Table 4.
The differentially expressed genes (RNA-seq analysis) of the sugar pathway (related routes were also considered) in two melon development stages. Statistical test evaluating the negative binomial distribution was applied using R package DeSeq2 (padj ≤0.05)
| Melonomics ID (v4.0) | Refseq ID | Short Name | Gene Name | Pathway (KEEG)a | Log2 FoldChangeb | padj |
|---|---|---|---|---|---|---|
| MELO3C010698.2 | XP_008444380.1 | CmAAG-LIKE1 | Alpha-galactosidase (Melibiase) Like 1 | – | 2.1853 | 3.723E-06 |
| MELO3C004346.2 | XP_008448578.1 | CmAGL2 | Alpha-glucosidase 2 | – | −2.2809 | 3.160E-03 |
| MELO3C005109.2 | XP_008465523.1 | CmAMN | Alpha-mannosidase | – | 2.4039 | 4.064E-06 |
| MELO3C035167.2 | XP_008463923.1 | CmAUXRF2 | Auxin response factor 2 | – | −2.1428 | 2.295E-02 |
| MELO3C021281.2 | XP_008458374.2 | CmBDXY | Beta-D-xylosidase 1-like | – | 2.7858 | 1.523E-19 |
| MELO3C020906.2 | XP_008438779.1 | CmCSREM | Chromatin structure-remodeling complex protein SYD isoform X1 | – | −0.8568 | 3.099E-02 |
| MELO3C034613.2 | XP_008459496.2 | CmCLPP | CLP protease regulatory subunit CLPX3, mitochondrial isoform X2 | – | −1.5961 | 6.544E-05 |
| MELO3C026854.2 | XP_008465290.2 | CmRNApol1 | DNA-directed RNA polymerase subunit | – | −1.1522 | 2.372E-02 |
| MELO3C016960.2 | XP_008452849.1 | CmRNApol2 | DNA-directed RNA polymerase subunit beta | – | −0.9456 | 4.024E-02 |
| MELO3C010495.2 | XP_008446732.1 | CmDNAJ1 | DnaJ protein homolog1 | – | −3.5189 | 1.593E-06 |
| MELO3C012052.2 | XP_008446732.1 | CmDNAJ2 | DnaJ protein homolog2 | – | −1.6851 | 4.110E-13 |
| MELO3C006726.2 | NP_001284475.1/XP_008438969.1 | CmGK | Galactokinase | – | 0.7983 | 9.738E-03 |
| MELO3C002363.2 | XP_008437427.1 | CmGLMT | Glucuronoxylan 4-O-methyltransferase 1 | – | 0.9286 | 4.704E-02 |
| MELO3C003459.2 | XP_008440310.1 | CmGLYT | Glycosyltransferases | – | 2.8172 | 2.076E-02 |
| MELO3C021249.2 | XP_008454693.1 | CmHEXT2 | Hexosyltransferase 2 | – | 2.0767 | 1.605E-07 |
| MELO3C015949.2 | XP_008447733.1 | CmHEXT1 | Hexosyltransferase 1 | – | −2.2774 | 1.159E-03 |
| MELO3C009735.2 | XP_008443230.1 | CmNFKB | NF-kappa-B-activating protein | – | −1.0229 | 3.657E-03 |
| MELO3C003497.2 | XP_008466126.1 | CmPGLMT1 | Phosphoglycerate mutase-like protein 1 | – | 2.0468 | 2.103E-02 |
| MELO3C022069.2 | XP_008459427.1 | CmEBGLUC | Probable endo-1,3(4)-beta-glucanase | – | 1.1135 | 1.504E-02 |
| MELO3C023253.2 | XP_008460901.1 | CmPCE1 | Probable pectinesterase1/pectinesterase inhibitor 51 | – | 5.7293 | 3.178E-03 |
| MELO3C023254.2 | XP_008460902.1 | CmPCE2 | Probable pectinesterase2/pectinesterase inhibitor 51 | – | 4.8748 | 4.918E-03 |
| MELO3C023627.2 | XP_008438007.1 | CmPGLC1 | Probable polygalacturonase1 | – | 6.3658 | 4.436E-02 |
| MELO3C011986.2 | XP_008446196.1 | CmPGLC2 | Probable polygalacturonase2 | – | 2.1382 | 1.028E-14 |
| MELO3C022542.2 | XP_016903497.1/XP_008466011.2 | CmKAN2 | Probable transcription factor KAN2 | – | −4.4866 | 1.861E-02 |
| MELO3C012479.2 | XP_008438929.1 | CmPARG1 | Protein argonaute 1 | – | −3.0169 | 1.142E-24 |
| MELO3C021378.2 | XP_008460254.1 | CmRIK | Protein RIK isoform X1 | – | −1.3787 | 1.360E-03 |
| MELO3C006266.2 | – | CmINH-LIKE3 | Putative invertase inhibitor LIKE3 | – | 2.3543 | 1.750E-14 |
| MELO3C008049.2 | – | CmINH2 | Invertase inhibitor | – | −1.2754 | 5.661E-03 |
| MELO3C014613.2 | XP_008449737.1 | CmUP1 | uncharacterized protein LOC103491528 | – | 1.0875 | 3.548E-02 |
| MELO3C004012.2 | XP_008451613.1 | CmUP2 | uncharacterized protein LOC103492844 | – | −1.0783 | 6.416E-03 |
| MELO3C027277.2 | XP_008462107.1 | CmEXPGLC | Exopolygalacturonase clone | cmo00040 | 2.4207 | 1.198E-03 |
| MELO3C008202.2 | XP_008441351.1 | CmRPE | Ribulose-phosphate 3-epimerase | cmo00040 | 1.0046 | 1.448E-02 |
| MELO3C004075.2 | XP_008452100.1 | CmXISM | Xylose isomerase | cmo00040 | 0.8185 | 3.558E-02 |
| MELO3C008467.2 | XP_008441609.2 | CmUGGP | UDP-sugar pyrophosphorylase |
cmo00040/ cmo00052/ cmo00520 |
−1.0021 | 3.830E-03 |
| MELO3C017213.2 | XP_008453254.1 | CmUG6D | UDP-glucose 6-dehydrogenase | cmo00040/ cmo00520 | 1.0501 | 4.919E-02 |
| MELO3C023110.2 | – | CmNAG2 | Neutral alpha galactosidase2 | cmo00052 | 1.0713 | 2.967E-03 |
| MELO3C011771.2 | XP_008445911.1 | CmAAG2 | Alpha-galactosidase (Melibiase)2 | cmo00052 | 1.5211 | 4.092E-02 |
| MELO3C032910.2 | XP_008440953.1 | CmATP-PPKN | ATP-dependent 6-phosphofructokinase (Phosphofructokinase) | cmo00052 | 1.1856 | 3.992E-02 |
| MELO3C009979.2 | XP_008443553.1 | Cm NAGLIKE2 | Galactinol-sucrose galactosyltransferase 5 | cmo00052 | 2.4512 | 2.042E-04 |
| MELO3C010314.2 | XP_008443958.1 | CmNAG3 | Galactinol-sucrose galactosyltransferase 6 isoform X1 | cmo00052 | −0.9338 | 2.874E-02 |
| MELO3C015912.2 | XP_008451468.1 | CmSCS | Stachyose synthase | cmo00052 | 2.4118 | 7.679E-04 |
| MELO3C005363.2 | NP_001284469.1 | CmAIN2 | Acid Invertase 2 (acid beta-fructofuranosidase-like) |
cmo00052/ cmo00500 |
2.3430 | 1.957E-08 |
| MELO3C005293.2 | XP_008467118.1 | CmPGIcyt | Phosphoglucomutase, cytoplasmic |
cmo00052/ cmo00500 |
0.8393 | 1.918E-02 |
| MELO3C017002.2 | XP_008452915.1 | CmAAML | Alpha-amylase (1,4-alpha-D-glucan glucanohydrolase) | cmo00500 | 0.9488 | 1.996E-02 |
| MELO3C012010.2 | XP_008446229.1 | CmTPS9 | Alpha-trehalose-phosphate synthase [UDP-forming] 9 | cmo00500 | 1.1210 | 8.375E-03 |
| MELO3C016121.2 | XP_008451866.1 | CmBAML | Beta-amylase | cmo00500 | −1.2463 | 6.429E-03 |
| MELO3C034277.2 | XP_008453064.1 | CmBGL18 | Beta-glucosidase 18-like | cmo00500 | 1.7017 | 1.035E-04 |
| MELO3C015214.2 | XP_008450452.1 | CmBGL24 | Beta-glucosidase 24 | cmo00500 | 4.5276 | 6.270E-04 |
| MELO3C021895.2 | XP_008459280.1 | CmEGLC | Endoglucanase-like | cmo00500 | 7.8063 | 3.544E-05 |
| MELO3C002024.2 | XP_008440956.1 | CmGBGL1 | Glucan endo-1,3-beta-glucosidase 1 | cmo00500 | −1.8416 | 4.230E-02 |
| MELO3C030768.2 | XP_016900389.1 | CmIBAML | Inactive Beta-amylase | cmo00500 | 1.7307 | 4.735E-02 |
| MELO3C015552.2 | XP_008450968.1 | CmSUS1 | Sucrose synthase 1 | cmo00500 | −1.2647 | 5.108E-05 |
| MELO3C025101.2 | XP_008463167.1 | CmSUS2 | Sucrose synthase 2 | cmo00500 | 3.8280 | 1.430E-41 |
| MELO3C009570.2 | XP_008442968.1 | CmSPP1 | Sucrose-phosphatase 1 | cmo00500 | 0.8290 | 4.230E-02 |
| MELO3C020357.2 | XP_008457154.1 | CmSPS2 | Sucrose-phosphate synthase 2 | cmo00500 | 1.6220 | 4.051E-03 |
| MELO3C006984.2 | XP_008439346.1 | CmTPP1 | Trehalose 6-phosphate phosphatase 1 | cmo00500 | 3.7901 | 4.521E-02 |
| MELO3C018715.2 | XP_016901732.1 | CmTPS7 | Trehalose-6-phosphate synthase 7 | cmo00500 | −0.6675 | 4.521E-02 |
| MELO3C013838.2 | XP_008448661.1 | CmTPS5 | Trehalose-6-phosphate synthase 5 | cmo00500 | −1.0657 | 6.854E-04 |
| MELO3C005858.2 | XP_008437557.1 | CmAEChit | Acidic endochitinase | cmo00520 | 2.1904 | 4.663E-05 |
| MELO3C009722.2 | XP_008443206.1 | CmALAR | Alpha-L-arabinofuranosidase 1-like isoform X2 | cmo00520 | 2.5093 | 2.053E-17 |
| MELO3C006704.2 | XP_008444611.1 | CmEP3-Like | Endochitinase EP3-like | cmo00520 | 2.1214 | 1.476E-02 |
| MELO3C005859.2 | XP_016903343.1 | CmHV-ALIKE | Hevamine-A-like | cmo00520 | 4.4816 | 5.239E-03 |
| MELO3C019691.2 | XP_016902486.1 | CmHEXT3 | Hexosyltransferase 3 | cmo00520 | 1.2974 | 1.711E-02 |
| MELO3C005640.2 | XP_008451740.1 | CmUGE3 | UDP-glucose epimerase 3 | cmo00520 | 1.5495 | 6.583E-07 |
| MELO3C022932.2 | XP_008460595.1 | CmAUXRF1 | Auxin response factor1 | cmo04075 | −0.7397 | 5.303E-03 |
| MELO3C003906.2 | XP_008450396.1 | CmER1 | Ethylene receptor 1 | cmo04075 | −1.2850 | 1.144e-06 |
| MELO3C006371.2 | XP_008461049.1 | CmAUXRS | Auxin-resposive protein | cmo04075 | −1.7529 | 1.147E-02 |
| MELO3C011021.2 | XP_008444821.1 | CmENDP | Endoplasmin homolog | cmo04141 | −0.7411 | 4.808E-02 |
a cmo00040: pentose and glucuronate interconversions; cmo00052: galactose metabolism; cmo00500: starch and sucrose metabolism; cmo00520: amino sugar and nucleotide sugar metabolism; cmo04075: plant hormone signal transduction; cmo04141: protein processing in endoplasmic reticulum
b The positive values are up-regulated genes and the negative values are down-regulated genes when considerate the 10 DAP stage