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Supplementary Table 2 Transcript derived fragments upregulated in ‘Dangui’ and homologous sequences No. Length (bp) Identity Functional category Functions or pathways Homologous sequence D1 102 83 Unkown Unkown Solanum lycopersicum uncharacterized LOC101253934 (LOC101253934), mRNA D2 110 90 Metabolism Synthesis of protein Syringa reflexa voucher Li 3614 trnK gene, partial sequence D3 107 71 Metabolism Tricarboxylic acid cycle Prunus cerasifera pyruvate decarboxylase (PDC) mRNA, complete cds D4 223 80 Metabolism Tricarboxylic acid cycle Solanum tuberosum ATP-citrate synthase alpha chain protein 2-like mRNA Signal transduction Signal transduction Response to stimulus Responsible for vegetative incompatibility Solanum tuberosum vegetative incompatibility protein HET-E-1- like mRNA Protein ubiquitination Solanum lycopersicum E3 ubiquitin-protein ligase UPL3-like mRNA Plant stress response Glycine max heat shock 70 kDa protein, mitochondrial-like (LOC100811003), mRNA Metabolism Phagocytosis Ricinus communis cysteine protease, putative, mRNA Catharanthus roseus allene oxide synthase mRNA, complete cds D5 204 68 D6 108 80 D7 352 78 D8 72 88 D9 110 75 Metabolism Resistance to pathogen，Jasmonic acid synthesis pathway D10 154 73 Metabolism Metabolism of a toxic substance Citrus sinensis carboxylesterase 1-like (LOC102608476), mRNA D11 81 85 Metabolism Catalyze glucosyl transfer Olea europaea putative glucosyltransferase mRNA Salt stress Solanum lycopersicum CBL-interacting protein kinase 14 (CIPK14), mRNA D12 117 78 Signal transduction D13 141 85 Metabolism Catalyze glycosyl transfer Forsythia x intermedia RengUGT11 mRNA for UDP-sugar:glycosyltransferase D14 158 80 Metabolism Fatty acid metabolism Vitis vinifera medium-chain-fatty-acid-CoA ligase-like (LOC100244843), mRNA D15 113 81 Metabolism Catalyze hydrolysis of fats Arabidopsis thaliana lipase class 3 family protein mRNA Protein ubiquitination Vitis vinifera U-box domain-containing protein 33-like (LOC100267999), mRNA Metabolic pathway of phenylpropanoid pathway Olea europaea isoflavone reductase-like protein mRNA Hormonal signal transduction Nicotiana tabacum LRR receptor-like protein kinase mRNA, complete cds Unkown Solanum tuberosum uncharacterized LOC102588097 (LOC102588097), mRNA Protein degradation Solanum lycopersicum proteasome subunit alpha type-2-B-like, mRNA Plant defence responses Ricinus communis ccr4-associated factor, putative, mRNA Unkown Citrus sinensis uncharacterized LOC102626856 (LOC102626856), mRNA D16 102 73 D17 108 93 D18 111 92 D19 203 82 Signal transduction Secondary metabolism Signal transduction Unkown D20 217 88 Metabolism D21 132 81 D22 166 83 Signal transduction Unkown D23 285 76 Metabolism Vesicular Transport Fragaria vesca subsp. vesca coatomer subunit zeta-1-like (LOC101300742), mRNA D24 145 78 Signal transduction Regulate physiological functions Catharanthus roseus adenosine-5’-phosphosulfate-kinase (CRakn) mRNA D25 199 79 Transport Transport of D-xylose Citrus sinensis D-xylose-proton symporter-like 2-like (LOC102610785), mRNA D26 130 84 Metabolism Photosynthesis Ricinus communis ribulose-bisphosphate carboxylase, putative, mRNA Phosphorylation of glycerol Solanum lycopersicum glycerol kinase-like (LOC101259139), mRNA Unkown Cucumis sativus uncharacterized LOC101207080 (LOC101207080), mRNA Solanum tuberosum probable protein phosphatase 2C 52-like (LOC102596312), mRNA D27 80 59 D28 119 70 Signal transduction Unkown D29 103 79 Metabolism D30 108 76 D31 154 77 D32 83 87 Photosynthesis and Energy Signal transduction Hydrolysis of phospholipids ATP hydrolysis Glycine max ATPase ASNA1 homolog (LOC100819315), mRNA Endocytic process Solanum lycopersicum clathrin interactor EPSIN 2-like (LOC101265874), mRNA Transport Phosphate transport Populus trichocarpa mitochondrial phosphate transporter family protein mRNA Stress signal transduction Solanum tuberosum CDPK-related kinase 1-like (LOC102591187), mRNA D33 117 85 Signal transduction D34 129 84 Metabolism Lipid metabolism Nicotiana tabacum mRNA for S-adenosyl-L-homocysteine hydrolase Hormonal signal transduction Solanum tuberosum probable receptor-like protein kinase At1g30570-like, mRNA D35 169 73 Signal transduction D36 129 80 Metabolism Protein degradation Citrus sinensis autophagy-related protein 3-like (LOC102615659), mRNA D37 93 78 Metabolism Store the iron Coffea arabica cultivar Mundo novo ferritin (Fer1) mRNA D38 97 80 Metabolism Translation initiation Glycine max translation initiation factor IF-2, mitochondrial-like mRNA D39 86 81 Metabolism Catalyze glycosyl transfer Vitis vinifera UDP-glycosyltransferase 74F2-like (LOC100242294), mRNA D40 105 89 Metabolism Plant isoprenoid pathway Eleutherococcus senticosus 3-hydroxy-3-methylglutaryl coenzyme A reductase mRNA D41 188 80 Protein degradation Olea europaea polyubiquitin OUB1 mRNA D42 97 74 Signal transduction Unkown Unkown Solanum tuberosum uncharacterized LOC102582751 (LOC102582751), mRNA D43 143 80 Unkown Unkown Solanum lycopersicum uncharacterized LOC101251041 (LOC101251041), mRNA D44 171 70 Metabolism Hydrolysis of proteins Ricinus communis serine carboxy peptidase, putative, mRNA D45 121 88 Metabolism Sugar metabolism Arabidopsis lyrata subsp. lyrata xylose isomerase family protein, mRNA D46 205 79 Metabolism Sugar metabolism D47 155 76 Metabolism Abiotic stress response in plants Medicago truncatula 2,3-bisphosphoglycerate-independent phosphoglycerate mutase mRNA Solanum tuberosum beta-1,4-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyl -transferase like mRNA D48 337 84 D49 88 76 D50 116 76 D51 169 72 D52 107 94 D53 94 79 D54 84 D55 146 Metabolism Response to stimulus Signal transduction Signal transduction Secondary metabolism Synthesis of cysteine Ricinus communis cysteine synthase, putative, mRNA Plant defense response Fragaria vesca subsp. vesca peroxidase 63-like (LOC101293677), mRNA Regulate endoplasmic reticulum calcium homeostasis Involved in mRNA export coupled transcription activation Oryzias latipes 78 kDa glucose-regulated protein-like (LOC101157378), mRNA Vitis vinifera enhancer of yellow 2 transcription factor homolog mRNA Synthesis of geraniol Olea europaea geraniol synthase 1 (GES1) mRNA Metabolism Sugar metabolism Picrorhiza kurrooa UDP-glucosyltransferase isoform 1 mRNA 80 Metabolism Synthesis of fatty acid Nicotiana tabacum acetyl-CoA carboxylase (ACC) mRNA 75 Metabolism Hydrolysis of phospholipids Solanum lycopersicum phospholipase PLDa2 (PLDa2), mRNA Regulate phenylpropanoid metabolic pathway Petunia exserta MYB transcription factor EOBII (EOBII) mRNA Catalyze the transfer of a methyl Solanum tuberosum methyltransferase-like protein 2-like (LOC102588464), mRNA D56 72 83 Signal transduction D57 88 75 Metabolism Supplementary Table 3 Transcript derived fragments upregulated in ‘Yingui’ and homologous sequences No. Length (bp) Identity Functional category Signal transduction Photosynthesis and Energy Y1 59 86 Y2 160 73 Y3 102 84 Metabolism Purine biosynthesis Y4 143 84 Transport Sugar transport Y5 95 96 Metabolism Encoding ribosomal proteins Fraxinus excelsior isolate frax207 rpl16-like (rpl16) gene Y6 75 73 Signal transduction Phosphorylation of proteins Zea mays putative protein kinase superfamily protein (LOC100279292), mRNA Y7 85 79 Metabolism Sugar metabolism Solanum tuberosum alkaline/neutral invertase CINV2-like (LOC102602949) mRNA Y8 68 84 Metabolism Sugar metabolism Coffea canephora sucrose synthase (SS2) mRNA, partial cds Y9 204 78 Metabolism Tricarboxylic acid cycle Ricinus communis 2-oxoisovalerate dehydrogenase, putative, mRNA ATP hydrolysis to generate energy Mitochondrial electron transport chain Functions or pathways Homologous sequence RNA editing Arabidopsis thaliana RNA recognition motif-containing protein mRNA Oxidative phosphorylation Vitis vinifera probable NADH dehydrogenase-like (LOC100253444), mRNA Populus balsamifera isolate WHR03 haplotype B amidophosphoribosyltransferase gene Solanum tuberosum probable sugar phosphate/phosphate translocator At2g25520-like mRNA Y10 200 73 Photosynthesis and Energy Y11 148 82 Transport Y12 176 77 Unkown Unkown Solanum tuberosum uncharacterized LOC102603976 (LOC102603976), mRNA Populus trichocarpa radical SAM domain-containing family protein mRNA Vitis vinifera calcium-transporting ATPase 10, plasma membrane- type-like , mRNA Solanum lycopersicum thylakoid membrane protein slr0575-like mRNA Y13 117 85 Metabolism Involved in many biological processes Y14 108 95 Response to stimulus Plant stress response Vitis vinifera calreticulin-like (LOC100256319), mRNA Y15 92 82 Metabolism Polyamine biosynthesis pathway Persea americana arginine decarboxylase gene Solanum lycopersicum probable acyl-activating enzyme 6-like mRNA Y16 95 79 Metabolism Catalyze the activation of carboxylic acids Y17 152 89 Defence response Pathogenesis-related Olea europaea pathogenesis-related thaumatin-like protein mRNA Signal transduction Signal transduction Response to stimulus Photosynthesis and Energy Efficient homologous recombination Citrus sinensis AP-5 complex subunit mu-like (LOC102630193), mRNA Regulate gene expression Glycine max BTB/POZ domain-containing protein At1g63850-like mRNA Plant stress response Solanum tuberosum probable indole-3-acetic acid-amido synthetase GH3.5-like mRNA Y18 144 81 Y19 94 82 Y20 92 85 Y21 102 94 Y22 92 97 Metabolism ATP hydrolysis to generate energy Triacylglyceride synthesis pathway Olea europaea putative apyrase mRNA Olea europaea cultivar Koroneiki diacylglycerol acyltransferase type 2 mRNA Oxidation decomposition of unsaturated fatty acids Involved in chloroplast and mitochondrial RNA processing Y23 117 89 Metabolism Y24 121 79 Metabolism Y25 74 55 Defence response DNA repair Fragaria vesca subsp. vesca DNA repair and recombination protein pif1, mRNA Y26 134 90 Metabolism Hydrolysis of phosphoinositide Solanum lycopersicum phosphoinositide phospholipase C 6-like mRNA Y27 74 84 Metabolism Transcription initiation Solanum tuberosum transcription initiation factor TFIID subunit 2-like mRNA Y28 110 82 Transport Potassium transport Solanum lycopersicum potassium transporter 4-like (LOC101262083), mRNA Y29 83 76 Transport Phospholipid transport Arabidopsis thaliana ALA-interacting subunit 3 mRNA Hydrolysis of proteins Arabidopsis thaliana ATP-dependent protease La (LON) domain protein mRNA Regulate gene expression Populus trichocarpa speckle-type POZ family protein (POPTR_0427s00200g) mRNA Signal transduction Signal transduction Solanum lycopersicum peroxisomal 2,4-dienoyl-CoA reductase-like mRNA Vitis vinifera pentatricopeptide repeat-containing protein At4g28010-like mRNA Y30 89 79 Y31 106 73 Y32 176 76 Metabolism Protein dephosphorylation Ricinus communis protein phosphatase 2a, regulatory subunit, putative, mRNA Y33 224 86 Signal transduction Transcription elongation Citrus sinensis transcription elongation factor B polypeptide 1-like mRNA Unsaturated fatty acid Metabolism Salicylic acid carboxyl methyl transfer Y34 111 86 Metabolism Y35 242 71 Metabolism Y36 261 70 Unkown Unkown Solanum tuberosum uncharacterized LOC102597453 (LOC102597453), mRNA Y37 73 84 Defence response Plant stress response Citrus sinensis pto-interacting protein 1-like (LOC102623610), mRNA ATP hydrolysis Solanum tuberosum phospholipid-transporting ATPase 3-like (LOC102587636), mRNA Unkown Solanum tuberosum uncharacterized LOC102589286 (LOC102589286), mRNA Secologanin synthsis Olea europaea cultivar Dolce d'Andria putative secologanin synthase (SLS2) mRNA Pathogen-associated protein Solanum lycopersicum PSTVd RNA-binding protein Virp1d (LOC543627), mRNA Y38 126 81 Photosynthesis and Energy Y39 141 79 Unkown Y40 135 91 Y41 75 81 Y42 181 80 Y43 116 84 Y44 90 87 Y45 194 69 Secondary metabolism Signal transduction Signal transduction Photosynthesis and Energy Response to stimulus Photosynthesis and Energy Phosphorylate phosphatidylinositol Cyanide resistant respiration pathway Olea europaea lipoxygenase mRNA Populus trichocarpa S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase (SAMT) mRNA Ricinus communis phosphatidylinositol 4-kinase, putative, mRNA Corylus heterophylla mitochondrial alternative oxidase 1A mRNA Plant stress response Camellia sinensis auxin response factor 1 mRNA Electron transport chain Hyoscyamus muticus cytochrome P450 hydroxylase (HPO) mRNA
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