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Table 1 Selected wound-responsive DEGs, grouped according to their putative role and their expression profile clustering

From: Transcriptomic analysis of wound xylem formation in Pinus canariensis

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
  1. FC: Fold-change. FDR: adjusted p-value by False Discovery Rate. In bold, statistically significant values