.5 21 84 19 17 0.3 1.1 CYP71B15, PAD3 251509࿝at At3 g59010 7.9E-05 9.0 124 74 70 218 1.7 0.3 CYP82F1 247882࿝at At5 g57785 7.9E-05 8.9 583 92 844 431 6.3 2.0 unknown 263098࿝at At2 g16005 7.9E-05 8.9 29 28 29 390 1.0 0.1 unknown 264404࿝at At2 g25160 1.1E-04 8.5 43 27 91 169 1.6 0.5 pectinesterase 245422࿝at At4 g17470 1.8E-04 8.0 77 65 66 265 1.2 0.2 CYP71A12 261474࿝at At1 g14540 1.8E-04 8.0 58 340 49 43 0.2 1.1 PER4 peroxidase 245306࿝at At4 g14690 2.0E-04 7.8 99 203 221 179 0.5 1.2 AP2-EREBP transcription factor, Rap2.1 249097࿝at At5 g43520 2.6E-04 7.5 104 190 118 49 0.5 2.4 glutathione S-transferase, AtGSTF6 245353࿝at At4 g16000 3.4E-04 7.2 123 337 256 286 0.4 0.9 unknown 253344࿝at At4 g33550 3.8E-04 7.1 428 158 332 374 2.7 0.9 lipid transfer protein 262119࿝s࿝at At1 g02930 4.3E-04 6.9 2191 6334 2213 1718 0.3 1.3 unknown 267411࿝at At2 g34930 4.5E-04 6.8 33 203 34 39 0.2 0.9 unknown 247215࿝at At5 g64905 7.8E-04 6.2 26 98 23 22 0.3 1.0 5 -adenylylphosphosulfate reductase 247949࿝at At5 g57220 7.8E-04 6.2 80 606 79 50 0.1 1.6 CYP81F2 252863࿝at At4 g39800 7.8E-04 6.2 557 212 495 506 2.6 1.0 peptide transporter PTR2-B 251248࿝at At3 g62150 7.8E-04 6.2 77 137 70 55 0.6 1.3 PGP21 259846࿝at At1 g72140 7.8E-04 6.2 45 56 28 103 0.8 0.3 tryptophan synthase alpha chain 255524࿝at At4 g02330 8.2E-04 6.0 85 113 101 42 0.7 2.4 pectinesterase 264745࿝at At1 g62180 8.2E-04 6.1 155 94 205 232 1.6 0.9 receptor kinase IRK1 264157࿝at At1 g65310 8.6E-04 5.9 344 184 433 822 1.9 0.5 unknown 264757࿝at At1 g61360 8.6E-04 6.0 91 127 97 63 0.7 1.5 unknown 245891࿝at At5 g09220 8.8E-04 5.9 605 380 773 147 1.6 5.2 amino acid transport protein AAP2 256601࿝s࿝at At3 g28290 8.8E-04 5.9 355 306 206 41 1.2 5.0 integrin-like 247293࿝at At5 g64510 8.8E-04 5.8 23 54 22 27 0.4 0.8 germin 256647࿝at At3 g13610 9.6E-04 5.7 77 539 81 48 0.1 1.7 At-XTH17 267101࿝at At2 g41480 1.0E-03 5.6 35 61 42 153 0.6 0.3 PER25 peroxidase 251884࿝at At3 g54150 1.1E-03 5.6 23 47 27 24 0.5 1.1 unknown 247723࿝at At5 g59220 1.4E-03 5.3 155 157 103 318 1.0 0.3 protein phosphatase 2C 262121࿝at At1 g02800 1.5E-03 5.2 84 61 90 207 1.4 0.4 endo-1,4-beta-glucanase 250446࿝at At5 g10770 1.6E-03 5.1 121 37 108 107 3.3 1.0 nucleoid DNA-binding protein cnd41 249459࿝at At5 g39580 1.7E-03 5.0 288 933 354 368 0.3 1.0 peroxidase, PER62 263402࿝at At2 g04050 1.7E-03 5.0 21 57 19 24 0.4 0.8 unknown 266783࿝at At2 g29130 1.7E-03 5.0 59 78 82 38 0.7 2.2 unknown 251847࿝at At3 g54640 1.7E-03 4.9 150 547 140 120 0.3 1.2 myo-inositol-1-phosphate synthase 261020࿝at At1 g26390 1.7E-03 4.9 21 168 19 21 0.1 0.9 vegetative storage protein Vsp1 246099࿝at At5 g20230 1.8E-03 4.8 54 697 45 102 0.1 0.4 blue copper binding protein 257206࿝at At3 g16530 1.8E-03 4.8 64 395 89 82 0.2 1.1 lectin 264968࿝at At1 g67360 1.8E-03 4.8 173 236 99 276 0.7 0.4 unknown 259878࿝at At1 g76790 2.1E-03 4.6 256 281 226 688 0.9 0.3 catechol O-methyltransferase COMT-like8 259616࿝at At1 g47960 2.1E-03 4.6 128 160 101 195 0.8 0.5 unknown 260015࿝at At1 g67980 2.1E-03 4.6 95 370 60 53 0.3 1.1 CCoAOMT6 259383࿝at At3 g16470 2.1E-03 4.6 1498 1468 1085 2261 1.0 0.5 lectin 245392࿝at At4 g15680 2.2E-03 4.6 29 28 82 25 1.0 3.3 glutaredoxin 263403࿝at At2 g04040 2.5E-03 4.4 25 113 28 29 0.2 0.9 unknown 258897࿝at At3 g05730 2.6E-03 4.3 289 273 550 71 1.1 7.8 unknown 263948࿝at At2 g35980 2.7E-03 4.3 35 115 28 21 0.3 1.4 unknown 261475࿝at At1 g14550 2.8E-03 4.2 22 120 22 21 0.2 1.0 peroxidase, PER5 252827࿝at At4 g39950 2.8E-03 4.2 82 515 100 153 0.2 0.7 CYP79B2 265670࿝s࿝at At2 g32210 2.8E-03 4.2 39 190 34 70 0.2 0.5 unknown 245506࿝at At4 g15700 3.1E-03 4.1 31 20 51 17 1.6 3.0 glutaredoxin 266978࿝at At2 g39430 3.1E-03 4.1 342 371 334 629 0.9 0.5 unknown 249481࿝at At5 g38900 3.1E-03 4.1 28 77 27 31 0.4 0.9 protein kinase 266746࿝s࿝at At2 g02930 3.4E-03 4.0 818 1671 719 400 0.5 1.8 glutathione S-transferase, AtGSTF3 260656࿝at At1 g19380 3.4E-03 3.9 244 360 265 193 0.7 1.4 laccase

Vert et al. www.pnas.org/cgi/content/short/0803996105 24 of 28 Adjusted log Affy AGI P value (odds) AB AM CB CM AB/AM CB/CM Annotation

254119࿝at At4 g24780 3.4E-03 3.9 156 88 210 211 1.8 1.0 pectate lyase 254313࿝at At4 g22460 3.7E-03 3.8 151 161 160 338 0.9 0.5 extensin 256736࿝at At3 g29410 3.7E-03 3.8 134 43 41 32 3.1 1.3 1-phosphatidylinositol-4-phosphate 5-kinase 266963࿝at At2 g39450 3.7E-03 3.8 482 303 266 407 1.6 0.7 asparaginyl endopeptidase 263126࿝at At1 g78460 3.7E-03 3.8 328 555 311 161 0.6 1.9 unknown 258941࿝at At3 g09940 4.0E-03 3.7 31 65 29 29 0.5 1.0 putative monodehydroascorbate reductase (NADH) 267384࿝at At2 g44370 4.1E-03 3.7 66 126 58 36 0.5 1.6 unknown 252214࿝at At3 g50260 4.3E-03 3.6 268 661 202 228 0.4 0.9 reticuline oxidase 264434࿝at At1 g10340 4.4E-03 3.6 61 93 70 47 0.7 1.5 unknown 250738࿝at At5 g05730 4.5E-03 3.5 200 532 201 171 0.4 1.2 anthranilate synthase 265443࿝at At2 g20750 4.5E-03 3.5 205 194 172 238 1.1 0.7 beta-expansin, AtEXPB1 253046࿝at At4 g37370 4.6E-03 3.5 43 132 36 37 0.3 1.0 CYP81D8 250826࿝at At5 g05220 4.8E-03 3.4 17 38 20 23 0.4 0.9 lipase 257248࿝at At3 g24150 4.9E-03 3.4 66 55 44 47 1.2 0.9 unknown 266265࿝at At2 g29340 4.9E-03 3.4 139 165 143 81 0.8 1.8 unknown 249832࿝at At5 g23400 4.9E-03 3.4 54 49 46 78 1.1 0.6 unknown 256522࿝at At1 g66160 4.9E-03 3.4 34 47 34 28 0.7 1.2 unknown 254432࿝at At4 g20830 6.0E-03 3.2 337 566 382 335 0.6 1.1 reticuline oxidase 254818࿝at At4 g12470 6.2E-03 3.1 989 1788 1035 844 0.6 1.2 plant U-box protein, AtPUB20 244921࿝s࿝at At2 g07674 6.2E-03 3.1 64 89 98 83 0.7 1.2 unknown 245352࿝at At4 g15490 6.4E-03 3.0 23 75 22 29 0.3 0.8 indole-3-acetate beta-glucosyltransferase 258589࿝at At3 g04290 6.4E-03 3.1 166 128 182 268 1.3 0.7 unknown 256306࿝at At1 g30370 6.5E-03 3.0 54 126 44 39 0.4 1.1 unknown 247431࿝at At5 g62520 6.8E-03 3.0 33 64 40 38 0.5 1.0 disease resistance protein RPP1-WsB 247582࿝at At5 g60760 6.8E-03 3.0 165 80 163 187 2.1 0.9 unknown 256376࿝s࿝at At1 g66690 6.8E-03 3.0 415 1533 305 173 0.3 1.8 unknown 264774࿝at At1 g22890 6.8E-03 2.9 214 168 248 84 1.3 3.0 unknown 247600࿝at At5 g60890 6.9E-03 2.9 86 74 76 100 1.2 0.8 unknown 251196࿝at At3 g62950 7.0E-03 2.9 61 43 86 33 1.4 2.6 glutaredoxin 245148࿝at At2 g45220 7.4E-03 2.8 372 918 242 220 0.4 1.1 pectinesterase 257890࿝s࿝at At3 g42570 7.4E-03 2.8 105 68 99 158 1.6 0.6 putative protein peroxidase 262045࿝at At1 g80240 7.4E-03 2.8 239 256 214 412 0.9 0.5 unknown 253643࿝at At4 g29780 7.6E-03 2.8 91 183 84 87 0.5 1.0 unknown 261005࿝at At1 g26420 7.6E-03 2.7 23 51 19 23 0.5 0.8 unknown 245250࿝at At4 g17490 7.9E-03 2.7 59 112 47 42 0.5 1.1 aniline dioxygenase 248932࿝at At5 g46050 8.0E-03 2.7 32 61 42 32 0.5 1.3 peptide transporter 260841࿝at At1 g29195 8.3E-03 2.6 273 269 203 356 1.0 0.6 unknown 265199࿝s࿝at At2 g36770 8.8E-03 2.6 28 44 33 35 0.6 0.9 glucosyl transferase 256337࿝at At1 g72060 8.8E-03 2.5 213 387 375 228 0.6 1.6 unknown 265075࿝at At1 g55450 8.8E-03 2.5 203 369 196 152 0.6 1.3 unknown 251456࿝at At3 g60120 8.9E-03 2.5 17 23 18 17 0.7 1.0 beta-glucosidase 253040࿝at At4 g37800 9.2E-03 2.5 48 26 112 84 1.8 1.3 At-XTH7 254327࿝at At4 g22490 9.5E-03 2.4 538 344 558 659 1.6 0.8 lipid transfer protein 261509࿝at At1 g71740 9.5E-03 2.4 332 286 291 440 1.2 0.7 unknown 266167࿝at At2 g38860 9.6E-03 2.4 260 810 237 215 0.3 1.1 unknown 254188࿝at At4 g23920 9.6E-03 2.4 46 74 34 40 0.6 0.9 UDPglucose 4-epimerase 257197࿝at At3 g23800 9.8E-03 2.4 287 242 302 79 1.2 3.8 ASL37 247095࿝at At5 g66400 9.9E-03 2.4 1034 3448 389 514 0.3 0.8 dehydrin 249942࿝at At5 g22300 9.9E-03 2.3 32 77 35 41 0.4 0.9 Nitrilase 4 254098࿝at At4 g25100 1.0E-02 2.3 509 827 1724 1300 0.6 1.3 253606࿝at At4 g30530 1.0E-02 2.3 339 671 444 444 0.5 1.0 AP2-EREBP transcription factor ERF6 262349࿝at At2 g48130 1.0E-02 2.3 51 60 33 72 0.9 0.5 lipid transfer protein 260097࿝at At1 g73220 1.0E-02 2.3 1130 1055 479 926 1.1 0.5 sugar transporter 259426࿝at At1 g01470 1.0E-02 2.3 1391 3767 1248 1768 0.4 0.7 terpene synthase 246108࿝at At5 g28630 1.0E-02 2.3 28 55 30 33 0.5 0.9 GDSL-motif lipase/acylhydrolase 263096࿝at At2 g16060 1.0E-02 2.2 1020 467 1451 1265 2.2 1.1 unknown 264346࿝at At1 g12010 1.1E-02 2.2 201 395 233 171 0.5 1.4 1-aminocyclopropane-1-carboxylate oxidase 250014࿝at At5 g17990 1.1E-02 2.2 173 316 175 147 0.5 1.2 anthranilate phosphoribosyltransferase 258388࿝at At3 g15370 1.1E-02 2.1 64 77 127 43 0.8 2.9 expansin, AtEXPA12 261135࿝at At1 g19610 1.1E-02 2.1 60 128 61 38 0.5 1.6 unknown 261937࿝at At1 g22570 1.1E-02 2.1 81 135 94 115 0.6 0.8 peptide transporter 266017࿝at At2 g18690 1.1E-02 2.1 345 910 461 411 0.4 1.1 unknown 266209࿝at At2 g27550 1.2E-02 2.1 176 152 118 48 1.2 2.5 similar to Terminal Flower 258938࿝at At3 g10080 1.2E-02 2.0 346 194 219 266 1.8 0.8 unknown

Vert et al. www.pnas.org/cgi/content/short/0803996105 25 of 28 Adjusted log Affy AGI P value (odds) AB AM CB CM AB/AM CB/CM Annotation

261076࿝at At1 g07420 1.2E-02 2.0 635 389 556 511 1.6 1.1 unknown 257295࿝at At3 g17420 1.2E-02 2.0 195 209 179 378 0.9 0.5 serine/threonine protein kinase 247880࿝at At5 g57780 1.2E-02 2.0 447 147 451 296 3.0 1.5 unknown 266720࿝s࿝at At2 g46790 1.3E-02 2.0 21 41 25 35 0.5 0.7 unknown 263629࿝at At2 g04850 1.3E-02 1.9 129 101 94 106 1.3 0.9 unknown 252482࿝at At3 g46670 1.3E-02 1.9 27 69 25 38 0.4 0.7 glucosyltransferase 249860࿝at At5 g22860 1.3E-02 1.9 226 128 146 150 1.8 1.0 prolylcarboxypeptidase-like protein 259331࿝at At3 g03840 1.3E-02 1.9 104 80 93 122 1.3 0.8 SAUR27 249817࿝at At5 g23820 1.3E-02 1.9 448 458 350 737 1.0 0.5 CLC-b chloride channel 265260࿝at At2 g43000 1.3E-02 1.9 24 69 24 24 0.3 1.0 NAC transcription factor 264025࿝at At2 g21050 1.4E-02 1.8 154 95 144 113 1.6 1.3 AUX1-like amino acid permease LAX2 267261࿝at At2 g23120 1.4E-02 1.8 763 2440 661 1103 0.3 0.6 unknown 259705࿝at At1 g77450 1.4E-02 1.8 286 768 215 303 0.4 0.7 NAC transcription factor 246821࿝at At5 g26920 1.5E-02 1.8 69 272 73 55 0.3 1.3 calmodulin-binding protein 245505࿝at At4 g15690 1.5E-02 1.7 48 37 89 29 1.3 3.0 glutaredoxin 254001࿝at At4 g26260 1.5E-02 1.7 23 64 25 33 0.4 0.8 unknown 262085࿝at At1 g56060 1.6E-02 1.7 37 119 48 48 0.3 1.0 unknown 266743࿝at At2 g02990 1.6E-02 1.6 47 86 75 95 0.5 0.8 unknown 263734࿝at At1 g60030 1.6E-02 1.6 31 42 34 71 0.7 0.5 phosphoribosylanthranilate transferase 245504࿝at At4 g15660 1.7E-02 1.6 18 17 31 18 1.1 1.7 glutaredoxin 255528࿝at At4 g02090 1.7E-02 1.6 270 184 237 258 1.5 0.9 unknown 251977࿝at At3 g53250 1.7E-02 1.5 111 36 149 71 3.1 2.1 SAUR57 253414࿝at At4 g33050 1.8E-02 1.5 149 273 119 129 0.5 0.9 unknown 248861࿝at At5 g46700 1.8E-02 1.5 270 270 295 440 1.0 0.7 unknown 256673࿝at At3 g52370 1.8E-02 1.5 49 41 45 67 1.2 0.7 unknown 257673࿝at At3 g20370 1.8E-02 1.4 243 268 155 260 0.9 0.6 unknown 249188࿝at At5 g42830 1.8E-02 1.4 47 178 43 47 0.3 0.9 N-hydroxycinnamoyl benzoyltransferase 263935࿝at At2 g35930 1.8E-02 1.4 82 193 69 82 0.4 0.8 plant U-box protein, AtPUB23 252652࿝at At3 g44720 1.8E-02 1.4 46 73 47 41 0.6 1.2 prephenate dehydratase 246368࿝at At1 g51890 1.8E-02 1.4 36 60 28 26 0.6 1.1 receptor kinase 260225࿝at At1 g74590 1.8E-02 1.4 63 127 41 27 0.5 1.5 serine carboxypeptidase II 265920࿝s࿝at At2 g15120 1.8E-02 1.4 116 268 92 72 0.4 1.3 unknown 263182࿝at At1 g05575 1.9E-02 1.4 124 168 100 80 0.7 1.3 unknown 254828࿝at At4 g12550 1.9E-02 1.3 429 488 405 219 0.9 1.9 CLCT protein (AIR1A) 253898࿝s࿝at At4 g27070 2.0E-02 1.3 247 527 262 251 0.5 1.0 tryptophan synthase beta-subunit (TSB2) 250277࿝at At5 g12940 2.0E-02 1.3 856 511 687 673 1.7 1.0 unknown 254907࿝at At4 g11190 2.0E-02 1.3 205 315 475 1704 0.7 0.3 unknown 251072࿝at At5 g01740 2.0E-02 1.3 1741 166 1634 319 10.5 5.1 sugar transporter 265645࿝at At2 g27370 2.0E-02 1.3 456 421 470 652 1.1 0.7 unknown 267307࿝at At2 g30210 2.0E-02 1.3 772 616 608 961 1.3 0.6 laccase 257130࿝at At3 g20210 2.0E-02 1.3 317 160 455 412 2.0 1.1 unknown 252576࿝s࿝at At3 g45450 2.0E-02 1.3 73 95 75 77 0.8 1.0 AtClpC 254014࿝at At4 g26120 2.0E-02 1.2 21 30 20 20 0.7 1.0 NPR1 247800࿝at At5 g58570 2.0E-02 1.2 38 54 38 35 0.7 1.1 unknown 262001࿝at At1 g33790 2.1E-02 1.2 316 460 239 146 0.7 1.6 EF-hand 261399࿝at At1 g79620 2.1E-02 1.2 99 68 54 65 1.5 0.8 sucrose-phosphate synthase 248435࿝at At5 g51210 2.1E-02 1.2 756 466 795 847 1.6 0.9 oleosin 248844࿝s࿝at At5 g46900 2.2E-02 1.2 872 1383 882 3282 0.6 0.3 subtilisin-like serine protease AtSubt4.12 251336࿝at At3 g61190 2.2E-02 1.2 64 103 54 57 0.6 1.0 unknown 264617࿝at At2 g17660 2.2E-02 1.1 26 86 20 33 0.3 0.6 unknown 247009࿝at At5 g67600 2.3E-02 1.1 1133 1950 1253 1188 0.6 1.1 adenosine-5-phosphosulfate-kinase 259479࿝at At1 g19020 2.4E-02 1.0 397 888 288 334 0.4 0.9 ribonuclease 250633࿝at At5 g07460 2.4E-02 1.0 48 119 46 36 0.4 1.3 peptide methionine sulfoxide reductase 252571࿝at At3 g45280 2.4E-02 1.0 22 20 36 16 1.1 2.2 syntaxin SYP72 260549࿝at At2 g43535 2.6E-02 1.0 1434 1437 931 2013 1.0 0.5 unknown 256066࿝at At1 g06980 2.6E-02 0.9 403 271 324 305 1.5 1.1 unknown 247651࿝at At5 g59870 2.6E-02 0.9 571 400 626 813 1.4 0.8 histone H2A 252265࿝at At3 g49620 2.6E-02 0.9 30 91 48 21 0.3 2.2 unknown 261022࿝at At1 g12260 2.6E-02 0.9 31 27 36 29 1.1 1.2 NAC transcription factor, VND4 248585࿝at At5 g49640 2.6E-02 0.9 21 32 26 24 0.7 1.1 unknown 259655࿝at At1 g55210 2.6E-02 0.9 283 292 289 487 1.0 0.6 unknown 259231࿝at At3 g11410 2.6E-02 0.9 538 509 431 709 1.1 0.6 protein phosphatase 2C, AtPP2CA 264846࿝at At2 g17850 2.6E-02 0.9 61 33 89 60 1.9 1.5 rhodanese protein AtStr17 250433࿝at At5 g10400 2.6E-02 0.9 112 75 110 138 1.5 0.8 histone H3

Vert et al. www.pnas.org/cgi/content/short/0803996105 26 of 28 Adjusted log Affy AGI P value (odds) AB AM CB CM AB/AM CB/CM Annotation

245904࿝at At5 g11110 2.6E-02 0.9 130 98 82 142 1.3 0.6 receptor kinase 247634࿝at At5 g60520 2.6E-02 0.9 47 22 26 21 2.1 1.2 unknown 256025࿝at At1 g58370 2.6E-02 0.9 170 187 230 122 0.9 1.9 xylan endohydrolase 249202࿝at At5 g42580 2.6E-02 0.9 26 27 24 43 1.0 0.6 CYP705A12 258434࿝at At3 g16770 2.6E-02 0.8 3232 3081 7904 4120 1.0 1.9 AP2 domain containing protein ERF72 253172࿝at At4 g35060 2.6E-02 0.8 634 643 611 1088 1.0 0.6 sugar transporter 249430࿝at At5 g39900 2.6E-02 0.8 27 21 21 25 1.3 0.8 AP2-EREBP transcription factor 247354࿝at At5 g63590 2.6E-02 0.8 215 187 162 225 1.1 0.7 flavonol synthase 262933࿝at At1 g65840 2.6E-02 0.8 269 333 256 476 0.8 0.5 polyamine oxidase 252870࿝at At4 g39940 2.6E-02 0.8 40 173 51 81 0.2 0.6 unknown 266820࿝at At2 g44940 2.6E-02 0.8 53 38 46 62 1.4 0.7 unknown 267457࿝at At2 g33790 2.6E-02 0.8 215 21 80 21 10.3 3.7 unknown 247755࿝at At5 g46900 2.7E-02 0.8 702 719 737 426 1.0 1.7 extA 264415࿝at At1 g43160 2.7E-02 0.8 98 159 104 75 0.6 1.4 AP2-EREBP transcription factor, Rap2.6 261439࿝at At1 g28395 2.8E-02 0.8 60 39 55 48 1.5 1.1 stearoyl-ACP desaturase 262873࿝at At1 g64700 2.8E-02 0.7 36 45 37 61 0.8 0.6 unknown 246036࿝at At5 g08370 2.8E-02 0.7 187 173 121 218 1.1 0.6 alpha-galactosidase 248100࿝at At5 g55180 2.9E-02 0.7 147 362 175 197 0.4 0.9 beta-1,3-glucanase 266992࿝at At2 g39200 2.9E-02 0.7 52 62 43 31 0.8 1.4 AtMLO12 258342࿝at At3 g22800 2.9E-02 0.7 55 87 46 35 0.6 1.3 extensin AtLRX6 265572࿝at At2 g28210 2.9E-02 0.7 17 35 18 19 0.5 0.9 carbonic anhydrase 245076࿝at At2 g23170 2.9E-02 0.7 133 141 687 361 0.9 1.9 unknown 245928࿝s࿝at At5 g24780 2.9E-02 0.7 16 13 16 36 1.2 0.5 reticuline oxidase 256751࿝at At3 g27170 3.0E-02 0.6 38 48 37 29 0.8 1.3 unknown 248703࿝at At5 g48430 3.0E-02 0.6 248 382 150 93 0.6 1.6 glycoprotein 246943࿝at At5 g25440 3.0E-02 0.6 105 157 86 90 0.7 1.0 serine/threonine protein kinase APK1 246415࿝at At5 g17160 3.0E-02 0.6 59 103 46 104 0.6 0.4 unknown 264280࿝at At1 g61820 3.0E-02 0.6 145 257 219 209 0.6 1.0 beta-glucosidase 259133࿝at At3 g05400 3.0E-02 0.6 203 106 252 256 1.9 1.0 unknown 245038࿝at At2 g26560 3.2E-02 0.5 148 653 101 88 0.2 1.1 patatin-like 252327࿝at At3 g48740 3.2E-02 0.5 2527 2837 4802 3235 0.9 1.5 unknown 259328࿝at At3 g16440 3.3E-02 0.5 217 134 205 81 1.6 2.5 lectin 261247࿝at At1 g20070 3.3E-02 0.5 108 451 106 176 0.2 0.6 unknown 245329࿝at At4 g14365 3.3E-02 0.5 25 82 22 24 0.3 0.9 unknown 251982࿝at At3 g53190 3.3E-02 0.5 89 72 81 97 1.2 0.8 pectate lyase 260969࿝at At1 g12240 3.3E-02 0.5 598 663 701 452 0.9 1.6 DNA-3-methlyadenine glycosylase (MAG) 251334࿝at At3 g61390 3.3E-02 0.5 32 32 34 21 1.0 1.7 unknown 254113࿝at At4 g24900 3.3E-02 0.5 114 109 85 105 1.0 0.8 unknown 266536࿝at At2 g16900 3.3E-02 0.5 92 143 83 84 0.6 1.0 unknown 264643࿝at At1 g08990 3.4E-02 0.4 32 27 31 41 1.2 0.8 glycosyltransferase 263063࿝s࿝at At2 g18140 3.4E-02 0.4 27 47 24 86 0.6 0.3 peroxidase, PER14 253600࿝at At4 g30810 3.4E-02 0.4 244 186 195 224 1.3 0.9 serine carboxypeptidase 251918࿝at At3 g54040 3.4E-02 0.4 285 444 304 184 0.6 1.7 unknown 254024࿝at At4 g25780 3.4E-02 0.4 783 481 714 907 1.6 0.8 unknown 246149࿝at At5 g19890 3.5E-02 0.4 29 37 39 24 0.8 1.7 peroxidase, PER59 245193࿝at At1 g67810 3.5E-02 0.4 512 1613 453 674 0.3 0.7 unknown 245610࿝at At4 g14380 3.5E-02 0.4 190 169 139 179 1.1 0.8 unknown 256877࿝at At3 g26470 3.5E-02 0.4 282 354 295 180 0.8 1.6 unknown 250680࿝at At5 g06570 3.6E-02 0.4 219 295 263 207 0.7 1.3 unknown 259553࿝x࿝at At1 g21310 3.6E-02 0.4 87 157 96 60 0.6 1.6 unknown 251109࿝at At5 g01600 3.6E-02 0.3 4025 7917 3790 3760 0.5 1.0 ferritin 266967࿝at At2 g39530 3.6E-02 0.3 115 87 104 41 1.3 2.6 unknown 263184࿝at At1 g05560 3.6E-02 0.3 133 241 113 110 0.6 1.0 glycosyltransferase 248074࿝at At5 g55730 3.6E-02 0.3 666 471 669 762 1.4 0.9 unknown 256017࿝at At1 g19180 3.7E-02 0.3 276 705 241 297 0.4 0.8 unknown 245362࿝at At4 g17460 3.8E-02 0.3 723 427 571 653 1.7 0.9 HD-ZIP HAT1 259897࿝at At1 g71380 3.8E-02 0.3 18 16 16 24 1.1 0.7 beta-glucanase 252908࿝at At4 g39670 3.8E-02 0.3 83 233 56 66 0.4 0.9 sphingosine transfer protein 253281࿝at At4 g34138 3.8E-02 0.3 206 443 180 197 0.5 0.9 unknown 251025࿝at At5 g02190 3.8E-02 0.2 123 69 120 83 1.8 1.4 chloroplast nucleoid DNA binding protein 263876࿝at At2 g21880 3.8E-02 0.3 215 332 140 351 0.6 0.4 RAS superfamily GTP-binding protein 267075࿝at At2 g41070 3.8E-02 0.2 197 140 152 76 1.4 2.0 bZIP12 258746࿝at At3 g05950 3.9E-02 0.2 91 350 43 81 0.3 0.5 unknown 264832࿝at At1 g03660 3.9E-02 0.2 66 54 72 40 1.2 1.8 unknown

Vert et al. www.pnas.org/cgi/content/short/0803996105 27 of 28 Adjusted log Affy AGI P value (odds) AB AM CB CM AB/AM CB/CM Annotation

267590࿝at At2 g39700 3.9E-02 0.2 257 380 346 889 0.7 0.4 alpha-expansin, AtEXPA4 247567࿝at At5 g61190 3.9E-02 0.2 55 72 43 44 0.8 1.0 C2H2 Zn finger transcription factor 261892࿝at At1 g80840 3.9E-02 0.2 56 50 63 31 1.1 2.0 AtWRKY40 251714࿝at At3 g56370 4.0E-02 0.2 170 157 176 240 1.1 0.7 leucine-rich receptor-like protein kinase 261719࿝at At1 g18380 4.1E-02 0.1 49 63 45 35 0.8 1.3 unknown 255860࿝at At5 g34940 4.1E-02 0.1 295 182 242 74 1.6 3.3 heparanase 251141࿝at At5 g01075 4.1E-02 0.1 84 81 85 145 1.0 0.6 unknown 266828࿝at At2 g22930 4.5E-02 0.0 20 27 21 35 0.8 0.6 glycosyltransferase 259443࿝at At1 g02360 4.5E-02 0.0 323 478 326 242 0.7 1.3 chitinase 248465࿝at At5 g51200 4.5E-02 0.0 306 197 277 258 1.6 1.1 unknown 264734࿝at At1 g62280 4.5E-02 0.0 113 79 86 36 1.4 2.3 unknown 256275࿝at At3 g12110 4.5E-02 0.0 146 163 131 232 0.9 0.6 actin 11 (ACT11) 247522࿝at At5 g61340 4.5E-02 0.0 103 88 91 138 1.2 0.7 unknown 251565࿝at At3 g58190 4.6E-02 0.0 18 21 21 41 0.9 0.5 ASL16

Vert et al. www.pnas.org/cgi/content/short/0803996105 28 of 28