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Figure S1. Heat Map of R (Pearson's Correlation Coefficient)

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Figure S1. Heat Map of R (Pearson's Correlation Coefficient) Figure S1. Heat map of r (Pearson’s correlation coefficient) value among different samples including replicates. The color represented the r value. Figure S2. Distributions of accumulation profiles of lipids, nucleotides, and vitamins detected by widely-targeted UPLC-MC during four fruit developmental stages. The colors indicate the proportional content of each identified metabolites as determined by the average peak response area with R scale normalization. PS1, 2, 3, and 4 represents fruit samples collected at 27, 84, 125, 165 Days After Anthesis (DAA), respectively. Three independent replicates were performed for each stages. Figure S3. Differential metabolites of PS2 vs PS1 group in flavonoid biosynthesis pathway. Figure S4. Differential metabolites of PS2 vs PS1 group in phenylpropanoid biosynthesis pathway. Figure S5. Differential metabolites of PS3 vs PS2 group in flavonoid biosynthesis pathway. Figure S6. Differential metabolites of PS3 vs PS2 group in phenylpropanoid biosynthesis pathway. Figure S7. Differential metabolites of PS4 vs PS3 group in biosynthesis of phenylpropanoids pathway. Figure S8. Differential metabolites of PS2 vs PS1 group in flavonoid biosynthesis pathway and phenylpropanoid biosynthesis pathway combined with RNA-seq results. Table S1. A total of 462 detected metabolites in this study and their peak response areas along the developmental stages of apple fruit. mix0 mix0 mix0 Index Compounds Class PS1a PS1b PS1c PS2a PS2b PS2c PS3a PS3b PS3c PS4a PS4b PS4c ID 1 2 3 Alcohols and 5.25E 7.57E 5.27E 4.24E 5.20E 2.99E 5.63E 2.21E 7.70E 3.10E 2.52E 2.82E 5.05E 2.30E 5.63E Mad216 Pantothenol -- polyols +03 +03 +03 +03 +03 +03 +03 +04 +03 +03 +03 +04 +03 +03 +03 Alcohols and 4.75E 4.94E 5.63E 5.45E 5.87E 5.79E 5.33E 4.37E 4.04E 6.23E 5.83E 5.01E 4.19E 4.52E 4.74E C00 Mad55 D-Sorbitol polyols +06 +06 +06 +06 +06 +06 +06 +06 +06 +06 +06 +06 +06 +06 +06 794 Alcohols and 1.41E 1.25E 1.48E 1.40E 1.37E 1.52E 1.47E 1.21E 1.12E 1.77E 1.61E 1.31E 1.13E 1.17E 1.26E C00 Mad56 D-Mannitol polyols +07 +07 +07 +07 +07 +07 +07 +07 +07 +07 +07 +07 +07 +07 +07 392 Alcohols and 3.31E 3.09E 2.93E 3.75E 3.58E 3.43E 4.65E 4.65E 3.37E 5.86E 5.72E 4.46E 2.82E 2.99E 3.08E C01 Mad805 Dulcitol polyols +06 +06 +06 +06 +06 +06 +06 +06 +06 +06 +06 +06 +06 +06 +06 697 Alcohols and 4.71E 3.10E 3.42E 9.00E 9.00E 9.00E 7.06E 7.99E 7.22E 7.58E 4.79E 5.93E 6.64E 1.25E 9.85E Mad850 1,5-Anhydro-D-glucitol -- polyols +04 +04 +04 +00 +00 +00 +04 +04 +04 +04 +04 +04 +04 +05 +04 1.40E 1.43E 1.63E 1.12E 1.15E 8.49E 2.45E 4.19E 5.20E 1.29E 8.42E 8.38E 2.29E 4.48E 3.98E C01 Mad100 Piperidine Alkaloids +06 +06 +06 +06 +06 +05 +05 +05 +05 +06 +05 +05 +06 +06 +06 746 1.57E 1.33E 1.44E 1.83E 2.01E 1.83E 2.90E 1.71E 1.29E 1.18E 6.25E 8.37E 1.01E 1.05E 7.15E Mad1121 Isohemiphloin Alkaloids -- +05 +05 +05 +05 +05 +05 +05 +05 +05 +05 +04 +04 +05 +05 +04 1.98E 2.35E 2.28E 1.04E 4.26E 5.14E 1.27E 1.46E 1.40E 9.63E 1.28E 1.10E 2.71E 2.99E 2.01E C00 Mad80 Betaine Alkaloids +05 +05 +05 +06 +05 +05 +05 +05 +05 +04 +05 +05 +05 +05 +05 719 1.08E 1.73E 8.09E 2.76E 3.14E 3.64E 8.24E 7.67E 7.35E 5.07E 9.00E 6.54E 1.38E 5.73E 4.46E C07 Mad221 Theobromine Alkaloids +04 +04 +03 +04 +04 +04 +03 +03 +03 +03 +00 +03 +04 +03 +03 480 2.44E 1.90E 2.37E 7.22E 6.53E 6.65E 1.02E 1.47E 1.71E 5.34E 3.58E 2.15E 2.55E 2.11E 1.26E C01 Mad72 Trigonelline Alkaloids +06 +06 +06 +06 +06 +06 +06 +06 +06 +05 +05 +05 +06 +06 +06 004 6.33E 6.22E 6.16E 9.96E 1.11E 1.11E 2.52E 3.38E 4.07E 1.99E 2.06E 4.05E 6.81E 4.41E 3.89E Mad1028 Aminophylline Alkaloids -- +05 +05 +05 +05 +06 +06 +05 +05 +05 +05 +05 +05 +05 +05 +05 Amino acid 1.55E 1.34E 1.74E 4.71E 4.86E 5.60E 1.49E 2.21E 3.16E 1.09E 1.87E 8.55E 1.75E 2.24E 1.65E Mad75 Aspartic acid di-O-glucoside -- derivatives +05 +05 +05 +04 +04 +04 +05 +05 +05 +05 +05 +04 +05 +05 +05 L-Glutaminyl-L-valyl-L-valyl- Amino acid 9.96E 1.16E 1.17E 4.04E 4.89E 4.89E 1.42E 1.30E 1.47E 2.05E 2.55E 2.13E 2.29E 1.74E 1.91E Mad489 -- L-cysteine derivatives +04 +05 +05 +04 +04 +04 +05 +05 +05 +05 +05 +05 +05 +05 +05 Amino acid 1.32E 1.25E 1.34E 5.53E 3.70E 3.35E 5.94E 1.02E 8.27E 1.14E 1.63E 1.50E 2.74E 2.16E 1.70E Mad1151 Acetyl tryptophan -- derivatives +07 +07 +07 +05 +05 +05 +06 +07 +06 +07 +07 +07 +07 +07 +07 Amino acid 6.52E 1.23E 8.65E 2.65E 1.64E 3.43E 6.56E 2.43E 5.33E 1.38E 1.89E 2.49E 2.69E 3.54E 3.38E Mad836 L-Glutamic acid O-glucoside -- derivatives +04 +05 +04 +05 +05 +05 +04 +04 +04 +04 +04 +04 +04 +04 +04 Amino acid 2.31E 2.82E 3.30E 1.32E 1.97E 2.94E 2.45E 5.41E 2.73E 3.92E 6.15E 3.67E 3.38E 2.08E 2.50E Mad1154 3-(2-Naphthyl)-D-alanine -- derivatives +04 +04 +04 +04 +04 +04 +04 +04 +04 +04 +04 +04 +04 +04 +04 Amino acid 1.19E 1.05E 1.03E 2.54E 2.16E 2.04E 8.21E 1.01E 1.15E 4.65E 3.18E 1.06E 6.75E 3.58E 2.68E C00 Mad881 Glutathione oxidized derivatives +05 +05 +05 +05 +05 +05 +04 +05 +05 +04 +04 +04 +04 +04 +04 127 Amino acid 1.67E 1.16E 1.32E 1.74E 1.34E 1.71E 8.57E 1.54E 2.10E 9.70E 1.45E 1.16E 1.34E 1.06E 1.50E C00 Mad197 L-Kynurenine derivatives +04 +04 +04 +04 +04 +04 +03 +04 +04 +03 +04 +04 +04 +04 +04 328 Amino acid 4.19E 5.16E 6.05E 3.16E 5.50E 3.39E 3.37E 2.84E 2.59E 1.02E 5.14E 1.40E 5.72E 3.52E 4.38E Mad1025 2,3-dimethylsuccinic acid -- derivatives +04 +04 +04 +04 +04 +04 +04 +04 +04 +05 +04 +05 +04 +04 +04 Amino acid 1.93E 2.10E 2.19E 4.33E 4.47E 4.36E 2.84E 2.51E 1.68E 5.19E 1.17E 3.72E 1.05E 8.75E 5.41E C00 Mad132 N-Acetyl-L-glutamic acid derivatives +05 +05 +05 +05 +05 +05 +05 +05 +05 +04 +05 +04 +05 +04 +04 624 Amino acid 1.68E 1.19E 7.34E 2.57E 1.06E 9.00E 9.00E 8.40E 1.05E 6.67E 9.76E 9.00E 9.00E 9.00E 4.09E C00 Mad121 γ-Glu-Cys derivatives +04 +04 +03 +04 +05 +00 +00 +03 +04 +03 +03 +00 +00 +00 +03 669 Amino acid 1.74E 1.59E 1.55E 5.47E 4.86E 7.88E 1.14E 1.40E 1.66E 6.71E 9.00E 5.14E 1.76E 1.27E 1.65E C00 Mad35 5-Aminovaleric acid derivatives +04 +04 +04 +04 +04 +04 +04 +04 +04 +03 +00 +03 +04 +04 +04 431 Amino acid 2.22E 2.44E 2.58E 4.14E 5.29E 3.12E 9.00E 2.21E 2.36E 6.97E 2.05E 2.57E 3.16E 2.16E 2.74E C02 Mad122 N6-Acetyl-L-lysine derivatives +04 +04 +04 +04 +04 +04 +00 +04 +04 +03 +04 +04 +04 +04 +04 727 Amino acid 9.63E 1.13E 1.06E 2.49E 2.18E 2.27E 6.29E 6.15E 8.60E 3.90E 4.78E 3.68E 4.74E 9.00E 9.00E Mad66 Glycyl-L-proline -- derivatives +03 +04 +04 +04 +04 +04 +03 +03 +03 +03 +03 +03 +03 +00 +00 Amino acid 4.10E 4.65E 4.36E 4.35E 5.12E 5.40E 5.84E 5.05E 5.39E 3.58E 1.89E 2.12E 3.22E 2.21E 2.21E Mad1016 Asp-phe -- derivatives +04 +04 +04 +04 +04 +04 +04 +04 +04 +04 +04 +04 +04 +04 +04 Amino acid 4.45E 4.53E 4.46E 3.74E 3.84E 5.34E 4.41E 4.71E 4.52E 4.45E 4.30E 3.04E 9.03E 5.22E 4.16E Mad893 Nα-Acetyl-L-glutamine -- derivatives +05 +05 +05 +05 +05 +05 +05 +05 +05 +05 +05 +05 +05 +05 +05 N-γ-Acetyl-N-2-Formyl-5- Amino acid 2.01E 1.85E 2.00E 5.11E 4.25E 3.27E 6.96E 9.35E 5.33E 7.56E 6.39E 6.54E 1.37E 4.15E 9.24E C05 Mad1148 methoxykynurenamine derivatives +04 +04 +04 +04 +04 +04 +03 +03 +03 +03 +03 +03 +04 +03 +03 642 Amino acid 1.41E 1.35E 1.48E 2.63E 2.12E 2.39E 1.15E 1.27E 1.43E 1.04E 7.40E 8.23E 6.04E 3.54E 3.53E Mad926 N-Propionylglycine -- derivatives +05 +05 +05 +05 +05 +05 +05 +05 +05 +05 +04 +04 +04 +04 +04 Amino acid 8.07E 9.79E 1.06E 2.04E 2.15E 2.27E 3.68E 7.67E 7.32E 3.68E 4.05E 2.78E 4.45E 4.60E 5.02E C01 Mad19 1-Methylhistidine derivatives +04 +04 +05 +05 +05 +05 +04 +04 +04 +04 +04 +04 +04 +04 +04 152 Amino acid 1.58E 1.52E 1.77E 4.29E 5.92E 5.53E 7.80E 1.03E 8.71E 7.66E 6.44E 9.00E 1.26E 7.35E 8.21E Mad190 N-Glycyl-L-leucine -- derivatives +04 +04 +04 +04 +04 +04 +03 +04 +03 +03 +03 +00 +04 +03 +03 Amino acid 3.49E 2.99E 3.34E 2.76E 4.00E 3.25E 1.61E 1.48E 1.53E 2.40E 2.32E 1.86E 5.55E 7.44E 9.59E Mad1112 N-Acetyl-l-leucine -- derivatives +04 +04 +04 +04 +04 +04 +04 +04 +04 +04 +04 +04 +04 +04 +04 Amino acid 2.01E 2.04E 2.08E 4.34E 6.48E 4.86E 4.58E 3.02E 2.63E 8.81E 6.62E 1.32E 1.54E 1.02E 1.28E C00 Mad786 2,6-Diaminooimelic acid derivatives +06 +06 +06 +06 +06 +06 +05 +05 +05 +04 +04 +05 +05 +05 +05 666 Amino acid 1.81E 1.77E 1.91E 1.54E 4.78E 8.55E 6.60E 4.31E 4.02E 2.12E 3.48E 6.09E 6.51E 1.38E 1.42E C00 Mad104 Glutathione reduced form derivatives +06 +06 +06 +06 +06 +03 +03 +06 +06 +06 +06 +03 +03 +06 +06 051 Amino acid 3.13E 6.28E 4.79E 4.95E 4.67E 6.34E 7.76E 5.90E 6.25E 5.34E 5.27E 4.66E 2.92E 1.72E 1.24E Mad915 S-(methyl)glutathione -- derivatives +04 +04 +04 +04 +04 +04 +04 +04 +04 +04 +04 +04 +04 +04 +04 S-(5'-Adenosy)-L- Amino acid 1.37E 1.17E 1.56E 2.06E 3.14E 1.77E 1.54E 1.72E 8.69E 6.59E 9.48E 9.00E 1.35E 6.85E 5.14E C00 Mad927 homocysteine derivatives +04 +04 +04 +04 +04 +04 +04 +04 +03 +03 +03 +00 +04 +03 +03 021 Amino acid 1.46E 8.34E 7.19E 1.30E 1.69E 1.80E 8.33E 9.48E 1.23E 2.74E 7.13E 5.67E 5.35E 4.96E 7.75E C00 Mad868 L-Pipecolic acid derivatives +04 +03 +03 +04 +04 +04 +03 +03 +04 +03 +03 +03 +03 +03 +03 408 Amino acid 4.66E 5.46E 4.94E 4.72E 5.31E 4.60E 2.81E 3.30E 4.24E 4.58E 7.55E 8.24E 2.56E 1.77E 3.25E C00 Mad53 L-Saccharopine derivatives +05 +05 +05 +05 +05 +05 +05 +05 +05 +05 +05 +05 +05 +05 +05 449 Amino acid 8.95E 8.14E 5.63E 9.08E 9.77E 1.17E 9.62E 1.04E 1.08E 6.92E 5.56E 4.54E 7.25E 1.18E 1.04E Mad17 3-N-Methyl-L-histidine -- derivatives +03 +03 +03 +03 +03 +04 +03 +04 +04 +03 +03 +03 +03 +04 +04 Amino acid 4.39E 3.80E 5.08E 1.09E 8.59E 1.10E 5.12E 2.95E 3.29E 1.75E 2.64E 2.22E 2.52E 2.35E 3.19E C00 Mad5 Histamine derivatives +05 +05 +05 +06 +05 +06 +05 +05 +05 +05 +05 +05 +05 +05 +05 388 Amino acid 3.15E 3.81E 3.26E 9.00E 9.00E 9.00E 4.71E 4.68E 5.77E 5.78E 4.66E 4.75E 3.51E 4.44E 5.55E Mad1029 N-Acetyl-L-tyrosine -- derivatives +04 +04 +04 +00 +00 +00 +04 +04 +04 +04
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