Supplemental Figure 1. Dubreuil et al. Plant Physiology (2017)

Figure S1. Heat map and cluster representation of the metabolite profile in the

different samples during chloroplast development. Each column represents the

metabolite change at a time point compared to its previous one (Log2(T/T-1).

Red and yellow colors indicate metabolites that accumulated or degraded

compared to the previous time point, respectively. Metabolites were color coded

based on their structure (organic acids in red, amino acids and derivatives in

blue, fatty acids in green and sugar derivatives in purple). Each column

represents a biological replicate.

02468

1012141618

0 6 9 24

Rel

ativ

e C

AO

/PP

2Aex

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sion

Col-0hy5glk1glk2

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2A e

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B

Supplemental Figure 2. Dubreuil et al. Plant Physiology (2017)

C

T1 v

s. T

0

T2 v

s. T

1

T4 v

s. T

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T5 v

s. T

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T7 v

s. T

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T10

vs. T

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T14

vs. T

10

A

-1 0 2.5

log2 (ratio)

HY5

GLK2

Time (h) Time (h)

LHCB1.1

CAO

Figure S2. (A) Gene expression heat map of HY5, GLK2, LHCB1.1 and CAO in

Arabidopsis cell culture. The counts for GLK1 were too low and the data was

therefore excluded. Each column represents the gene expression at a time point

compared to its previous one (Log2(T/T-1). Red color indicates genes that were

upregulated and yellow color indicates genes that were downregulated compared

to the previous time point. (B) LHCB1.1 (C) CAO expression following a shift

to light in hy5 and glk1glk2 seedlings. Gene expression was normalized to

PROTEIN PHOSPHATASE 2A SUBUNIT A3, PP2A (At1g13320) and related to

the amount present in the dark. Each data point represents the mean (±SD) of at

least 3 independent replicates.

Supplemental Figure 3. Dubreuil et al. Plant Physiology (2017)

A B

GRMZM2G104549 AC208915.3 FG010 GRMZM2G120619

GRMZM2G351977 GRMZM2G155216

AT1G29920.1 AT2G34430.1

AC207722.2 FG009 AT3G27690.1

99

60

75

99

9281

0.05

GRMZM2G455413 GRMZM2G086723 GRMZM2G427369

ATCG00020.1 GRMZM5G844143

GRMZM2G004224 GRMZM2G152576 ATCG00270 ATCG00680.1

100

100

0.1

ZmPSBA Cluster

AtLHCB1.1

Figure S3. Phylogenetic analysis of the Zea mays family genes, showing the phylogenetic

relationships among LHCBs (A) and PSBAs (B) in Zea mays and Arabidopsis.

Both of unrooted phylogenetic trees were generated using full-length protein sequences from Zea

mays and Arabidopsis. Full-length protein sequences were obtained from the Arabidopsis

Information Resource (http://www.arabidopsis.org/) and Phytozome ver. 12.0

(https://phytozome.jgi.doe.gov/pz/portal.html). Protein sequences were aligned and the unrooted

phylogenetic trees were constructed with MEGA 7.0.

AtLHCB1.4

AtLHCB2.4

AtPSBA

AtPSBD

AtPSBB

ZmLHCB (a)

ZmLHCB (b)

A

Supplemental Figure 4. Dubreuil et al. Plant Physiology (2017)

B

C D

Dark 12h 24h 48h

0

100

200

300

400

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0 1 3 6 9 12 24 480

102030405060708090

0 1 3 6 9 12 24 48

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ativ

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LHCB1.1 LHCB2.4

Time (h) Time (h)

Figure S4. De-etiolation of Arabidopsis seedlings.

(A) Representative photographs of 5-day-old dark grown seedlings shifted to

light. (B) Electron microscope images of etioplasts developing into chloroplasts

following light exposure. Images were chosen from at least two independent

experiments for each developmental stage. Scale bar=0.5 µm. (C) Relative

expression of LHCB1.1 and (D) LHCB2.4. Gene expression was normalized to

PROTEIN PHOSPHATASE 2A SUBUNIT A3, PP2A (At1g13320) and related to

the amount present in the dark. Each data point represents the mean (±SE) of at

least 3 independent replicates.

3h 9h 12h 24h

0 7 14 14

A

Supplemental Figure 5. Dubreuil et al. Plant Physiology (2017)

F

D

B

E

1% suc 3% suc

C

Time(days) 1% suc 3% suc

Time (days)Fv/Fm 0.67 ± 0.03 0.72 ± 0.03 0.54 ± 0.06φPSII 0.45 ± 0.05 0.48 ± 0.04 0.17 ± 0.06NPQ 0.07 ± 0.05 0.32 ± 0.06 0.04 ± 0.04qL 0.42 ± 0.11 0.46 ± 0.00 0.17 ± 0.06

3% suc147 14

1% suc

0 7 14 140

20

40

60

80

Time (days)

Chl

orop

hyll

cont

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(µg

g-1 F

W)

0 14 14-100

0

100

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400

Time (days)O2 e

volu

tion

(nm

ol/m

in/g

FW

)

1% suc 3% sucChl aChl b

1% suc 3% suc

LHCB1.13 % suc1 % suc

Time (days) 0 1 2 3 4 5 6 7

LHCB2.4

*

******

**

*

**

*

*

Rel

ativ

e ge

ne e

xpre

ssio

nR

elat

ive

gene

exp

ress

ion 1500

1000

500

0

300

200

100

0

ML AL AL MLon on off off

00.20.40.60.8

11.2

0 50 100 150 200 250 300

3% suc1% suc

Chl

orop

hyll

fluor

esce

nce

ratio

Time (s)

Figure S5. High sucrose concentration inhibits chloroplast development. (A) Ultrastructure of

chloroplasts of 14-day-old cells cultured in MS + 1% sucrose and MS + 3% sucrose.

Representative electron microscopy images shown from at least two independent experiments.

Scale bar: 0.5 μm. (B) The 7- and 14-day cells compared to the control (T0) and 14-day cells

cultured in MS + 3% sucrose. (C) Chlorophyll fluorescence parameters measured in 7- and 14-

day-cells. All values are means (± SD) of three independent experiments with three biological

replicates per experiment. (D) Chlorophyll content 7- and 14-day-cells compared to the dark grown

cells. (E) Oxygen evolution rate in 14-day-cells. All values are means (± SD) of three independent

experiments with three biological replicates per experiment. (F) Relative LHCB1.1 and LHCB2.4

expression in cells cultured in MS + 1% sucrose (open bars) and MS + 3% sucrose (black bars).

Gene expression was normalized to Ubiquitin like protein (At4g36800) and related to the amount

present in the dark. Each data point represents the mean (±SE) of at least 6 independent replicates.

Asterisk indicates significant difference between 1% and 3% sucrose conditions (t test; *, P < 0.05;

**, P < 0.01; ***, P < 0.001).

Supplementary Table 1List of identified metabolites with their normalized peak areas in every samples

Values correspond to the average of two technical replicates

daybiological replicates 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 22 amino adipic acid 5646.93 5642.35 4736.43 5614.97 5222.88 5237.55 1942.94 1450.34 1774.53 1804.23 1902.25 1465.89 6435.74 2610.98 5312.88 3637.38 5283.33 15704.4 73308 76218.2aconitic acid 43191 47849.1 48093.8 52748.2 57441.6 47335.3 15685 16489.7 15693.2 17780.2 19622.3 14388 16902 15193.9 14274.7 16682.6 13994.7 16220.1 15058.7 14793.8agmatine 6280.39 2580.82 3869.14 3499.64 9404.2 4028.86 20593.5 21077.8 20508.9 24380.6 23119.3 19069.7 13703.1 8056.45 11312.3 7116.37 10109.8 13855.5 16384.1 13950.4alanine 1594421 1508299 1843139 1669930 1642043 1890339 942620 922028 896389 720987 818694 815783 806367 1207629 656671 1012765 578419 550974 571157 665573allantoin (major) 10309.5 6682.39 17659.8 10389.7 11013.1 22206.6 32093.6 14846.4 16810.5 23634.3 38174.6 26970 19076.4 25593.8 18534.8 20029.4 30474 30656.8 101163 64906.4allothreonine 310651 284251 314630 310740 302970 316663 432284 380405 409351 373154 405963 369422 280259 257602 269866 260320 253075 259993 351330 381715arginine 79967 78820.9 100164 86573.8 85446.5 96267.4 146190 138692 139640 141354 158987 134016 35126.6 37289.5 27451 42035.7 29388.3 24259.1 53863.8 63004.7asparagine (minor) 51136.6 49231.5 70389 49620.2 45446.8 50049.6 100933 101596 106085 108864 105110 92211.5 92712.6 96224.5 78671.1 93568.2 76125.4 61190.3 188340 186081beta-alanine (major) 54551.2 54026.1 49240 55202.2 53078.9 52858.3 31867.3 33669.5 32018.1 36584 30926.7 30093.7 53961.4 50619.7 42261.9 53155 37913.4 35269.6 98818.8 114261citric acid (saturation) 734915 625490 749838 688906 788620 790139 309245 252072 265946 247121 273732 268782 315301 473528 277917 369527 275939 278472 207046 218343dehydroascorbic acid (major) 216511 217511 214822 223305 198626 226543 237793 215786 218874 221410 209204 193298 231388 190270 200588 229311 207994 226177 150320 180374ethanolamine (saturation) 709960 645318 706223 694401 696301 799706 779509 597195 672495 623437 532392 589481 676270 645794 632383 579366 573200 547411 556035 524667fucose (major) 67227.4 67318.8 62795.2 68359.6 66479.2 62053.9 7720.99 7794.18 7207.4 7615.1 6345.78 6418.89 6483.97 4052.01 4670.46 5355.62 4024.85 4682.53 17274.9 19684.1fumaric acid 56835.8 68264.4 66920.4 68595.5 58567.8 71073.6 116678 115794 116500 114300 109245 104272 11914.9 19605.4 10005.1 12466.6 7135.27 6767.67 7354.15 10778.2GABA 321429 286665 360899 326003 332530 367981 118949 102709 133799 69185.9 93211.3 118621 89811 96979.3 162414 93458.9 98759.3 156482 84380.4 74547.4glucose-6-P (major) 4409.74 4439.99 9476.58 9954.35 10805 7642.66 33870.8 28517 30002.6 42551.8 28563.3 25157.5 21457.1 16613.9 36400.9 21417.7 22564.1 35001 9765.33 9571.29glutamic acid 190969 187422 218986 197334 187249 203413 236136 195184 197490 208210 214896 199168 211479 224849 198507 224014 206424 190026 210198 218091glyceric acid 215125 209911 218498 204517 197237 199243 82858.8 89214.9 83867.3 97433.6 81228.7 83202 26018.9 24769 22109.9 35154.8 20193.8 25443.3 10973.6 12834.1glycine (major) 274503 260804 290342 288089 298062 310740 248603 248671 256025 255930 226024 229546 128336 147142 115476 134688 98094.2 104570 94468.6 123073histidine 4687.9 2408.43 7247.21 3779.39 3703.95 6340.24 53946.6 4592.01 38972.2 8454.72 53154 43283 3078.12 8642.7 2877.93 2712.87 4183.78 4702.24 39291.5 62527homoserine 304.12 315.178 325.631 304.35 283.325 299.214 279.555 262.8 258.011 312.554 297.37 259.283 207.755 247.376 113.984 296.698 100.387 88.1974 68.1308 98.3588isoleucine 87957.5 83453.3 93998.4 90066.9 86367.2 91679.5 85284.5 75861.8 78926.3 82121 78100.3 77828.8 76184.8 65594.1 83394 74093.3 87699.8 119928 160254 164686lactic acid 650139 558387 431353 610112 638882 634697 7514.51 32873.3 70690 2289.61 4200.61 21386.4 3593.95 30983.3 14943.6 5120.82 5174.03 1575.08 2041.67 4483.01leucine 16546.6 14825.4 21575.1 16469 13555.5 14650 15265.8 14668.1 14986.4 14138.2 13592.8 13099 18222.1 12695 19301.5 14237.3 27825.4 53241 35030.8 47420.9linoleic acid 3326.46 2836.26 28931.3 3506.2 3352.91 16985.8 31419.8 19809.3 23377.7 23488.6 29017.5 29739.9 28158.2 35708.9 29055 29552 24836.1 28687.4 31716.2 22428.6lysine 15163.7 14920.7 14823.3 17155.7 17215.3 15669.7 61871 51807.1 60393.6 59024.5 63007.9 56346.8 44974.7 22632.5 43990.1 29069.4 45053 56914 53489.8 113129malic acid 390164 371824 417937 396278 382183 403227 291028 257800 259609 256098 281653 259739 167816 194793 182607 190094 151345 198874 73466.2 107571myo-inositol (saturation) 264509 267406 319367 269290 264280 282725 349838 290770 313434 293948 323119 305483 335641 370963 330799 358245 328270 318589 246176 266227oleic acid 2903.2 2962.03 52859 3424.91 3215.98 34529.9 86594.7 49435.9 54219.4 58670.3 61219.1 69807.3 80365.2 98368.6 77578.6 82689.9 58152.3 62570.5 71432.3 60604.2ornithine (major) 8671.77 8534.09 14255.2 9034.31 8007.02 8937.6 138409 114100 126398 120938 124107 120791 8588.76 14080.6 7821.08 7690.49 6394.08 5993.8 13774.2 13997.9phenylalanine 52550.8 51324.6 51891.4 53358.4 52287 53514.9 36069.4 34551.5 34254.1 39396.4 37251.2 33721.3 55993.8 37026.4 54834.9 40589 54427.8 67756.8 131261 119972phosphoric acid 44203.1 41822.5 48609 50301.5 44522.1 51705 176623 138564 153289 132671 153684 145972 117802 136175 106942 121476 100590 99731.9 107488 113525proline 63131 64670.1 65424.5 66202.3 66590.6 68063.9 85735.6 88313.7 90452.3 97197.3 84019.2 79189.3 50559.8 50360.2 42955.9 43732.6 37401.5 37105.8 41407.1 53561.6pyroglutamic acid 663046 574878 690208 631687 722593 691961 1004613 827330 891148 865040 900475 815390 876347 988070 715818 843755 715594 604787 726241 780831serine (saturation) 819361 764949 841478 874111 939367 987104 686025 619960 664746 630077 578576 549779 494602 617504 450846 451125 396967 314398 405608 465599sinapinic acid 28.125 30.2577 92.8528 26.2485 72.3753 78.8163 162.899 141.304 139.208 142.837 171.391 151.24 435.444 392.058 349.229 333.173 277.264 253.162 503.956 502.037sorbose (major; saturation) 672901 594154 849604 680362 642473 807218 195440 184351 194494 194837 187529 183926 259783 468488 153974 493224 108338 78926.1 74167.3 121100stearic acid 2808.53 3364.31 69359.8 3465.9 40963 41019.4 108855 55009.6 56368.1 57799.5 66315.5 79257 97561.3 97914.5 81405.9 89559 70804.1 68570.1 66642.1 58883.8succinic acid 388323 352325 421943 381864 372895 415419 139210 146521 149473 132880 118861 132636 112507 253371 126814 185933 117552 95162.9 74060.2 84359.7sugar monoP 0 0 4416.27 3752.08 4419.38 2441.21 10071 8942.55 7409.78 16615.5 9769.8 9075.22 7945.02 7685.84 11021.8 9233.59 6238.41 8595.05 2549.31 3012.47tryptophan 1163.12 1951.93 21775.6 1559.35 1705.23 18453 22038.4 13183.4 13268.6 14230 13159 21433.5 27635 25213.3 31908.9 25150.2 25341.7 37146 63730.6 61002.4tyrosine 53703.3 71667.2 36443.1 46560.7 38645.6 25773.7 17208.8 12642 19654.9 15102.2 20513 19540.8 3404.06 15329.1 2194.7 2350.65 8508.41 17831.6 48562.7 92671.1uracil 23774 24165.1 23362 22811.7 20765.4 23875.2 8429.25 8261.11 9777.42 7057.8 7411.98 8737.15 16140 15118.9 15945.7 17167.7 12983.9 19541.8 3240.99 4916.26urea 4716.42 4005 4976.9 5383.09 5509.47 5911.86 6145.36 4360.84 5008.44 4514.13 4629.91 4851.57 6724.01 5212.27 5993.29 6398.52 7083.45 8239.39 9949.9 8174.07uric acid 102.075 211.809 158.022 132.277 121.795 116.419 80.2879 87.0301 92.2722 88.498 75.0849 82.2979 863.627 788.768 705.641 860.735 599.459 574.096 409.783 745.366uridine 3314.2 703.864 3758.4 1562.23 1287.29 1980.85 2962.08 6356.09 6846.72 2057.59 2469.07 2806.67 3011.33 3890.4 3592.19 3283.5 3490.01 3269.65 1273.96 1720.38valine 46961.3 46041 49312.1 48617.1 47760.9 47068.5 28749.9 29071.3 28419.8 29826.6 29904.7 25844.4 55802.7 48336.7 56544.8 45076.2 59657.2 83034 193060 202035

0 1 4 5

3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 6 1 2 3 4 5 674687 68935.5 66953.2 74414.1 44691.7 57512.4 40852.2 50081.7 40894.3 35986.2 22968 22637.2 19749.2 28088 18163.5 21406.7 18081.5 14416.5 9567.36 18513 13502.5 8687.89

15784.6 13218.7 18251.9 19072.2 13441.1 11178.3 14027.1 13666.9 14384.2 14158.2 9657.83 10427 9783.33 16078 9793.92 12082.8 10587.6 9382.18 9073 10451.4 9812.79 8283.0815461.5 13255.3 20561.4 17189.9 22783.3 16248.9 24216.9 15366 22992.9 30351.2 30465.8 26954.8 28346.3 24106.4 26917.8 26248.9 21621.5 27231.4 37291.4 26729.7 38629.4 36434.7676697 476594 589672 653549 196868 259068 246096 247316 257246 229494 144673 157565 184433 86066.1 67441.8 129087 194659 163911 218736 256340 255741 260408104371 94391.7 77186.9 104751 209793 210290 195503 189430 216577 198710 296663 223975 249951 207421 193350 189976 236265 210013 240605 205939 233069 269477397302 332900 356580 349676 250481 312053 297793 251985 285186 281847 177997 171009 183261 234423 160630 189917 146765 105863 115476 139414 126683 134249

51661.3 47427.8 50260.6 50270 99911.3 118307 92766.8 91967.2 97511.1 60859.2 41405.3 29821 35006.7 54869.3 32085.3 49579.5 44630.3 35340.3 33093.8 44225 38814.6 39324.4167031 179979 122400 161882 309709 295066 257243 281632 271979 270022 433183 358211 360285 378818 314856 294409 284484 310491 344891 334477 337599 349903

84370.7 92615.3 83693.4 74401.5 7408.12 9490.71 7614.51 6894.97 7725.51 6454.66 3889.99 3932.16 4542.05 5011.46 3689.14 5058.87 5315.13 3918.86 3931 6009.85 5968.73 5236.12185954 219143 173144 204307 126960 148081 77269.1 119891 70814.3 68603 96247.8 83983.5 82813.7 116972 81898.2 86640.4 119836 118780 99345.9 127209 86931.6 86845.4157648 131962 133677 187498 65767.3 52950.3 62533.4 59368.2 69275.7 65955.5 28975.6 34636.3 46683.1 46451.1 37017.9 44004.8 23969.2 23216.4 18783.1 29038.3 22231.8 19792.6552349 539308 649198 553119 618171 613963 633858 579739 564480 606531 479045 501657 593525 555715 431700 449972 404243 414609 460129 517269 495155 454973

18709.1 16043.5 20352.6 19293.5 23905.2 20952 23800.3 21835.9 23380.4 22032.7 6627.44 9536.89 8665.64 8708.99 7138.84 7797.69 9124.82 7851.84 6723.1 7309.98 7440.01 6268.1912905.9 6625.29 11169.4 10135.4 9037.97 9784.87 9806.94 6880.93 9980.02 10201.4 8533.98 6201 5278.1 7224.46 5688.95 4926.1 8294.57 7081.47 7613.8 5866.69 6245.56 7821.17122768 76168 72150.8 113466 55362.5 75146.2 117359 126799 136829 136568 27124.7 28088.4 30321.3 20476.9 19058.5 20646.6 50373.1 35208.5 66804.4 68945.5 112731 111001

7673.16 13528.9 12562.8 12478.4 6912.55 3320.31 3088.84 1235.63 2777.06 2453.09 4730.33 4925.01 3831.55 9579.14 8974.7 7709.86 2787.65 2411.07 1229.3 1151.51 425.359 627.223193074 206621 185941 190305 209878 225430 187926 187482 183938 178040 251571 222744 235639 250753 193358 200659 173839 182567 193300 198953 183102 190856

9580.61 10798.8 11365.5 12607.7 12549.7 9755.29 13720.9 9017.65 14967.2 15939.6 18851.9 17331.3 14443.4 15157.5 16709.9 16652.3 21892.3 16865.8 18414.9 17241.8 18762.5 22429.899625.5 87366.2 92254.6 98979.9 42235.5 44167.5 56013.7 39720.2 65580.3 48809.9 29755 26642.2 30736.5 48614.5 34590.3 37763.5 54496.1 28407.1 38047.1 35608.5 36697 40597.657746.4 36208.9 40263.7 57335.6 10224.5 66597.5 84835.5 13134.7 108180 50117.9 48299.2 35063.2 50390.3 81289.6 38675.9 39358.8 84292.1 40999 72343.3 52916.5 44146 5273.0351.2549 74.6098 49.3633 44.3704 18.4405 6.37266 13.625 3.93761 12.0768 5.92476 16.1773 9.57318 6.97964 3.05904 3.25253 7.15681 17.3562 18.9253 8.4719 6.12628 20.7927 8.70392185488 167139 153524 173066 53089.2 62034.9 59658.9 55727.4 62254.5 57201.7 59007.5 51277.4 49288.7 54760.4 47374.9 49817.4 68548.6 49540.9 56247.9 49157.1 55141.3 50192.5

3586.81 1293.97 3503.82 3137.03 1924.41 6355.67 5706.84 16757.8 1172.82 3986.87 2709.43 1920.78 1454.32 1906.61 674.252 1049.1 1432.01 1975.92 739.82 4169.43 1226.83 821.6140307.1 35479.1 36989 39697.4 9641.01 9769.64 9003.34 9781.41 9768.51 9844.81 7138.55 6658.16 6856.23 7740.71 5922.13 7073.92 22102.1 6496.12 7248.45 8328.29 8009.45 7783.77

29557 22868.5 39724 25275.1 42275.5 34673.7 31100.5 29572.7 23431.1 26622.2 29723.2 21599.5 22984.5 25721.1 23179.3 17821.7 24495.5 21642 25210.4 21948.5 26061.8 29091.5107308 46472.2 107036 105349 3037.59 39732 70109.2 3171.59 78098.2 30333.4 15035.7 13350.5 19274.7 33077.5 12976.7 18533.2 36446.8 10196.5 19064.9 13672.9 11193.7 999.771

72527.6 59821.4 76203.7 101575 48069 53766.5 48684.3 45839.7 39339.2 43173.7 43197.1 46502.9 48201.3 64178.3 43340.5 60814.7 61816 49884.6 32203.8 37132.6 38370.5 37811.5235331 239418 248871 232494 127409 186571 137436 137210 148499 126336 103097 101098 103964 105846 80222.4 104039 58947.1 42281.2 42010.3 48213.4 48647 48279

63074.5 56427 80679.6 54693.7 90771.6 77989.8 60584.6 59198.6 45038.4 62948.3 66719.9 50687.2 54470.5 60572.9 49550.8 42776.3 53230.6 48157.7 57991.3 53093.8 62603.2 66212.415527.3 12984.9 16105.5 14512.5 33101.2 43575.4 34060.3 30240.4 28673 20196.4 10725.4 8416.71 13151.9 10137.4 7401.65 11709.3 10297.3 7830.16 8213 9584.95 6443.91 9298.82132228 122594 142370 144510 148722 139948 151663 136142 149498 150784 143803 130463 130852 135802 112798 112847 118461 127709 135710 135140 137987 146647111259 102974 116580 114242 138421 137984 135410 139041 131099 136190 168027 152767 152042 160296 133881 140637 144509 149192 152729 158069 162339 153359

43775.4 39306.9 39074.1 37209.2 16247.8 21193.7 16513.9 17039.1 17463.9 14610.3 12545.6 10774.1 11064.4 10905.2 9076.31 10954.7 19690.1 11037.5 13133 13247.5 13231.8 12174.3689486 732829 731658 599501 761810 841361 744768 749227 705275 673896 963762 868369 986076 928231 737575 778351 693657 727227 741579 769930 714149 750299530651 365280 482111 405858 319176 350450 319995 321123 295426 284259 218984 203585 215399 258567 186995 209291 205152 167512 188637 190266 178222 190241

489.706 390.951 647.837 386.253 650.806 541.236 652.591 306.115 549.743 231.898 76.897 83.8594 69.7787 50.4027 59.6975 46.2276 45.3894 55.0071 44.7389 37.2863 51.5185 31.52568506.3 74613.9 78737.2 65086.1 69304.9 64309.2 67478.2 57823.5 60835.3 49064.6 38960.8 48243.6 48164.1 48756.8 39108.7 41199.4 52369.8 40549.9 36095.8 42242 36636.7 2560860377.7 60852 76382.9 56062.3 80678.1 83123.7 72225.3 57314.9 54266.7 78403.6 102863 55962.6 80004.4 71962.6 52959.3 47682.2 51083.6 47835.2 53693.9 55318.5 59230.5 62659.271985.8 81165.5 70326.3 71238.4 79239.6 83935 77978.9 70898.6 82356.2 87267.6 95584.4 79554.5 75840.5 77062.6 60334.2 64049.8 64793.1 54920 80392.3 92405.1 77910.2 85463.92033.42 2978.1 3293.54 2710.61 2216.78 1484.04 1349.5 1052.02 1311.84 1345.94 1733.66 1872.13 1947.09 3126.16 2660.21 2557.89 1623.65 1646.44 1384.86 1308.64 1423.85 1036.7866335.5 57477.8 71954.6 75294.7 97953.9 105742 97504.8 92884.2 82739.6 94180.8 52165.2 46565.7 44591.2 47105 40502.1 43587.7 52662.4 42987.5 44391.1 55139.3 52266.6 50612.6107713 37808.8 111354 113982 3015.1 22447 36931.1 3133.02 40660.1 19131.8 7956.93 8758.52 10803.6 14895 7627.86 7780 23991.3 7373.66 10972.3 9836.66 8937.11 1418.66

3560.39 3570.61 3116.25 3468.8 4321.23 4338.69 5298.41 6007.58 7920.39 9595.11 5338.72 4523.33 5871.72 3182.49 2701.3 2654.1 7783.25 6056.18 5764.08 5687.44 7635.72 6221.17736.65 8251.24 8334.77 14651.5 14298.4 11530.7 13902.5 11839.1 26090.9 22122.7 25173.7 26014.1 20617.3 31921.1 36309.6 42710.3 44172.7 48095.1 50184 27569.9 57288.5 57224.5376.544 413.162 342.7 354.316 119.834 173.183 108.229 115.015 102.507 91.5425 48.5786 47.7863 55.7346 71.5266 58.1781 57.4628 46.7651 40.8822 41.7587 50.487 47.226 48.51841492.77 1232.38 1625.91 2042.6 1591.25 1933.64 1956.63 2279.29 1914.5 1415.9 1672.67 1973.76 1589.69 1539.52 1246.8 1543.59 1667.1 1438.49 2048.6 2040.24 2313.93 1267.09215293 188615 218305 205842 34867.4 42924.9 38540.6 34886.5 38712.2 37041.1 35711.7 30758.9 31456.7 36201.9 28416.4 34552.7 48338.8 26253.2 31623.1 32178.2 30530.3 31462.7

145 7 10

Supplementary Table 2. List of primers used for the RT-PCR analysis.

Gene name Locus Sequence

LHCB1.1_F At1g29920 CGGAAAGTGAGCCAAGTTCT

LHCB1.1_R At1g29920 TGAAAGTCTCTACCATCCACCA

LHCB2.4_F At3g27690 GCCATCCAACGATCTCCTC

LHCB2.4_R At3g27690 TGGTCCGTACCAGATGCTC

qCAO_F AT1G44446 ACCCTCCTCTTCAACCACTGC

qCAO_R AT1G44446 AGCTTTTCGCACCCGTGTTTGT

qZm2G351977-F GRMZM2G351977 GCAAGTGAGCGAGGGCATAT

qZm2G351977-R GRMZM2G351977 TCTGAGCCCATGCTCCCTT

qZm2G120619-F GRMZM2G120619 GGAGGGAATAGATTGCAAGCG

qZm2G120619-R GRMZM2G120619 CTACAGCCTCGAGCAGAGAC

qZm2G427369-F GRMZM2G427369 CGTATTTATTATCGCCTTCATCGC

qZm2G427369-R GRMZM2G427369 CATCAACAGATGCAGCTTCCC

Supplementary data Theory section with details of the mathematical calculations.

Two-component positive feedback loop Assume that we have two components A and B that are direct or indirect exerting positive regulation upon each other. More A gives more synthesis of B, more B gives more synthesis of A. Mathematically we can formulate it as

𝑑𝐴𝑑𝑡 = 𝑎𝑓! 𝐵 − 𝑏𝐴,

𝑑𝐵𝑑𝑡 = 𝑐𝑓! 𝐴 − 𝐵

where the functions fA,B are monotonically increasing with a maximal value less than or equal to one. a and c are the maximal synthesis rates of A and B, respectively, and b the decay rate constant of A. We have scaled time with the decay rate constant of B to reduce the number of parameters, making all units of time measured relative to the half-life of B. If the functions are monotonically increasing with maximum of one the system will as time evolve end up in the steady state A=a/b and B=c. Typically fA,B would have a sigmoidal shape and could be represented e.g. by a Hill-type function depending on the details of the regulation. Such functions can typically be linearized for small values (see e.g. [1]). Thus for small values we approximately have that

𝑑𝐴𝑑𝑡 = 𝑎𝐵 − 𝑏𝐴,

𝑑𝐵𝑑𝑡 = 𝑐𝐴 − 𝐵

the solution can be shown to be

𝐵 𝑡 = 𝐶!𝑒!!! + 𝐶!𝑒!!! , 𝐴 𝑡 = 1𝑐𝑑𝐵𝑑𝑡 + 𝐵

where the constants C1,2 are determined by initial values and

𝑟!,! = −1+ 𝑏2 ±

1+ 𝑏 !

4 + 𝑎𝑐 − 𝑏

Ignoring the fast decaying mode r2 gives

𝐵 𝑡 = 𝐶!𝑒!!! , 𝐴 𝑡 = 𝐵(𝑡)𝑐 𝑟! + 1

and 𝐵/𝐴 = !!!!!

showing that the ratio will be constant making B a linear function of A with time. Thus plotting B versus A will show a straight line for small values and will eventually saturate in the non-linear regime. In figure 1 below we have plotted A and B versus time in the left panel and in the right panel B vs A and the asymptote cx/(r1+1) (dashed line).

Figure1Mutualpositivefeedbackloop.(a)EvolutionofAandBwithtimeand(b)ratioB/A.Thedashedlineareplottedwithslopec/(r1+1)

0 0.5 1Time [a.u]

1

1.5

2

2.5

3

3.5

Con

c [a

.u]

A B

1 1.5 2 A [a.u]

1

2

3

4

B [a

.u]

[1] Lacramioara Bintu, Nicolas E Buchler, Hernan G Garcia, Ulrich Gerland, Terence Hwa, Jané Kondev, Rob Phillips, Transcriptional regulation by the numbers: models, Current Opinion in Genetics & Development, Volume 15, Issue 2, April 2005, Pages 116-124