Supplemental Data Murata et al. (2008) The leaf 'Epidermome' of Catharanthus roseus reveals its biochemical specialization

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1 Supplemental Data Murata et al. (2008) The leaf 'Epidermome' of Catharanthus roseus reveals its biochemical specialization Supplemental Table 1: CROLF1NG genes related to isoprenoid biosynthesis. Gene Name Description Hit ID Evalue Pathway MCT CL1072Contig1 4-diphosphocytidyl-2-C-methyl-D-erythritol synthase [Stevia rebaudiana] gi MEP HMGR 006-B11 3-hydroxy-3-methylglutaryl coenzyme A reductase [Eucommia ulmoides] gi MVA AACT1 CL684Contig1 3-ketoacyl-CoA thiolase 2, peroxisomal precursor, putative [Oryza sativa (japonica cultivar-group)] gi MVA AACT2 CL222Contig1 acetoacetyl-coa thiolase [Picrorhiza kurrooa] gi MVA HMGS CL207Contig1 HMG-CoA synthase 2 [Hevea brasiliensis] gi MVA GPS 008-A07 geranyl pyrophosphate synthase [Lycopersicon esculentum] gi MEP/MVA FPS CL1065Contig1 Farnesyl pyrophosphate synthase [Gentiana lutea] gi MEP/MVA IPPI CL192Contig1 isopentenyl pyrophosphate isomerase [Gentiana lutea] gi MEP/MVA Supplemental Table 2: CROLF1NG genes related to downstream terpenoid biosynthesis. Category Name Description Hit ID Evalue cyclase CL50Contig1 putative beta-amyrin synthase [Centella asiatica] gi CYP CL247Contig1 squalene monooxygenase 1 [Medicago truncatula] gi kinase CL700Contig1 phytol kinase [Glycine max] gi cyclase CL914Contig1 Cycloartenol Synthase [Panax ginseng] gi phosphatidate cytidylyltransferase [Arabidopsis kinase 142-D09 thaliana] gi kinase 033-H06 phytol kinase [Glycine max] gi geranyl pyrophosphate synthase [Lycopersicon 008-A07 esculentum] gi cyclase 149-B03 beta-amyrin synthase [Panax ginseng] gi Supplemental Table 3: CROLF1NG genes related to flavonoid biosynthesis. Gene Category Name Description Hit ID Evalue CL3Contig2 2-Hydroxyisoflavanone dehydratase [Glycyrrhiza echinata] gi dehydrogenase CL124Contig1 chalcone reductase [Sesbania rostrata] gi CHR dehydrogenase CL124Contig1 chalcone reductase [Sesbania rostrata] gi (16OMT) methyltransferase CL314Contig1 flavonoid 4'-O-methyltransferase [Catharanthus roseus] gi acyltransferase CL536Contig1 quercetin 3-O-glucoside-6''-O-malonyltransferase [Verbena x hybrida] gi F3H dioxygenase CL445Contig1 flavanone 3-hydroxylase [Allium cepa] gi C4H CYP CL965Contig1 cinnamate 4-hydroxylase (CYP73) [Catharanthus roseus] gi FLS dioxygenase 007-A04 flavonol synthase [Eustoma grandiflorum] gi F3H dioxygenase 169-C12 flavanone 3-hydroxylase [Eustoma grandiflorum] gi CHS/STS acyltransferase 134-A11 Chalcone and stilbene synthases, N-terminal [Medicago truncatula] gi CHS/STS acyltransferase 134-G10 Chalcone and stilbene synthases, N-terminal [Medicago truncatula] gi dioxygenase 158-G10 strong similarity to naringenin 3-dioxygenase [Arabidopsis thaliana] gi DFR reductase 018-B01 2'-hydroxy isoflavone/dihydroflavonol reductase homolog [Glycine max] gi PAL 128-E08 phenylalanine ammonia lyase [Catharanthus roseus] gi DFR reductase 149-B07 2'-hydroxy isoflavone/dihydroflavonol reductase homolog [Glycine max] gi glycosyltransferase 035-F05 putative anthocyanidine rhamnosyl-transferase [Capsicum annuum] gi Genes that are shown in bold characters are the clones with perfect amino acid sequence identity at with known Catharanthus genes. Note that the 16OMT is actually involved in the biosynthesis or the MIA, 16-methoxytabersonine.

2 Supplemental Table 4: CROLF1NG genes related to lipid biosynthesis. Name Category Description Hit ID Evalue CL5Contig1 LTP lipid transfer protein [Helianthus annuus] gi CL26Contig1 LTP putative lipid transfer protein [Solanum tuberosum] gi CL33Contig1 LTP lipid transfer protein precursor [Davidia involucrata] gi CL84Contig1 NADP-ME malate dehydrogenase [Nicotiana tabacum] gi CL135Contig1 CoA ligase 3-ketoacyl-CoA synthase [Gossypium hirsutum], CUT1 gi CL217Contig1 hydrolase carboxylic ester hydrolase/ hydrolase, acting on ester bonds [Arabidopsis thaliana] gi CL215Contig1 FA desaturase stearoyl-acyl carrier protein desaturse [Sesamum indicum] gi CL295Contig1 hydrolase carboxylic ester hydrolase/ hydrolase, acting on ester bonds [Arabidopsis thaliana] gi CL308Contig1 LTP lipid transfer protein, putative [Arabidopsis thaliana] gi CL371Contig1 Enolase (2-phosphoglycerate dehydratase) [Ricinus communis] gi CL483Contig1 FA desaturase sphingolipid delta-8 desaturase [Primula farinosa] gi CL386Contig1 putative phosphoglycerate mutase [Oryza sativa (japonica cultivar-group)] gi CL391Contig1 FA elongase fatty acid elongase-like protein (cer2-like) [Arabidopsis thaliana] gi CL435Contig1 lipid binding Cytosolic fatty-acid binding; Actin-crosslinking proteins [Medicago truncatula] gi CL473Contig1 FA elongase fatty acid elongase-like protein (cer2-like) [Arabidopsis thaliana] gi CL1042Contig1 FA desaturase chloroplast fatty acid desaturase 6 [Olea europaea subsp. europaea] gi CL966Contig1 lipase catalytic/ hydrolase [Arabidopsis thaliana] gi CL876Contig1 hydrolase Lipolytic enzyme, G-D-S-L [Medicago truncatula] gi CL1080Contig1 dehydrogenase ACX4 (ACYL-COA OXIDASE 4); oxidoreductase [Arabidopsis thaliana] gi CL1106Contig1 CoA ligase putative long-chain acyl-coa synthetase [Arabidopsis thaliana] gi CL696Contig1 FA desaturase Omega-3 fatty acid desaturase, chloroplast precursor gi CL684Contig1 thiolase 3-ketoacyl-CoA thiolase 2, peroxisomal precursor, putative, expressed [Oryza sativa (japonica cultivar-group)] gi CL823Contig1 acyltransferase 3-ketoacyl-ACP synthase [Cuphea pulcherrima] gi CL459Contig1 NADP-ME malate dehydrogenase [Glycine max] gi CL797Contig1 lipid binding lipid binding [Arabidopsis thaliana] gi CL746Contig1 esterase acyl-coa thioesterase/ catalytic/ hydrolase [Arabidopsis thaliana] gi CL746Contig1 hydrolase acyl-coa thioesterase/ catalytic/ hydrolase, acting on ester bonds [Arabidopsis thaliana] gi CL589Contig1 LTP lipid transfer protein [Helianthus annuus] gi CL864Contig1 NADP-ME putative 3-isopropylmalate dehydratase, small subunit [Arabidopsis thaliana] gi CL986Contig1 LTP Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor [Medicago truncatula] gi B08 CoA ligase acyl-coa synthetase [Brassica napus] gi E03 Tetrafunctional protein of glyoxysomal fatty acid beta-oxidation [Brassica napus] gi G06 lipoxygenase [Nicotiana attenuata] gi F08 esterase phospholipase D-alpha [Cucumis melo var. inodorus] gi D02 LTP glycolipid transfer protein-like [Oryza sativa (japonica cultivar-group)] gi E12 NADP-ME 3-isopropylmalate dehydratase large subunit [Medicago truncatula] gi G04 CoA ligase acyl-activating enzyme 17 [Arabidopsis thaliana] gi C01 FA elongase putative fatty acid elongase [Tropaeolum majus] gi C04 ATPase, coupled to transmembrane movement of ions, phosphorylative mechanism [Arabidopsis thaliana] gi H01 esterase phospholipase D delta isoform 1a [Gossypium hirsutum] gi B07 FA desaturase stearoyl-acp desaturase, chloroplast precursor [Olea europaea] gi F06 phospholipid hydroperoxide glutathione peroxidase [Lycopersicon esculentum] gi E02 CoA ligase putative beta-ketoacyl-coa synthase [Oryza sativa (japonica cultivar-group)] gi F12 putative sulfolipid synthase [Oryza sativa (japonica cultivar-group)] gi A04 esterase Esterase/lipase/thioesterase [Medicago truncatula] gi

3 043-B07 putative phospholipid cytidylyltransferase [Arabidopsis thaliana] gi F04 NADP-ME cytosolic malate dehydrogenase [Lycopersicon esculentum] gi H12 vacuolar proton ATPase proteolipid subunit-like protein [Solanum tuberosum] gi C12 lipase triacylglycerol lipase like protein [Arabidopsis thaliana] gi D09 lipid binding lipid binding [Arabidopsis thaliana] gi G08 lipid binding lipid binding [Arabidopsis thaliana] gi G08 lipid binding lipid binding [Arabidopsis thaliana] gi E03 LTP lipid transfer protein [Catharanthus roseus] gi C02 lipid binding Cytosolic fatty-acid binding; Actin-crosslinking proteins [Medicago truncatula] gi E07 acyltransferase acyltransferase [Arabidopsis thaliana] gi E07 DAG synthase Monogalactosyldiacylglycerol synthase [Medicago truncatula] gi F01 putative sulfolipid synthase [Oryza sativa (japonica cultivar-group)] gi E03 lipase triacylglycerol lipase [Arabidopsis thaliana] gi E03 lipase triacylglycerol lipase [Arabidopsis thaliana] gi C02 FA desaturase microsomal delta-12 oleate desaturase [Olea europaea] gi FA 018-B11 dehydratase putative beta-hydroxyacyl-acp dehydratase [Oryza sativa (japonica cultivar-group)] gi

4 Supplemental Table 5: CROLF1NG genes related to methyltransferases. Gene Name Description Hit ID Evalue (LAMT) CL57Contig1 SAM dependent carboxyl methyltransferase [Medicago truncatula] gi Methionine synthase CL69Contig1 methionine synthase (Vitamin-B12-independent methionine synthase isozyme) [Catharanthus roseus] gi CL166Contig1 gamma-tocopherol methyltransferase [Lycopersicon esculentum] gi CL557Contig1 SHM4 (SERINE HYDROXYMETHYLTRANSFERASE 4); glycine hydroxymethyltransferase [Arabidopsis thaliana] gi CL530Contig1 phosphoethanolamine N-methyltransferase [Lycopersicon esculentum] gi CL1003Contig1 putative methyltransferase [Oryza sativa (japonica cultivar-group)] gi CL1104Contig1 putative methyltransferase [Solanum tuberosum] gi B05 SHM1 (SERINE HYDROXYMETHYLTRANSFERASE 1); glycine hydroxymethyltransferase [Arabidopsis thaliana] gi H11 Aminomethyltransferase, mitochondrial precursor [Solanum tuberosum] gi SMT 169-E03 S-methyltransferase [Catharanthus roseus] gi (S)-coclaurine-N-methyltransferase/cyclopropane-fatty-acyl-phospholipid synthase [Arabidopsis 027-E08 thaliana] gi C04 phosphoethanolamine N-methyltransferase [Lycopersicon esculentum] gi F08 DNA (cytosine-5)-methyltransferase [Lycopersicon esculentum] gi G08 gamma-tocopherol methyltransferase [Helianthus annuus] gi D05 glycine hydroxymethyltransferase [Arabidopsis thaliana] gi B08 Aminomethyltransferase, mitochondrial precursor [Flaveria pringlei] gi D12 O-methyltransferase [Mesembryanthemum crystallinum] gi COMT 101-B09 caffeic acid O-methyltransferase [Catharanthus roseus] gi F03 O-methyltransferase, family 2 [Medicago truncatula] gi A02 O-methyltransferase [Mesembryanthemum crystallinum] gi D02 SAM (and some other nucleotide) binding motif; Skb1 methyltransferase [Medicago truncatula] gi Genes shown in bold characters are clones with perfect amino acid sequence identity at with known Catharanthus genes or with genes characterized in the present study (LAMT).

5 Supplemental Table 6: CROLF1NG genes related to acyltransferases. While DAT appears to be the only acyltransferase involved in vindoline biosynthesis several putative acyltransferases including one with similarity to vinorine synthase from Rauvolfia serpentina (Bayer et al., 2004) were identified. Vinorene synthase catalyzes the formation of vinorine, which is an intermediate for the antiarrhythmic drug ajmaline in Rauvolfia, also shows some similarity (20%) to DAT from Catharanthus and to salutaridinol acyltransferase (Grothe et al, 2001) from Papaver somniferum. The biological role of this enzyme in relation to MIA biosynthesis should be considered. Bayer, A., Ma, X., and Stöckigt, J. (2004). Acyltransfer in natural product biosynthesis: functional cloning and molecular analysis of vinorine synthase. Bioorg. Med. Chem. 12, Grothe, T., Lenz, R., and Kutchan, T.M. (2001). Molecular Characterization of the Salutaridinol 7-O-Acetyltransferase Involved in Morphine Biosynthesis in Opium Poppy Papaver somniferum. J. Biol. Chem. 276, Supplemental Table 6: Acyltransferases in CROLF1NG Name Description Hit ID Evalue CL101Contig1 1-acylglycerol-3-phosphate O-acyltransferase/ acyltransferase [Arabidopsis thaliana] gi CL334Contig1 N-hydroxycinnamoyl-CoA:tyramine N-hydroxycinnamoyl transferase THT7-8 [Lycopersicon esculentum] gi CL429Contig1 Phospholipid/glycerol acyltransferase [Medicago truncatula] gi CL943Contig1 lecithine cholesterol acyltransferase-like protein [Medicago truncatula] gi CL928Contig1 putative dihydrolipoamide S-acetyltransferase [Arabidopsis thaliana] gi CL646Contig1 glutamate N-acetyltransferase [Arabidopsis thaliana] gi E02 putative malonyl-coa:acyl carrier protein transacylase [Arabidopsis thaliana] gi C05 3-oxoacyl-[acyl-carrier-protein] synthase-like protein [Arabidopsis thaliana] gi E03 3-oxoacyl-[acyl-carrier-protein] synthase [Capsicum chinense] gi A05 dihydrolipoamide S-acetyltransferase, putative [Arabidopsis thaliana] gi E12 acetyl Co-A acetyltransferase [Hevea brasiliensis] gi B05 N-acetyltransferase [Arabidopsis thaliana] gi B08 vinorine synthase [Rauvolfia serpentina] gi G11 1-acylglycerol-3-phosphate O-acyltransferase/ acyltransferase [Arabidopsis thaliana] gi H10 N-acetyltransferase [Arabidopsis thaliana] gi F07 Phospholipid/glycerol acyltransferase [Medicago truncatula] gi E02 putative malonyl-coa:acyl carrier protein transacylase [Arabidopsis thaliana] gi C05 3-oxoacyl-[acyl-carrier-protein] synthase-like protein [Arabidopsis thaliana] gi E03 3-oxoacyl-[acyl-carrier-protein] synthase [Capsicum chinense] gi A05 dihydrolipoamide S-acetyltransferase, putative [Arabidopsis thaliana] gi

6 Supplemental Table 7: CROLF1NG genes related Cytochrome P450-dependent monooxygenases (CYPs). Multiple steps in MIA biosynthesis involve reactions catalyzed by CYPs. There are three CYPs that have been cloned and functionally characterized: namely G10H (represented by 1 in CROLFING), SLS (represented 25 times in CROLFING) and T16H (represented 4 times in CROLFING) (Table 1). In addition, deoxyloganin 7 hydroxylase (DL7H) enzyme activity was first identified in C. roseus microsomes (Irmler et al., 2000) that converted 7-deoxyloganin into loganin only in the presence of NADPH. Although more studies are required, the CYPs represented by CL19Contig3 (represented 5 times in CROLFING) and 110-F10 (represented 1 time in CROLFING) could be good DL7H candidates (Supplemental Table 7). For example the CYP represented by CL19Contig3 shows 100%, 98 % and 97 % amino acid sequence identity to CYP72B (AAA ), CYP72C (AAA ) and to SLS (AAA ), respectively. Name Description Hit ID Evalue CL19Contig4 Secologanin synthase [Catharanthus roseus] gi SLS (CYP72A) G10H-like CL34Contig1 cytochrome P450 [Catharanthus roseus] gi (Kelly) CL146Contig1 cytochrome P450 [Solanum tuberosum] gi CL19Contig3 cytochrome P450 gi CYP72B CL201Contig1 cytochrome P450 [Catharanthus roseus] gi CYP96 CL219Contig1 CYP77A3p [Glycine max] gi CL288Contig1 cytochrome P450 [Catharanthus roseus] gi T16H CL241Contig1 cytochrome P450 [Catharanthus roseus] gi G10H-like (Kelly) CL399Contig1 cytochrome P450 monooxygenase CYP716A [Medicago truncatula] gi CL19Contig2 cytochrome P450 gi CYP72 CL965Contig1 cinnamate 4-hydroxylase (CYP73) [Catharanthus roseus] gi CL19Contig1 cytochrome P450 gi CYP72 CL1119Contig1 cytochrome P450 monooxygenase CYP716A [Medicago truncatula] gi F10 cytochrome P450 gi CYP72C 027-H04 cytochrome P450 [Catharanthus roseus] gi G10H-like (Kelly) 102-F12 cytochrome P450 monooxygenase CYP72B [Medicago truncatula] gi B05 cytochrome P450 71D2 [Catharanthus roseus] gi CYP71D2 028-H03 cytochrome P450 monooxygenase CYP82A [Medicago truncatula] gi A08 cytochrome P450 [Cicer arietinum] gi F10 putative cytochrome P450 [Glycine max] gi B01 CYP77A2 [Solanum melongena] gi Gene

7 Supplemental Table 8: CROLF1NG genes related to glycosyltransferases Glycosylation of natural products will significantly increase their water solubility, their stability, and will affect their subcellular localization and/or transport between cells (Gachon et al., 2005). The biosynthesis of MIAs involves a glucosylation for the conversion of 7-deoxyloganetic acid into 7-deoxyloganic acid that has yet to be characterized in detail. This 7-deoxyloganetic acid 1-O-glycosyltransferase (7DLGT), first detected in extracts from Lonicera japonica cell cultures (Yamamoto et al., 2002), appears to play an important role in stabilizing reactive iridoid intermediates that accumulate in certain members of the family. While this gene remains to be cloned, its suggested localization to Catharanthus leaf epidermis (Murata and De Luca, 2005) suggests that the 23 putative glycosyltransferases (GTs) from the CROLF1NG dataset could harbor 7DLGT (Supplemental Table 8). In this context, it is interesting that only one of these putative GTs (CL972Contig1) found in both the CROLF1NG (2 s) and root tip (CrUniGene) dataset could be a good putative 7DLGT candidate to investigate. Gachon, C.M.M., Langlois-Meurinne, M., and Saindrenan, P. (2005). Plant secondary metabolism glycosyltransferases: the emerging functional analysis. Trends Plant Sci.10, Name Description Hit ID Evalue CL398Contig1 alpha-1,6-xylosyltransferase [Gossypium raimondii] gi CL795Contig1 transferase, transferring glycosyl groups [Arabidopsis thaliana] gi CL647Contig1 4-alpha-glucanotransferase precursor [Solanum tuberosum] gi CL585Contig1 QUA1 (QUASIMODO1); transferase, transferring glycosyl groups / transferase, transferring hexosyl groups [Arabidopsis thaliana] gi CL773Contig1 transferase, transferring glycosyl groups [Arabidopsis thaliana] gi CL1000Contig1 putative glycosyltransferase [Ipomoea trifida] gi CL972Contig1 glycosyltransferase 1 [Ipomoea trifida] gi D11 transferase, transferring glycosyl groups / transferase, transferring hexosyl groups [Arabidopsis thaliana] gi B08 putative oligosaccharyl transferase STT3 protein [Vitis vinifera] gi F09 putative glycosyltransferase [Nicotiana benthamiana] gi C11 UDP-glucose glucosyltransferase [Catharanthus roseus] gi D10 glycosyltransferase 10 [Ipomoea trifida] gi E03 arbutin synthase [Rauvolfia serpentina] gi H06 glucosyltransferase-2 [Vigna angularis] gi A04 UDP-glycosyltransferase/ transferase, transferring glycosyl groups / transferase, transferring hexosyl groups [Arabidopsis thaliana] gi F12 cyclo-dopa 5-O-glucosyltransferase [Celosia cristata] gi C11 putative glucosyltransferase-2 [Oryza sativa (japonica cultivar-group)] gi G02 UDP-glycosyltransferase/ transferase, transferring glycosyl groups [Arabidopsis thaliana] gi C02 UDP-glucose:salicylic acid glucosyltransferase [Nicotiana tabacum] gi E10 UDP-glucose glucosyltransferase [Fragaria x ananassa] gi F05 putative anthocyanidine rhamnosyl-transferase [Capsicum annuum] gi A03 thiohydroximate S-glucosyltransferase [Brassica rapa subsp. pekinensis] gi B10 UDP-glucose glucosyltransferase [Catharanthus roseus] gi

8 Supplemental Table 9: CROLF1NG genes related to 2-oxoglutarate dependent dioxygenases. Dioxygenases are involved in the oxidation of diverse class of metabolites including flavonoids, carotenoids and lipids. In addition to four dioxygenases listed as flavonoid biosynthesis-related genes in Supplemental Table 3, five other genes with similarity to known dioxygenases were identified (Supplemental Table 9). In the case of the MIA biosynthesis, the hydroxylation of deacetoxyvindoline was shown to be catalyzed by the dioxygenase D4H (Vázquez-Flota et al., 1997), but this gene was not represented in the dataset. This is not surprising since previous studies localized both D4H and DAT to Catharanthus mesophyll idioblasts and laticifers (St. Pierre et al., 1999). Vazquez-Flota, F., De Carolis, E., Alarco, A.M., and De Luca, V. (1997). Molecular cloning and characterization of desacetoxyvindoline-4-hydroxylase, a 2-oxoglutarate dependent-dioxygenase involved in the biosynthesis of vindoline in Catharanthus roseus (L.) G. Don. Plant Mol Biol 34, Name Description Hit ID Evalue CL221Contig1 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase 3 (Aci-reductone dioxygenase 3) gb AAW [Arabidopsis thaliana] gi CL836Contig1 Glyoxalase/bleomycin resistance protein/dioxygenase [Medicago truncatula] gi CL885Contig1 2-nitropropane dioxygenase-like protein [Arabidopsis thaliana] gi F09 putative prolyl 4-hydroxylase, alpha subunit [Arabidopsis thaliana] gi E04 Glyoxalase/bleomycin resistance protein/dioxygenase [Medicago truncatula] gi

9 Supplemental Table 10: CROLF1NG genes related to transcription factors. Transcriptional control of gene expression is a key regulatory step in triggering morphological and biochemical changes that lead to specialized cells for MIA biosynthesis. The CROLF1NG dataset contained all three previously characterized ORCA3, ZCT2 and BPF1, respectively, classified into AP2/ERF, Zinc finger and bhlh type transcription factors (Table 1). The transcriptional activator ORCA3 is known to activate multiple MIA biosynthesis genes in Catharanthus cell cultures (van der Fits and Memelink, 2000) including the leaf epidermis localized TDC and STR (Table 1, St. Pierre et al., 1999). On the other hand, ZCT2 repressed the transcription of the reporter genes that were fused to TDC and STR promoter sequences (Pauw et al., 2004), suggesting that ZCT2 might act as a transcriptional repressor, while the biological function of BPF1 is still not clear (van der Fitz et al., 2000). Extensive studies with these transcription factors, however, only revealed the complexity of the transcriptional regulation of MIA pathway genes. For example, ORCA3 did not seem to play a major role in controlling the expression of all the MIA pathway genes (van der Fitz and Memelink, 2000). While ORCA3 itself seems to be expressed throughout the leaf tissue (Murata and De Luca, 2005), the expression of SGD was not affected by overexpression of ORCA3 (van der Fits and Memelink, 2000), indicating that ORCA3 might not be involved in the activation of transcription of SGD in leaf epidermis. These data imply that other transcription factors are probably required for SGD expression as well as later steps in MIA biosynthesis in leaf epidermal cells. Category Name Description Hit ID Evalue TF CL250Contig1 ribonuclease/ transcriptional repressor [Arabidopsis thaliana] gi TF CL214Contig1 unknown protein [Oryza sativa (japonica cultivar-group)] gi TF CL504Contig1 unknown protein [Arabidopsis thaliana] gi TF CL1109Contig1 SPL14 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 14); DNA binding / transcription factor [Arabidopsis thaliana] gi TF 149-G04 transcription regulator [Arabidopsis thaliana] gi TF 142-A06 transcription factor DP1 [Populus tremula x Populus tremuloides] gi TF 053-H01 putative CCR4-associated factor [Arabidopsis thaliana] gi TF 031-F06 transcriptional activator [Arabidopsis thaliana] gi TF 015-A06 Transcriptional factor B3 [Medicago truncatula] gi TF, AP2 CL258Contig1 Ethylene-responsive transcription factor 4 [Nicotiana sylvestris] gi TF, AP2 CL936Contig1 ethylene-responsive element binding protein [Nicotiana tabacum] gi TF, AP2 CL915Contig1 DNA binding / transcription factor [Arabidopsis thaliana] gi TF, AP2 118-A07 AP2-domain DNA-binding protein [Catharanthus roseus], ORCA3 gi TF, AP2 015-D04 AP2-domain DNA-binding protein [Catharanthus roseus] gi TF, AP2 130-G03 putative AP2/EREBP transcription factor [Arabidopsis thaliana] gi TF, AP2 064-E09 Pathogenesis-related transcriptional factor and ERF [Medicago truncatula] gi TF, AP2 027-D09 ethylene-responsive element binding protein [Nicotiana tabacum] gi TF, bhlh CL1107Contig1 transcription factor [Arabidopsis thaliana] gi TF, bhlh CL1070Contig1 DNA binding / transcription factor [Arabidopsis thaliana] gi TF, bhlh 112-E02 DNA binding / transcription factor [Arabidopsis thaliana] gi TF, bhlh 110-E08 DNA binding / transcription factor [Arabidopsis thaliana] gi TF, bhlh 104-F03 DNA binding / transcription factor [Arabidopsis thaliana] gi TF, bhlh 057-A08 hypothetical protein [Arabidopsis thaliana] gi TF, bhlh 010-C09 DNA binding / transcription factor [Arabidopsis thaliana] 1

10 TF, bhlh 010-C09 DNA binding / transcription factor [Arabidopsis thaliana] gi TF, bzip CL918Contig1 DNA binding / transcription factor [Arabidopsis thaliana] gi TF, bzip 125-H11 DNA binding / transcription factor [Arabidopsis thaliana] gi TF, bzip 119-G01 bzip transcription factor, bzip_1 [Medicago truncatula] gi TF, bzip 104-F10 Eukaryotic transcription factor, DNA-binding [Medicago truncatula] gi TF, CCAAT 010-A04 transcription factor [Arabidopsis thaliana] gi TF, CSN6a 119-D02 transcription factor-like; similar to CH6 and COP9 complex subunit 6 [Arabidopsis thaliana] gi TF, GRAS 015-E07 SCARECROW transcriptional regulator-like [Arabidopsis thaliana] gi TF, GRAS 126-G08 SCL3; transcription factor [Arabidopsis thaliana] gi TF, GRAS 015-E07 SCARECROW transcriptional regulator-like [Arabidopsis thaliana] gi TF, GT D05 GT-like trihelix DNA-binding protein, putative [Arabidopsis thaliana] gi TF, helicase 035-F02 putative SNF2 subfamily ATPase [Arabidopsis thaliana] gi TF, HMG CL723Contig1 HMG protein [Catharanthus roseus] gi TF, HMG 154-G09 HMG protein [Catharanthus roseus] gi TF, HSF 005-A10 heat stress transcription factor HSFA9 [Helianthus annuus] gi TF, MADS CL361Contig1 MADS box transcription factor [Ipomoea batatas] gi TF, MYB CL87Contig1 myb-related transcription factor LBM2 [Nicotiana tabacum] gi TF, MYB 128-A08 MYB-like DNA-binding protein [Catharanthus roseus], BPF1 gi TF, MYB 047-E02 DNA binding / transcription factor [Arabidopsis thaliana] gi TF, NAC CL613Contig1 BTF3 [Nicotiana benthamiana] gi TF, NAC 011-E12 NAC2; transcription factor [Arabidopsis thaliana] gi TF, polii CL384Contig1 putative transcription initiation factor [Oryza sativa (japonica cultivar-group)] gi TF, polii 037-A11 ATP binding / RNA polymerase II transcription factor [Arabidopsis thaliana] gi TF, polii coactivator 056-D12 KIWI; DNA binding / transcription coactivator [Arabidopsis thaliana] gi TF, SNF5 007-F09 BSH [Arabidopsis thaliana] gi TF, SWI/SNF 141-A03 putative SWI/SNF family transcription activator [Arabidopsis thaliana] gi TF, TFIIe CL1113Contig1 Transcription initiation factor IIE beta subunit, putative, expressed [Oryza sativa (japonica cultivar-group)] gi TF, WRKY CL954Contig1 transcription factor WRKY4 [Petroselinum crispum] gi TF, WRKY CL857Contig1 WRKY transcription factor NtEIG-D48 [Nicotiana tabacum] gi TF, WRKY CL666Contig1 DNA-binding protein 3 [Nicotiana tabacum] gi TF, ZF CL98Contig1 transcription factor [Arabidopsis thaliana] gi TF, ZF CL822Contig1 nucleic acid binding / transcription factor/ zinc ion binding [Arabidopsis thaliana] gi TF, ZF CL1028Contig1 transcription factor lim1 [Eucalyptus camaldulensis] gi TF, ZF 158-E02 zinc finger DNA-binding protein [Catharanthus roseus], ZCT2 gi TF, ZF 131-H04 Transcription factor jumonji, jmjc [Medicago truncatula] gi REF6 (RELATIVE OF EARLY FLOWERING 6); nucleic acid binding / transcription factor/ zinc ion binding TF, ZF 021-B06 [Arabidopsis thaliana] gi TF, ZF-HD CL934Contig1 transcription factor [Arabidopsis thaliana] gi TF, ZF-HLH CL988Contig1 YABBY-like transcription factor GRAMINIFOLIA [Antirrhinum majus] gi Genes that are shown in bold characters are the clones with perfect amino acid sequence identity at with known Catharanthus genes