Table 1.
Selected wound-responsive DEGs, grouped according to their putative role and their expression profile clustering
| Cluster | ID | Seq. Description | H1 | H2 | H3 | |||
|---|---|---|---|---|---|---|---|---|
| FC | FDR | FC | FDR | FC | FDR | |||
| Defense and stress response genes | ||||||||
| A | Contig18804 | disease resistance response protein 206-like | 395.78 | 0.00 | 37.14 | 0.00 | 52.52 | 0.00 |
| A | Contig19053 | pathogenesis-related protein pr-4b-like | 96.55 | 0.00 | 23.91 | 0.00 | 19.77 | 0.00 |
| A | Contig22185 | major allergen pru ar 1-like | 138.29 | 0.00 | 13.75 | 0.00 | 4.94 | 0.01 |
| A | Contig22375 | pathogenesis-related protein pr-4-like | 343.24 | 0.00 | 7.69 | 0.00 | 7.38 | 0.00 |
| A | Ppnisotig12265 | antimicrobial peptide 1-like | 72.52 | 0.00 | 16.88 | 0.00 | 12.84 | 0.00 |
| A | Ppnisotig13133 | pathogenesis-related protein pr-4-like | 206.36 | 0.00 | 6.43 | 0.00 | 5.13 | 0.00 |
| A | Ppnisotig13431 | disease resistance response protein 206-like | 133.78 | 0.00 | 24.75 | 0.00 | 31.68 | 0.00 |
| B | Contig00602 | defensin ec-amp-d2-like | 11.27 | 0.00 | 2.07 | 0.12 | -1.42 | 0.65 |
| B | Contig02906 | nematode resistance hspro2-like | 7.81 | 0.01 | -1.23 | 0.94 | -2.12 | 0.11 |
| B | Contig03079 | lactoylglutathione lyase glyoxalase i family protein | 3.96 | 0.04 | 1.97 | 0.20 | -1.36 | 0.75 |
| B | Contig09180 | thioredoxin h-type | 6.82 | 0.01 | 1.52 | 0.44 | 1.39 | 0.55 |
| B | Contig19857 | nematode resistance hspro2-like | 9.88 | 0.00 | -1.33 | 0.83 | -2.56 | 0.06 |
| B | Contig20555 | phenylalanine ammonia-lyase-like | 14.41 | 0.00 | 3.19 | 0.03 | -1.08 | 1.11 |
| C | Contig13499 | (-)-camphene tricyclene chloroplastic-like | 2.17 | 0.17 | 2.14 | 0.12 | 2.81 | 0.01 |
| D | Contig00126 | basic endochitinase a-like | 15.25 | 0.00 | -1.20 | 0.55 | 0.34 | 1.13 |
| D | Contig10307 | endochitinase a-like | 65.05 | 0.00 | 3.40 | 0.02 | 1.49 | 0.47 |
| D | Contig17617 | defensin ec-amp-d2-like | 44.89 | 0.00 | 1.32 | 0.40 | -1.23 | 0.69 |
| D | Contig21216 | endochitinase a-like | 92.45 | 0.00 | 2.28 | 0.08 | 2.51 | 0.02 |
| D | Contig23442 | chitinase 1-like | 29.31 | 0.00 | 2.12 | 0.37 | -1.65 | 0.41 |
| D | Ppnisotig00751 | endochitinase pr4-like | 85.39 | 0.00 | 3.16 | 0.02 | 1.28 | 0.78 |
| D | Ppnisotig01747 | peroxidase 12-like | 97.76 | 0.00 | 1.74 | 0.28 | 1.53 | 0.37 |
| D | Ppnisotig06171 | glutathione s-transferase f9-like | 41.49 | 0.00 | 2.48 | 0.05 | 1.55 | 0.36 |
| D | Ppnisotig08058 | endochitinase pr4-like | 89.60 | 0.00 | 1.15 | 1.04 | 1.12 | 1.08 |
| H | Contig03270 | geranylgeranyl pyrophosphate chloroplastic-like | 1.61 | 0.46 | 1.48 | 0.45 | 2.57 | 0.03 |
| H | Contig08417 | abietadienol abietadienal oxidase-like | 1.10 | 1.12 | 2.08 | 0.11 | 2.64 | 0.02 |
| H | Ppnisotig10634 | geranylgeranyl pyrophosphate chloroplastic-like | -1.26 | 1.00 | 2.54 | 0.04 | 2.92 | 0.01 |
| Cell-wall matrix development and/or carbohydrates metabolism | ||||||||
| G | Contig06476 | caffeoyl- o-methyltransferase | -1.27 | 0.97 | -3.59 | 0.04 | -1.44 | 0.61 |
| G | Contig15857 | cellulose synthase-like protein d3 | 1.38 | 0.78 | -1.14 | 1.08 | -3.00 | 0.04 |
| G | Contig17013 | probable xyloglucan endotransglucosylase hydrolase protein 23 | -1.24 | 0.93 | -6.29 | 0.00 | -7.64 | 0.00 |
| G | Contig21865 | galactinol--sucrose galactosyltransferase-like | 2.27 | 0.18 | -2.03 | 0.21 | -3.39 | 0.03 |
| H | Contig00603 | beta-xylosidase alpha-l-arabinofuranosidase 2-like | -0.57 | 1.10 | 2.46 | 0.07 | 2.58 | 0.03 |
| H | Contig03225 | expansin alpha | -2.10 | 0.20 | 2.64 | 0.04 | 1.99 | 0.13 |
| H | Contig05066 | probable pectate lyase 15-like | -5.21 | 0.01 | 2.08 | 0.20 | 3.24 | 0.01 |
| H | Contig05424 | probable xyloglucan endotransglucosylase hydrolase protein 8-like | -1.78 | 0.37 | 2.55 | 0.04 | 2.18 | 0.06 |
| H | Contig09907 | probable xyloglucan endotransglucosylase hydrolase protein 32 | -1.86 | 0.32 | 2.14 | 0.09 | 2.95 | 0.01 |
| H | Contig10173 | endoglucanase 24-like | -3.26 | 0.05 | 1.58 | 0.46 | 2.58 | 0.03 |
| H | Contig13281 | probable pectinesterase 68-like | -1.56 | 0.60 | 2.18 | 0.09 | 3.40 | 0.01 |
| H | Contig18777 | endoglucanase 24-like | -1.69 | 0.41 | 2.54 | 0.04 | 5.32 | 0.00 |
| H | Contig18811 | expansin alpha | -1.59 | 0.58 | 3.42 | 0.01 | 4.98 | 0.00 |
| I | Contig00766 | xyloglucan endotransglucosylase hydrolase protein 9-like | -17.49 | 0.00 | -1.36 | 0.72 | -1.24 | 0.78 |
| I | Contig02447 | caffeoyl- o-methyltransferase-like | -6.41 | 0.01 | 1.17 | 0.75 | -1.58 | 0.34 |
| I | Contig03231 | probable carboxylesterase 15-like | -4.22 | 0.03 | -1.63 | 0.38 | -1.39 | 0.68 |
| I | Contig08356 | udp-glycosyltransferase 85a2-like | -44.90 | 0.00 | 1.62 | 0.28 | 1.45 | 0.46 |
| I | Contig11436 | probable polygalacturonase non-catalytic subunit jp650-like | -13.41 | 0.00 | 1.46 | 0.47 | 1.52 | 0.44 |
| I | Contig13611 | beta-xylosidase alpha-l-arabinofuranosidase 2-like | -4.92 | 0.02 | 0.35 | 1.08 | 1.39 | 0.56 |
| I | Contig19457 | xyloglucan endotransglucosylase hydrolase protein 9-like | -14.61 | 0.00 | -1.41 | 0.66 | -1.31 | 0.68 |
| L | Contig00654 | cellulose synthase a catalytic subunit 3 | -8.70 | 0.00 | -1.86 | 0.26 | -1.57 | 0.54 |
| L | Contig01405 | protein cobra-like | -6.74 | 0.01 | -2.06 | 0.20 | -2.27 | 0.09 |
| L | Contig01916 | xyloglucan glycosyltransferase 4-like | -1.45 | 0.71 | -1.36 | 0.60 | -4.36 | 0.01 |
| Hormone signalling | ||||||||
| B | Contig00715 | 1-aminocyclopropane-1-carboxylate oxidase-like | 5.91 | 0.01 | 1.63 | 0.51 | 1.77 | 0.19 |
| B | Contig03482 | salicylic acid-binding protein 2-like | 5.92 | 0.01 | 1.99 | 0.14 | 1.40 | 0.57 |
| C | Contig00524 | 1-aminocyclopropane-1-carboxylate oxidase-like | 1.69 | 0.38 | 3.80 | 0.02 | 2.65 | 0.02 |
| C | Ppnisotig12073 | 1-aminocyclopropane-1-carboxylate oxidase-like isoform x1 | 3.27 | 0.05 | 2.48 | 0.05 | 2.29 | 0.04 |
| D | Contig14053 | salicylic acid-binding protein 2-like | 22.28 | 0.00 | 3.04 | 0.04 | 3.76 | 0.00 |
| I | Contig16100 | 1-aminocyclopropane-1-carboxylate oxidase | -4.81 | 0.02 | 2.54 | 0.04 | 2.45 | 0.04 |
| Transcriptional regulation of meristem activity | ||||||||
| B | Contig00787 | nac domain-containing protein 2-like | 9.26 | 0.00 | -1.02 | 0.85 | -1.26 | 0.79 |
| B | Contig12353 | early nodulin-like protein 1 | 9.58 | 0.00 | -1.48 | 0.61 | -2.80 | 0.05 |
| B | Contig20304 | homeobox-leucine zipper protein athb-13-like | 3.82 | 0.04 | 1.31 | 0.72 | 1.24 | 0.86 |
| D | Contig13895 | nac transcription factor 29-like | 22.81 | 0.00 | 1.08 | 1.07 | 1.20 | 0.64 |
| G | Contig09007 | exordium like 2 | -0.36 | 1.17 | -3.66 | 0.03 | -4.59 | 0.01 |
| H | Contig06813 | wuschel-related homeobox 4-like | -1.76 | 0.34 | 1.49 | 0.47 | 2.61 | 0.02 |
| H | Contig14178 | clavata3 esr-related 12 family protein | -3.46 | 0.05 | 1.70 | 0.41 | 2.45 | 0.03 |
| L | Contig05551 | probable wrky transcription factor 51-like | -2.28 | 0.19 | -3.39 | 0.04 | -2.23 | 0.15 |
| L | Contig12050 | transcription factor myb46-like | -9.05 | 0.00 | -2.05 | 0.18 | -2.11 | 0.22 |
| Non annotated genes and unknown functions | ||||||||
| A | Contig03506 | hypothetical protein SELMODRAFT_115352 | 63.88 | 0.00 | 20.85 | 0.00 | 12.74 | 0.00 |
| B | Contig09209 | ---NA--- | 13.90 | 0.00 | 1.35 | 0.82 | -1.67 | 0.36 |
| B | Contig22448 | ---NA--- | 12.00 | 0.00 | 1.31 | 0.68 | -1.40 | 0.64 |
| B | Contig24621 | ---NA--- | 12.34 | 0.00 | 0.36 | 1.01 | -1.81 | 0.30 |
| D | Contig19474 | ---NA--- | 22.81 | 0.00 | 1.49 | 0.64 | 0.36 | 1.09 |
| D | Contig20761 | predicted protein | 24.06 | 0.00 | 1.29 | 0.75 | 1.80 | 0.20 |
| D | Contig22397 | ---NA--- | 31.25 | 0.00 | 2.29 | 0.09 | 1.10 | 1.10 |
| D | Contig23569 | ---NA--- | 36.23 | 0.00 | 2.55 | 0.06 | -2.05 | 0.27 |
| F | Contig03012 | ---NA--- | 7.04 | 0.01 | -7.98 | 0.00 | -4.60 | 0.01 |
| F | Contig03111 | ---NA--- | 5.57 | 0.02 | -3.12 | 0.12 | -2.77 | 0.05 |
| G | Contig12685 | uncharacterized loc101213469 | 1.34 | 0.82 | -1.79 | 0.31 | -6.43 | 0.00 |
| G | Contig20076 | ---NA--- | 2.71 | 0.12 | 0.11 | 1.03 | -7.76 | 0.00 |
| G | Contig23934 | ---NA--- | 1.31 | 0.79 | -2.74 | 0.08 | -9.51 | 0.00 |
| G | Contig24690 | ---NA--- | 1.55 | 0.53 | -2.30 | 0.17 | -8.11 | 0.00 |
| H | Contig12627 | ---NA--- | -1.94 | 0.28 | 4.42 | 0.00 | 8.62 | 0.00 |
| H | Contig21346 | ---NA--- | -1.02 | 1.19 | 7.69 | 0.00 | 7.90 | 0.00 |
| I | Contig02729 | ---NA--- | -11.85 | 0.00 | 2.03 | 0.19 | 1.70 | 0.23 |
| I | Contig13781 | ---NA--- | -12.25 | 0.00 | -1.08 | 1.01 | 1.09 | 0.88 |
| I | Contig16419 | ---NA--- | -13.45 | 0.00 | 1.55 | 0.31 | -0.45 | 0.83 |
| I | Contig19504 | ---NA--- | -12.31 | 0.00 | -1.05 | 1.03 | 1.13 | 0.90 |
| L | Contig02798 | uncharacterized loc101210414 | -1.25 | 0.99 | -1.78 | 0.29 | -5.06 | 0.01 |
| L | Contig10360 | ---NA--- | -9.23 | 0.00 | -2.42 | 0.12 | -1.69 | 0.36 |
| L | Contig12514 | ---NA--- | -9.36 | 0.00 | -2.14 | 0.17 | -1.35 | 0.33 |
| L | Contig14134 | ---NA--- | -1.64 | 0.55 | -9.50 | 0.00 | -3.12 | 0.04 |
| L | Contig14477 | ---NA--- | -10.08 | 0.00 | -2.38 | 0.12 | -2.15 | 0.12 |
| L | Contig20478 | ---NA--- | -1.33 | 0.86 | -5.43 | 0.01 | -2.76 | 0.04 |
| L | Contig34794 | PREDICTED: uncharacterized protein LOC101509257 | -10.94 | 0.00 | -3.20 | 0.04 | -2.59 | 0.10 |
FC: Fold-change. FDR: adjusted p-value by False Discovery Rate. In bold, statistically significant values