Table S2. Enriched GO Categories in Biological Process for the Shared Degs

Table S2. Enriched GO categories in biological process for the shared DEGs

photosynthesis (GO ID:15979)

Fold Change ProbeID AGI Col-0(R) pifQ(D) Name Description /Col-0(D) /Col-0(D) A_84_P19035 AT1G30380 17.07 4.9 PSAK; PSAK (PHOTOSYSTEM I SUBUNIT K) A_84_P21372 AT4G12800 8.55 3.57 PSAL; PSAL (photosystem I subunit L) PSBP-1; PSBP-1 (OXYGEN-EVOLVING A_84_P20343 AT1G06680 12.27 3.85 PSII-P; ENHANCER PROTEIN 2); poly(U) binding OEE2; LHCB6; LHCB6 (LIGHT HARVESTING COMPLEX A_84_P14174 AT1G15820 23.9 6.16 CP24; PSII); chlorophyll binding A_84_P11525 AT1G79040 16.02 4.42 PSBR; PSBR (photosystem II subunit R) FAD5; ADS3; FAD5 (FATTY ACID DESATURASE 5); A_84_P19290 AT3G15850 4.02 2.27 FADB; oxidoreductase JB67; GAPA (GLYCERALDEHYDE 3- GAPA; PHOSPHATE DEHYDROGENASE A A_84_P19306 AT3G26650 4.6 3.43 GAPA-1; SUBUNIT); glyceraldehyde-3-phosphate dehydrogenase A_84_P193234 AT2G06520 14.01 3.89 PSBX; PSBX (photosystem II subunit X) LHB1B1; LHB1B1 (Photosystem II light harvesting A_84_P160283 AT2G34430 89.44 32.95 LHCB1.4; complex gene 1.4); chlorophyll binding PSAN (photosystem I reaction center subunit A_84_P10324 AT5G64040 26.14 7.12 PSAN; PSI-N); calmodulin binding LHB1B2; LHB1B2 (Photosystem II light harvesting A_84_P207958 AT2G34420 41.71 12.26 LHCB1.5; complex gene 1.5); chlorophyll binding LHCA2 (Photosystem I light harvesting A_84_P19428 AT3G61470 10.91 5.36 LHCA2; complex gene 2); chlorophyll binding A_84_P22465 AT1G31330 32.37 6.58 PSAF; PSAF (photosystem I subunit F) chlorophyll A-B binding protein CP29 A_84_P190244 AT5G01530 16.45 5.27 LHCB4 (LHCB4) A_84_P15184 AT1G08380 16.64 4.4 PSAO; PSAO (photosystem I subunit O)

generation of precursor metabolites and energy (GO ID:6091)

A_84_P21372 AT4G12800 8.55 3.57 PSAL; PSAL (photosystem I subunit L) PSBP-1; PSBP-1 (OXYGEN-EVOLVING A_84_P20343 AT1G06680 12.27 3.85 PSII-P; ENHANCER PROTEIN 2); poly(U) binding OEE2; A_84_P16683 AT4G26390 -5.22 -2.78 pyruvate kinase, putative A_84_P11525 AT1G79040 16.02 4.42 PSBR; PSBR (photosystem II subunit R) FAD5; ADS3; FAD5 (FATTY ACID DESATURASE 5); A_84_P19290 AT3G15850 4.02 2.27 FADB; oxidoreductase JB67; LHB1B1; LHB1B1 (Photosystem II light harvesting A_84_P160283 AT2G34430 89.44 32.95 LHCB1.4; complex gene 1.4); chlorophyll binding GAPC-2; glyceraldehyde-3-phosphate A_84_P13402 AT1G13440 3.08 2.83 GAPC-2; dehydrogenase PSAN (photosystem I reaction center subunit A_84_P10324 AT5G64040 26.14 7.12 PSAN; PSI-N); calmodulin binding LHB1B2; LHB1B2 (Photosystem II light harvesting A_84_P207958 AT2G34420 41.71 12.26 LHCB1.5; complex gene 1.5); chlorophyll binding A_84_P297434 AT4G04640 6.18 2.62 ATPC1 ATPC1 (ATP synthase gamma chain 1) GAPA-2; glyceraldehyde-3-phosphate A_84_P15540 AT1G12900 8.25 4.83 GAPA-2; dehydrogenase LHCA2 (Photosystem I light harvesting A_84_P19428 AT3G61470 10.91 5.36 LHCA2; complex gene 2); chlorophyll binding A_84_P15184 AT1G08380 16.64 4.4 PSAO; PSAO (photosystem I subunit O)

response to abiotic stimulus (GO ID:9628)

TUB1 (tubulin beta-1 chain); structural A_84_P10530 AT1G75780 -3.61 -2.04 TUB1; molecule A_84_P21376 AT4G13790 -4.19 -3.29 auxin-responsive protein, putative A_84_P15595 AT3G49970 -3.9 -2.35 phototropic-responsive protein, putative HFR1; REP1; HFR1 (LONG HYPOCOTYL IN FAR-RED); A_84_P17015 AT1G02340 -2.74 -3.3 RSF1; DNA binding / transcription factor FBI1; A_84_P15788 AT4G38840 11.11 2.26 auxin-responsive protein, putative FAD5; ADS3; FAD5 (FATTY ACID DESATURASE 5); A_84_P19290 AT3G15850 4.02 2.27 FADB; oxidoreductase JB67; DRT112 (DNA-damage-repair/toleration A_84_P14351 AT1G20340 11.32 4.71 DRT112; protein 112); copper ion binding / electron carrier A_84_P270930 AT2G39730 12.85 3.63 RCA; RCA (RUBISCO ACTIVASE) A_84_P18568 AT4G25050 10.15 3.21 ACP4; ACP4 (ACYL CARRIER PROTEIN 4) HLS1; A_84_P19566 AT4G37580 -6 -2.97 COP3; HLS1 (HOOKLESS 1); N-acetyltransferase UNS2; GAPA (GLYCERALDEHYDE 3- GAPA; PHOSPHATE DEHYDROGENASE A A_84_P19306 AT3G26650 4.60 3.43 GAPA-1; SUBUNIT); glyceraldehyde-3-phosphate dehydrogenase ATP synthase delta chain, chloroplast, A_84_P12848 AT4G09650 8.64 2.92 putative / H(+)-transporting two-sector ATPase, delta (OSCP) subunit, putative PIL1 (PHYTOCHROME INTERACTING A_84_P521683 AT2G46970 -14.68 -11.74 PIL1; FACTOR 3-LIKE 1); transcription factor RPT2 (ROOT PHOTOTROPISM 2); protein A_84_P519833 AT2G30520 10.45 4.96 RPT2; binding APX1; APX1 (ASCORBATE PEROXIDASE 1); L- A_84_P16329 AT1G07890 2.33 2.34 CS1; ascorbate peroxidase MEE6; A_84_P255380 AT1G16850 -2.37 -3.8 unknown protein ATHB-2 (ARABIDOPSIS THALIANA HAT4; A_84_P16749 AT4G16780 -4.15 -2.9 HOMEOBOX PROTEIN 2); DNA binding / ATHB2; transcription factor NIA2; CHL3; A_84_P16255 AT1G37130 2.42 2.04 NIA2-1; NIA2 (NITRATE REDUCTASE 2) NR; NR2; PIL2; PIL2 (PHYTOCHROME INTERACTING A_84_P13757 AT3G62090 -2.65 -2.19 PIF6; FACTOR 3-LIKE 2) RD20 (RESPONSIVE TO DESSICATION A_84_P21026 AT2G33380 -8.92 -5.67 RD20; 20); calcium ion binding ATCAMBP25 (ARABIDOPSIS THALIANA ATCAMBP2 A_84_P124252 AT2G41010 -2.35 -2.11 CALMODULIN (CAM)-BINDING 5; PROTEIN OF 25 KDA); calmodulin binding response to endogenous stimulus (GO ID:9719)

A_84_P21376 AT4G13790 -4.19 -3.29 auxin-responsive protein, putative A_84_P23698 AT1G22690 10.66 3.40 gibberellin-responsive protein, putative A_84_P147268 AT1G29490 2.12 2.29 auxin-responsive family protein A_84_P15788 AT4G38840 11.11 2.26 auxin-responsive protein, putative A_84_P12859 AT4G12410 -3.34 -2.44 auxin-responsive family protein A_84_P21359 AT4G09530 -10.14 -5.31 auxin-responsive family protein A_84_P19956 AT1G76190 2.23 2.23 auxin-responsive family protein A_84_P19997 AT1G74670 12.04 4.79 gibberellin-responsive protein, putative HLS1; A_84_P19566 AT4G37580 -6.00 -2.97 COP3; HLS1 (HOOKLESS 1); N-acetyltransferase UNS2; GAPA (GLYCERALDEHYDE 3- GAPA; PHOSPHATE DEHYDROGENASE A A_84_P19306 AT3G26650 4.60 3.43 GAPA-1; SUBUNIT); glyceraldehyde-3-phosphate dehydrogenase LOX2; A_84_P15574 AT3G45140 76.30 6.94 LOX2 (LIPOXYGENASE 2) ATLOX2; IAA29 (indoleacetic acid-induced protein 29); A_84_P55550 AT4G32280 -3.31 -2.92 IAA29; transcription factor ACS5; ACS5 (ACC SYNTHASE 5); 1- A_84_P23570 AT5G65800 -8.15 -3.44 ETO2; aminocyclopropane-1-carboxylate synthase CIN5; ARF18 (AUXIN RESPONSE FACTOR 18); A_84_P10920 AT3G61830 -4.94 -2.10 ARF18; transcription factor A_84_P24123 AT3G53250 2.84 2.94 auxin-responsive family protein RD20 (RESPONSIVE TO DESSICATION A_84_P21026 AT2G33380 -8.92 -5.67 RD20; 20); calcium ion binding A_84_P21449 AT4G34770 -3.6 -3.36 auxin-responsive family protein

response to biotic stimulus (GO ID:9607)

protease inhibitor/seed storage/lipid transfer A_84_P18533 AT4G12470 -3.17 -2.08 protein (LTP) family protein A_84_P13052 AT5G28010 2.30 2.77 Bet v I allergen family protein A_84_P13916 AT4G36430 -5.41 -2.49 peroxidase, putative LOX2; A_84_P15574 AT3G45140 76.30 6.94 LOX2 (LIPOXYGENASE 2) ATLOX2; A_84_P17616 AT4G23670 3.31 2.77 major latex protein-related / MLP-related A_84_P19508 AT4G23680 2.81 3.72 major latex protein-related / MLP-related A_84_P215028 AT3G25770 20.66 4.34 AOC2; AOC2 (ALLENE OXIDE CYCLASE 2) A_84_P16094 AT1G23130 4.87 2.76 Bet v I allergen family protein ATCEL2 (Arabidopsis thaliana Cellulase 2); A_84_P24081 AT1G02800 -6.06 -2.2 CEL2; hydrolase, hydrolyzing O-glycosyl compounds CPN60B (CHAPERONIN 60 BETA); ATP CPN60B; A_84_P16083 AT1G55490 2.63 2.08 binding / protein binding / unfolded protein LEN1; binding ESM1 (EPITHIOSPECIFIER MODIFIER 1); A_84_P22166 AT3G14210 12.47 4.6 ESM1; carboxylesterase A_84_P19409 AT1G24020 3.95 4.16 MLP423; MLP423 (MLP-LIKE PROTEIN 423) carbohydrate metabolic process (GO ID:5975)

ESP; A_84_P17086 AT1G54040 8.35 21.72 ESR; ESP (EPITHIOSPECIFIER PROTEIN) TASTY; phosphoglucomutase, putative / glucose A_84_P19000 AT1G70820 17.49 2.81 phosphomutase, putative ATGOLS7 (ARABIDOPSIS THALIANA GALACTINOL SYNTHASE 7); transferase, A_84_P15183 AT1G60450 -3.74 -2.02 ATGOLS7; transferring glycosyl groups / transferase, transferring hexosyl groups A_84_P16683 AT4G26390 -5.22 -2.78 pyruvate kinase, putative GATL10 (Galacturonosyltransferase-like 10); polygalacturonate 4-alpha- A_84_P554567 AT3G28340 -2.44 -2.25 GATL10; galacturonosyltransferase/ transferase, transferring hexosyl groups A_84_P19216 AT2G21330 4.54 2.27 fructose-bisphosphate aldolase, putative ESM1 (EPITHIOSPECIFIER MODIFIER 1); A_84_P22166 AT3G14210 12.47 4.6 ESM1; carboxylesterase GAPA (GLYCERALDEHYDE 3- GAPA; PHOSPHATE DEHYDROGENASE A A_84_P19306 AT3G26650 4.60 3.43 GAPA-1; SUBUNIT); glyceraldehyde-3-phosphate dehydrogenase ATGH9B13 (ARABIDOPSIS THALIANA A_84_P17557 AT4G02290 -4.13 -2.69 GLYCOSYL HYDROLASE 9B13); hydrolase, hydrolyzing O-glycosyl compounds ATGH9B8 (ARABIDOPSIS THALIANA A_84_P14433 AT2G32990 -3.27 -2.15 GLYCOSYL HYDROLASE 9B8); hydrolase, hydrolyzing O-glycosyl compounds GAPC-2; glyceraldehyde-3-phosphate A_84_P13402 AT1G13440 3.08 2.83 GAPC-2; dehydrogenase ATGH9C3 (ARABIDOPSIS THALIANA A_84_P14743 AT4G11050 -2.65 -2.71 GLYCOSYL HYDROLASE 9C3); hydrolase, hydrolyzing O-glycosyl compounds GAPA-2; glyceraldehyde-3-phosphate A_84_P15540 AT1G12900 8.25 4.83 GAPA-2; dehydrogenase A_84_P219118 AT4G38970 7.71 3.07 fructose-bisphosphate aldolase, putative ATGH9B12 (ARABIDOPSIS THALIANA A_84_P22068 AT2G44570 -6.78 -2.78 GLYCOSYL HYDROLASE 9B12); hydrolase, hydrolyzing O-glycosyl compounds

response to stress (GO ID:6950)

A_84_P20750 AT5G19890 -7.37 -2.63 peroxidase, putative A_84_P18528 AT4G11290 -3.38 -2.04 peroxidase, putative A_84_P14392 AT2G43550 7.79 2.88 trypsin inhibitor, putative disease resistance protein (CC-NBS-LRR A_84_P17213 AT1G58410 -3.52 -2.01 class), putative A_84_P15788 AT4G38840 11.11 2.26 auxin-responsive protein, putative A_84_P16094 AT1G23130 4.87 2.76 Bet v I allergen family protein CPN60B (CHAPERONIN 60 BETA); ATP CPN60B; A_84_P16083 AT1G55490 2.63 2.08 binding / protein binding / unfolded protein LEN1; binding disease resistance protein-related / LRR A_84_P11544 AT1G33590 2.05 2.22 protein-related protease inhibitor/seed storage/lipid transfer A_84_P18533 AT4G12470 -3.17 -2.08 protein (LTP) family protein ATP synthase delta chain, chloroplast, putative A_84_P12848 AT4G09650 8.64 2.92 / H(+)-transporting two-sector ATPase, delta (OSCP) subunit, putative

A_84_P13052 AT5G28010 2.3 2.77 Bet v I allergen family protein LOX2; A_84_P15574 AT3G45140 76.3 6.94 LOX2 (LIPOXYGENASE 2) ATLOX2; GAPC-2; glyceraldehyde-3-phosphate A_84_P13402 AT1G13440 3.08 2.83 GAPC-2; dehydrogenase A_84_P21103 AT2G41480 -5.35 -2.65 peroxidase A_84_P19508 AT4G23680 2.81 3.72 major latex protein-related / MLP-related A_84_P17616 AT4G23670 3.31 2.77 major latex protein-related / MLP-related APX1; APX1 (ASCORBATE PEROXIDASE 1); L- A_84_P16329 AT1G07890 2.33 2.34 CS1; ascorbate peroxidase MEE6; A_84_P255380 AT1G16850 -2.37 -3.8 unknown protein A_84_P215028 AT3G25770 20.66 4.34 AOC2; AOC2 (ALLENE OXIDE CYCLASE 2) A_84_P23433 AT1G49570 -5.31 -2.54 peroxidase, putative RD20 (RESPONSIVE TO DESSICATION A_84_P21026 AT2G33380 -8.92 -5.67 RD20; 20); calcium ion binding THI1; A_84_P23525 AT5G54770 13.39 2.02 THI1 (THIAZOLE REQUIRING) TZ; ATCAMBP25 (ARABIDOPSIS THALIANA ATCAMBP A_84_P124252 AT2G41010 -2.35 -2.11 CALMODULIN (CAM)-BINDING 25; PROTEIN OF 25 KDA); calmodulin binding A_84_P19409 AT1G24020 3.95 4.16 MLP423; MLP423 (MLP-LIKE PROTEIN 423)

lipid metabolic process (GO ID:6629)

A_84_P13857 AT4G28780 15.15 5.91 GDSL-motif lipase/hydrolase family protein A_84_P501534 AT4G31380 -3.22 -2.78 FLP1; FLP1 (FPF1-LIKE PROTEIN 1) A_84_P20781 AT1G02205 -3.34 -3.61 CER1; CER1 (ECERIFERUM 1) FAD5; ADS3; FAD5 (FATTY ACID DESATURASE 5); A_84_P19290 AT3G15850 4.02 2.27 FADB; oxidoreductase JB67; A_84_P18568 AT4G25050 10.15 3.21 ACP4; ACP4 (ACYL CARRIER PROTEIN 4) A_84_P19729 AT5G51210 -8.12 -3.02 OLEO3; OLEO3 (OLEOSIN3) A_84_P294704 AT1G54010 2.28 3.37 myrosinase-associated protein, putative LOX2; A_84_P15574 AT3G45140 76.3 6.94 LOX2 (LIPOXYGENASE 2) ATLOX2; A_84_P100416 AT1G59030 9.4 2.4 carboxylesterase/ lipase CYP86A4 (cytochrome P450, family 86, A_84_P19852 AT1G01600 -3.49 -2.58 CYP86A4; subfamily A, polypeptide 4); oxygen binding A_84_P20671 AT1G29660 7.03 6.01 GDSL-motif lipase/hydrolase family protein A_84_P215028 AT3G25770 20.66 4.34 AOC2; AOC2 (ALLENE OXIDE CYCLASE 2) A_84_P14479 AT2G40250 -2.37 -3.13 GDSL-motif lipase/hydrolase family protein