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1 Supplementary Tables 1
2 Supplementary Table 1: The 11 genes in the geneset for Case Study 1 At1g62570 At1g09350 At1g60470 At2g47180 At4g17090 At5g20830 At2g16890 At3g51240 At3g55120 At4g27560 At5g08640 flavin-containing monooxygenase family protein / FMO family protein galactinol synthase, putative galactinol synthase, putative galactinol synthase, putative beta-amylase (CT-BMY) / 1,4-alpha-D-glucan maltohydrolase sucrose synthase / sucrose-udp glucosyltransferase (SUS1) UDP-glucuronosyl/UDP-glucosyl transferase family protein naringenin 3-dioxygenase / flavanone 3-hydroxylase (F3H) chalcone-flavanone isomerase / chalcone isomerase (CHI) glycosyltransferase family protein flavonol synthase 1 (FLS1) 2
3 Supplementary Table 2: The 14 genes in the geneset for Case Study 2 At5g18170 At1g28670 At2g35690 At1g55920 At4g22690 At1g10360 At1g16410 At2g22330 At2g23600 At2g29340 At4g15550 At5g24160 At5g14740 At3g01500 glutamate dehydrogenase 1 (GDH1) lipase acyl-coa oxidase, putative serine O-acetyltransferase, putative cytochrome P450 family protein glutathione S-transferase, putative cytochrome P450, putative cytochrome P450, putative hydrolase, alpha/beta fold family protein short-chain dehydrogenase/reductase (SDR) family protein UDP-glucose:indole-3-acetate beta-d-glucosyltransferase (IAGLU) squalene monooxygenase 1,2 / squalene epoxidase 1,2 (SQP1,2) carbonic anhydrase 2 / carbonate dehydratase 2 (CA2) (CA18) carbonic anhydrase 1, chloroplast / carbonate dehydratase 1 (CA1) 3
4 Supplementary Table 3: The 113 senescent-responsive genes in the geneset for Case Study 3 At1g07600 At1g09500 At1g13990 At1g14400 At1g18210 At1g19570 At1g20620 At1g21670 At1g30420 At1g30460 At1g35160 At1g47128 At1g51200 At1g52040 At1g52880 At1g53580 At1g53750 At1g58360 At1g59870 At1g63010 At1g67840 At1g68820 At1g70900 At1g71950 At1g73260 At1g73325 At1g73750 metallothionein-like protein 1A (MT-1A) (MT-Q) (MT-2) cinnamyl-alcohol dehydrogenase family / CAD family ubiquitin-conjugating enzyme 1 (UBC1) calcium-binding protein, putative dehydroascorbate reductase, putative catalase 3 (SEN2) ATP-binding cassette transport protein, putative zinc finger (CCCH-type) family protein / YT521-B-like family protein protein GF14 phi (GRF4) cysteine proteinase (RD21A) / thiol protease zinc finger (AN1-like) family protein jacalin lectin family protein no apical meristem (NAM) family protein hydroxyacylglutathione hydrolase, putative / glyoxalase II, putative 26S proteasome AAA-ATPase subunit (RPT1a) amino acid permease I (AAP1) ABC transporter family protein SPX (SYG1/Pho81/XPR1) domain-containing protein ATP-binding region, ATPase-like domain-containing protein membrane protein, putative trypsin and protease inhibitor family protein / Kunitz family protein trypsin and protease inhibitor family protein / Kunitz family protein Continued on next page 4
5 Supplementary Table 3: Continued At1g75280 At1g75380 At1g78080 At1g78380 At2g05540 At2g20860 At2g21660 At2g21950 At2g22240 At2g23980 At2g25450 At2g26560 At2g39900 At2g42690 At2g43290 At2g43770 At2g45210 At3g02040 At3g03720 At3g07590 At3g09390 isoflavone reductase, putative wound-responsive protein-related AP2 domain-containing transcription factor RAP2.4 glutathione S-transferase, putative glycine-rich protein lipoic acid synthase (LIP1) glycine-rich RNA-binding protein (GRP7) SKP1 interacting partner 6 (SKIP6) inositol-3-phosphate synthase isozyme 2 / myo-inositol-1-phosphate synthase 2 / MI-1-P synthase 2 / IPS 2 cyclic nucleotide-regulated ion channel / cyclic nucleotide-gated channel (CNGC6) 2-oxoglutarate-dependent dioxygenase, putative patatin, putative LIM domain-containing protein lipase, putative calmodulin-like protein (MSS3) transducin family protein / WD-40 repeat family protein auxin-responsive protein-related glycerophosphoryl diester phosphodiesterase family protein amino acid permease family protein small nuclear ribonucleoprotein D1, putative / snrnp core protein D1, putative / Sm protein D1, putative metallothionein protein, putative (MT2A) At3g12120 omega-6 fatty acid desaturase, endoplasmic reticulum (FAD2) / delta-12 desaturase At3g15580 autophagy 8i (APG8i) At3g15730 phospholipase D alpha 1 / PLD alpha 1 (PLDALPHA1) (PLD1) / choline phosphatase 1 At3g16640 translationally controlled tumor family protein Continued on next page 5
6 Supplementary Table 3: Continued At3g17790 At3g22600 At3g23920 At3g25480 At3g25760 At3g26100 At3g44100 At3g44300 At3g44720 At3g46000 At3g48000 At3g51130 At3g51730 At3g52800 At3g55430 At3g62550 At4g01610 At4g03280 At4g11360 At4g11600 At4g11910 At4g12290 At4g13250 At4g16190 At4g16740 At4g18280 acid phosphatase type 5 (ACP5) protease inhibitor/seed storage/lipid transfer protein (LTP) family protein beta-amylase, putative / 1,4-alpha-D-glucan maltohydrolase, putative rhodanese-like domain-containing protein early-responsive to dehydration stress protein (ERD12) regulator of chromosome condensation (RCC1) family protein MD-2-related lipid recognition domain-containing protein / ML domain-containing protein nitrilase 2 (NIT2) prephenate dehydratase family protein actin-depolymerizing factor, putative (ADF2) aldehyde dehydrogenase (ALDH2) saposin B domain-containing protein zinc finger (AN1-like) family protein glycosyl hydrolase family 17 protein / beta-1,3-glucanase, putative universal stress protein (USP) family protein cathepsin B-like cysteine protease, putative cytochrome B6-F complex iron-sulfur subunit, chloroplast / Rieske iron-sulfur protein / plastoquinol-plastocyanin reductase (petc) zinc finger (C3HC4-type RING finger) family protein (RHA1b) glutathione peroxidase, putative copper amine oxidase, putative short-chain dehydrogenase/reductase (SDR) family protein cysteine proteinase, putative terpene synthase/cyclase family protein glycine-rich cell wall protein-related Continued on next page 6
7 Supplementary Table 3: Continued At4g24220 At4g27020 At4g27830 glycosyl hydrolase family 1 protein At4g30210 NADPH-cytochrome p450 reductase, putative / NADPH-ferrihemoprotein reductase, putative At4g30270 At4g30440 At4g32940 At4g35750 At4g37390 At4g37990 At4g39090 At4g39670 At5g01600 At5g02380 At5g08410 At5g10650 At5g10860 At5g11520 At5g13170 At5g17220 At5g18100 At5g19540 At5g24160 At5g24770 At5g24780 At5g34850 MERI-5 protein (MERI-5) (MERI5B) / endo-xyloglucan transferase / xyloglucan endo-1,4-beta-d-glucanase (SEN4) NAD-dependent epimerase/dehydratase family protein vacuolar processing enzyme gamma / gamma-vpe Rho-GTPase-activating protein-related auxin-responsive GH3 family protein mannitol dehydrogenase, putative (ELI3-2) cysteine proteinase RD19a (RD19A) / thiol protease ferritin 1 (FER1) metallothionein protein 2B (MT-2B) ferredoxin-thioredoxin reductase, putative zinc finger (C3HC4-type RING finger) family protein CBS domain-containing protein aspartate aminotransferase, chloroplast / transaminase A (ASP3) (YLS4) nodulin MtN3 family protein glutathione S-transferase, putative superoxide dismutase [Cu-Zn] / copper/zinc superoxide dismutase (CSD3) squalene monooxygenase 1,2 / squalene epoxidase 1,2 (SQP1,2) vegetative storage protein 2 (VSP2) vegetative storage protein 1 (VSP1) calcineurin-like phosphoesterase family protein Continued on next page 7
8 At5g43850 At5g48380 At5g53350 Supplementary Table 3: Continued acireductone dioxygenase (ARD/ARD ) family protein leucine-rich repeat family protein / protein kinase family protein ATP-dependent Clp protease ATP-binding subunit ClpX1 (CLPX) At5g53730 harpin-induced family protein / HIN1 family protein / harpin-responsive family protein At5g54250 At5g57655 At5g59310 At5g60360 At1g05340 cyclic nucleotide-regulated ion channel / cyclic nucleotide-gated channel (CNGC4) xylose isomerase family protein lipid transfer protein 4 (LTP4) cysteine proteinase, putative / AALP protein (AALP) Concluded 8
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A WT siz1-2 siz1-3 B WT siz1-2 siz1-3 -Pi C +Pi WT siz1-2 siz1-3 D WT siz1-2 siz1-3 E +Pi, 0.05 M IAA -Pi, 0.05 M IAA WT siz1-2 siz1-3 WT siz1-2 siz1-3 F +Pi, 2.5 M NPA -Pi, 2.5 M NPA Supplemental Figure
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0.004 SW nm 0.04 0.03 nm nm 0.16 0.1 nm nm 0.40 0.3 nm nm 0.80 0.5 nm 1.6 1 nm 16 10 nm 160 100 nm 0 nm 0.04 nm 0.16 nm 0.40 nm 0.80 nm 1.6 nm 16 nm 160 nm Spectral counts 0 nm 0.04 nm 0.16 nm 0.40 nm
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