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Table 1 Genes differentially expressed during organogenic nodule formation in hop.

From: Organogenic nodule development in hop (Humulus lupulus L.): Transcript and metabolic responses

GenBank Acc. No. E value Annotation 24 h vs 0 15d vs 0 28d vs 0 28d vs 28dWH Clone ID/contig
   Defense response, response to stress, response to chemical stimulus, abiotic and biotic stimuli      
ES437675 1,00E-81 cationic peroxidase [Nelumbo nucifera] -3.81 -1.44   2.01 Hlct1
ES437719 9,00E-119 peroxidase [Vigna angularis] 2.73 1.53 1.79 2.03 Hl4206
ES437713 2,00E-87 peroxidase [Populus trichocarpa]   2.16 1.66   Hl4578
ES437767 2,00E-13 SAG21 (Senescence-Associated Gene 21) [Arabidopsis thaliana] 1.87 2.09 1.87 -1.91 Hl4571
ES437753 4,00E-77 Senescence-associated [Medicago truncatula] 4.06 4.32 3.46   Hl1471
ES437674 0.0 M. domestica ribulose-1.5-bisphosphate carboxylase/oxygenase activase -13.29 -5.38 -2.97   Hlct810
ES437696 1,00E-64 major allergen Pru p 1 [Prunus persica] 6.05 3.5 1.95   Hl1695
ES437747 2,00E-48 major allergen Pru p 1 [Prunus persica] 5.94 3.74 2.56   Hlct313
ES437764 2,00E-140 Solanum tuberosum clone 054G03 Hsp90-2-like mRNA 2.02 2.81 3.1   Hlct1560
ES437687 2,00E-23 putative gamma-thionin [Castanea sativa] 5.21 1.55   -1.87 Hl1925
ES437729 5,00E-20 mandelonitrile lyase [Arabidopsis thaliana]   -1.46 NA 4.06 Hl2222
ES437733 3,00E-152 Thiazole biosynthetic enzyme, chloroplast precursor -3.34 -3.29 -2.49 -2.35 Hl3328
ES437789 2,00E-162 Humulus lupulus chitinase 1.74 2.52 2.38   Hlct1044
ES437688 1,00E-65 glutathione S-transferase GST 12 [Glycine max] 4.2 2.63 2.62   Hl1525
ES437709 1,00E-16 early flowering 3 [Mesembryanthemum crystallinum] 1.56 1.82 2.64   Hl3446
ES437740 1,00E-12 nematode responsive protein [Arabidopsis thaliana] 2.64 4.57 3.12   Hl4497
EF624245 6,00E-124 putative phenylalanine ammonia-lyase [Rhizophora mangle] 1.95 1.56 NA   Hlpal
ES437730 3,00E-32 Populus tremula × Populus tremuloides aux/IAA protein -1.41 -1.54 -2.5 2.55 Hl4491
   Macromolecule metabolic processes      
ES437720 6,00E-10 Solanum tuberosum extensin 1.97 7.03 4.44   Hlct117
AY795910 0.0 Humulus lupulus beta-1.3-glucanase 3.81 3.37 3.28   Hlgluc5
EF593131 2,00E-79 Pectin methylesterase 1 [Pyrus communis]   1.65    Hl52
ES437689 4,00E-121 Populus tremula xyloglucan endotransglycosylase/hydrolase precursor XTH-30 3.48 5.3 6.87   Hl3465
ES437757 0.0 Nicotiana tabacum ZIP -5.77 -3.4 NA NA Hl4167
EF624249 5,00E-158 sucrose synthase [Glycine max] 3.01 1.9 1.5   Hlsuc
   Cellular metabolic processes      
ES437727 1,00E-56 RNA binding [Arabidopsis thaliana] 2.15 2.19 2.32   Hl417
ES437761 4,00E-161 Avr9/Cf-9 induced kinase 1 [Nicotiana tabacum] 2.46 2.53 3.17   Hl3459
ES437769 6,00E-20 Plant lipid transfer protein/Par allergen [Medicago truncatula] 2.66 2.71 1.76   Hl3157
ES437798 1,00E-156 Hevea brasiliensis latex plastidic aldolase-like protein -9.51 -4.32 -2.85   Hlct77
ES437772 1,00E-94 ribonuclease/transcriptional repressor [Arabidopsis thaliana]   -1.44 -2.67 NA Hl4319
ES437711 8,00E-81 pfkB-type carbohydrate kinase family protein, putative expressed [Oryza sativa] 3.54 2.49 2.8   Hl3980
ES437721 0.0 putative dTDP-glucose 4-6-dehydratase [Arabidopsis thaliana] NA 2.07 2.23   Hl4620
ES437736 0.0 Arabidopsis thaliana mRNA for glyceraldehyde-3-phosphate dehydrogenase C subunit 2.31 2.5 1.53   Hlct23
ES437788 2,00E-152 fructose-bisphosphate aldolase-like protein [Solanum tuberosum] NA 1.91   -1.87 Hlct3973
ES437680 6,00E-63 glyceraldehyde-3-phosphate dehydrogenase A subunit, photosynthetic isoform [Glycine max] -10.78 -5.17    Hl263
ES437780 6,00E-83 glycerophosphodiesterase-like protein [Nicotiana tabacum] -1.6   -1.58 2.65 Hl3510
ES437786 1,00E-95 epoxide hydrolase/hydrolase [Arabidopsis thaliana]    NA 3.18 Hl1072
ES437692 0.0 C. blumei kinetoplast met gene for cobalamine-independent methionine synthase 3.56 2.13 1.45   Hlct4592
ES437722 4,00E-09 S-adenosylmethionine decarboxylase [Malus × domestica] NA NA 2.6 NA Hl3196
ES437681 0.0 Elaeagnus umbellata S-adenosyl-L-methionine synthetase (SAMS2) mRNA 1.55 2.35 1.48 -1.68 Hlct214
ES437707 1,00E-80 Vitis vinifera 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase 3.25 2.31 NA   Hl1812
ES437758 3,00E-85 Capsicum annuum nucleoside diphosphate kinase 4.72 5.1 5.03   Hl1543
ES437763 3,00E-82 MAP kinase-like protein [Gossypium hirsutum] -1.89 -1.66 -2.08 2.48 Hl4516
ES437718 5,00E-58 Protein kinase; Type I EGF [Medicago truncatula] -1.46 -1.62 -4.38 7.51 Hl4559
ES437766 5,00E-77 Putative phosphatase 2A inhibitor [Arabidopsis thaliana] -1.68 -1.92 -1.67 2.35 Hl2273
   Primary metabolic process      
ES437723 5,00E-11 Corylus avellana lipid transfer protein precursor    1.95 1.99 Hl2898
ES437779 1,00E-14 Lipoxygenase [Medicago truncatula] 3.35 2.42    Hllox6
ES437705 2,00E-31 Lipoxygenase [Nicotiana attenuata]    -3.26 4 Hl2195
   Transcription and DNA and RNA metabolism      
ES437679 2,00E-32 ZFP4 (ZINC FINGER PROTEIN 4); nucleic acid binding/transcription factor/zinc ion binding [Arabidopsis thaliana] 3.83 2.99 3.35   Hl1813
ES437796 1,00E-43 histone H2B1 [Gossypium hirsutum] 2.66 2.57 2.36   Hl2418
ES437677 2,00E-62 A. thaliana histone H4 gene 3.76 1.94 1.73 2.03 Hlct2847
   Signal transduction      
ES437693 5,00E-70 Medicago truncatula small G-protein ROP9 6.54 7.27 6.23   Hl1506
ES437706 3,00E-118 Populus tomentosa calmodulin 1.71 2.09 1.4   Hl2815
   Cellular component organization and biogenesis      
ES437700 1,00E-39 Gossypium hirsutum RAC-like G-protein Rac1 2.04 2.02 1.98   Hl1537
ES437797 1,00E-113 Camellia sinensis alpha tubulin 1 (Tua1)    -5.7 7.36 Hl2210
ES437690 6,00E-12 Arabidopsis thaliana POK (POKY POLLEN TUBE) -8.51 -2.97 -1.62 1.99 Hl3610
   Protein metabolism      
ES437748 8,00E-36 ribosome inactivating protein Euserratin 2 precursor [Euphorbia serrata] 1.7   1.71 2.86 Hl3627
ES437712 6,00E-76 A. thaliana structural constituent of ribosome (AT5G28060) 2.82 2 2.3   Hl1643
ES437716 5,00E-113 Cicer arietinum mRNA for ribosomal protein RL5 (rl5 gene) 3.63 5.31 5.35   Hl1520
ES437765 3,00E-57 structural constituent of ribosome [Arabidopsis thaliana]    -1.44 3.03 Hl3805
ES437756 5,00E-41 Triticum aestivum ribosomal protein L39 2.8 2.54 2.2   Hl4115
ES437773 2,00E-55 40S RIBOSOMAL PROTEIN S20 homolog [Arabidopsis thaliana] 2.85 NA 2.29 NA Hl1619
ES437744 6,00E-56 ribosomal protein L30 [Lupinus luteus] 3.72 3.71 2.83   Hlct1532
ES437739 3,00E-26 G. hirsutum mRNA for ribosomal protein 41, large subunit (RL41) 4.22 2.17 1.57   Hlct1769
ES437701 7,00E-15 putative subtilisin-like serine proteinase [Arabidopsis thaliana] 1.45 1.88 2.2   Hl1547
ES437775 8,00E-18 Trifolium pratense RNA for putative zinc dependent protease NA NA 2.63 NA Hl1923
ES437778 3,00E-21 protein binding/ubiquitin-protein ligase/zinc ion binding [Arabidopsis thaliana] NA 1.88 2.17   Hl1495
ES437685 6,00E-25 ATP binding/protein binding [Arabidopsis thaliana] -1.47 -1.62 -3.24 3.09 Hl2061
   Photosynthesis and carbon utilization      
ES437710 7,00E-165 oxygen evolving complex 33 kDa photosystem II protein [Nicotiana tabacum] -10.45 -4.95 -2.56   Hlct484
ES437702 5,00E-88 Arachis hypogaea photosystem I psaH protein -7.75 -4.86 -2.28   Hlct829
ES437794 2,00E-46 photosystem I reaction center subunit × psaK [Nicotiana tabacum] -6.29 NA -2.68 NA Hlct526
ES437741 0.0 Glycine max cv. Dare photosystem II type I chlorophyll a/b-binding protein (lhcb1*7) gene -9.9 -6.33 -2.84 1.66 Hlct54
ES437745 1,00E-144 chlorophyll ab binding protein [Gossypium hirsutum], light harvesting complex -11.69 -5.89 -2,43 1.86 Hlct362
ES437704 1,00E-95 photosystem II 23 kDa polypeptide [Nicotiana tabacum] -7.41 -4.34 -1.89   Hl2435
ES437703 2,00E-131 chlorophyll a/b binding protein [Solanum tuberosum] -6.91 -5.95 -2.97   Hlct1969
ES437759 2,00E-07 LHCII type I chlorophyll a/b binding protein [Vigna radiata] -18.13 -8.33 -3.71 1.78 Hl240
ES437783 6,00E-118 chloroplast pigment-binding protein CP26 [Nicotiana tabacum] -3.02 -3.13 -3.48 2.92 Hl4149
ES437793 1,00E-86 PSI type III chlorophyll a/b-binding protein [Arabidopsis thaliana] -4.96 -4.08 -2.35   Hl2281
ES437755 3,00E-118 LHCII type III chlorophyll a/b binding protein [Vigna radiata] NA -7.85 -3.04   Hl3332
ES437760 5,00E-79 putative chloroplast chlorophyll a/b-binding protein [Carya cathayensis] -7.19 -4.82 -2.67   Hl1396
ES437673 7,00E-85 small subunit ribulose-1.5-bisphosphate carboxylase/oxygenase [Fagus crenata] -13.36 -6.44 -2.49   Hlct105
ES437715 1,00E-128 chlorophyll a/b-binding protein CP24 precursor [Vigna radiata] -7.11 -5.46 -2.79   Hlct1168
ES437762 1,00E-130 chlorophyll a/b-binding protein [Solanum lycopersicum] -9.86 -6.57 -2.75   Hlct2446
ES437697 1,00E-74 Potato mRNA for light inducible tissue-specific ST-LS1 gene -11.42 -4.33 -2.33   Hlct30
ES437781 4,00E-07 putative photosystem I reaction centre PSI-D subunit precursor [Solanum tuberosum] -1.78 -1.85 -1.74 3.03 Hl3804
ES437771 7,00E-68 subunit of photosystem I [Cucumis sativus] -4.84 -4.02 -2.08   Hlct2254
   Generation of precursor metabolites and energy      
ES437678 7,00E-24 putative photosystem I reaction center subunit IV [Arabidopsis thaliana] -4.51 -3.63 -1.85   Hl4247
ES437751 8,00E-87 Pachysandra terminalis glycolate oxidase -7.94 -3.22 -2.46   Hl1696
ES437768 2,00E-39 putative steroid binding protein [Arabidopsis thaliana] -1.9    -1.87 Hl1863
ES437752 3,00E-62 F1-ATP synthase delta subunit [Ipomoea batatas] NA 2.35 2.87   Hl1512
ES437695 2,00E-138 Gossypium hirsutum vacuolar H+-ATPase subunit B 2.52 2.82 2.8   Hl3429
ES437683 8,00E-94 vacuolar-type H+-ATPase (v-ATPase) subunit D [Arabidopsis thaliana] 1.61 1.85 2.33   Hl3612
   Secondary metabolic process      
ES437792 7,00E-72 NADPH-protochlorophyllide oxidoreductase [Cucumis sativus] -4.21 -3.95 -2.26   Hlct395
ES437754 2,00E-173 Malus × domestica cinnamic acid hydroxylase (C4H1) 2.03 2.24 1.67   Hlct225
ES437670 7,00E-93 iron ion binding/isopenicillin-N synthase/flavonol synthase [Arabidopsis thaliana] 2.44 5.27 2.33   Hl3668
   Other classes      
ES437676 1,00E-55 protein transporter [Arabidopsis thaliana] -1.47 -1.84 -2.25 4.29 Hl1064
ES437750 3,00E-22 Gossypium hirsutum hybrid proline-rich protein 2   2.43    Hlct2443
ES437749 1,00E-08 metallothionein 1a [Populus balsamifera subsp. trichocarpa × Populus deltoides] 1.74 2.61 2.13   Hlct1310
ES437717 7,00E-54 Fagus sylvatica glycine-rich protein 2 2.55 2.08   NA Hl1692
   Unknown function      
ES437698 3,00E-16 nectarin IV [Nicotiana langsdorffii × Nicotiana sanderae], xyloglucan-specific fungal endoglucanase-inhibitor   -1.46 -1.79 2.69 Hl3829
ES437708 2,00E-67 Stress protein DDR48, related [Medicago truncatula] 1.65 2.22 2.9   Hl3456
ES437737 6,00E-78 hypothetical protein OsJ_005893 [Oryza sativa], sodium/calcium exchanger protein 2.11 3.17 3.52   Hlct2641
ES437724 2,00E-25 putative type-1 pathogenesis-related protein [Oryza sativa] 2.16 2.43 3.51   Hl697
ES437672 5,00E-08 Kunitz inhibitor ST1-like [Medicago truncatula] 5.39 2.28 2.95   Hl2037
ES437684 2,00E-65 thioredoxin-dependent peroxidase [Nelumbo nucifera] 1.62 2.23 1.44   Hl3152
ES437732 1,00E-28 cystatin-like protein [Citrus × paradisi] 1.63 1.91 NA -1.6 Hl285
ES437734 1,00E-11 metal ion binding [Arabidopsis thaliana] -1.5   -1.77 3.84 Hl3490
ES437777 4,00E-93 Platanus × acerifolia putative zinc-binding protein 1.88 2.11 2.24   Hl481
ES437738 1,00E-24 hypothetical protein OsI_022889 [Oryza sativa], AN1-like Zinc finger   1.98 2.27   Hlct1522
ES437774 7,00E-28 S locus F-box protein with the low allelic sequence polymorphism 2-Sf [Prunus mume]   -7.04 -5.52 5.47 Hl4049
ES437770 3,00E-98 acireductone dioxygenase-like protein [Brassica juncea] 1.56 2.23 1.93   Hl3444
ES437691 2,00E-31 auxin-repressed protein-like protein ARP1 [Manihot esculenta] -10.78 -1.93 -1.49 2.23 Hlct188
ES437694 2,00E-25 putative auxin-repressed protein [Prunus armeniaca] -6.17 -4.13 -2.35 2.08 Hl1264
ES437742 1,00E-65 Mannose/glucose-specific lectin NA 2.25 1.81 -2.96 Hl1960
ES437746 2,00E-08 pore-forming toxin-like protein Hfr-2 [Triticum aestivum] -5.82 -4.68 -3.22   Hlct272
ES437782 4,00E-22 carbohydrate binding [Arabidopsis thaliana] -6.94 -3.46 -1.57   Hl2175
ES437726 1,00E-15 Triticum aestivum acidic ribosomal protein    -2.07 2.3 Hl3792
ES437790 8E-17 Similar to threonine endopeptidase [Arabidopsis thaliana] 5.27 7.32 5.53 2.51 Hl3859
ES437784 7,00E-28 unknown protein [Arabidopsis thaliana] 1.8 2.16 2.87   Hl3471
ES437776 4,00E-50 unknown protein [Arabidopsis thaliana] -2.28 -2.1 -2.32 2.08 Hl2053
ES437787 4,00E-51 unknown protein [Arabidopsis thaliana] 1.58 -3.72 -2.41 2.82 Hl3322
   No identity      
ES437699     3.19 2.99 1.83 Hl3362
ES437682    12.98 22.04 9.41   Hlct85
ES437795      -1.65 -3.23 Hlct367
ES437791    -1.45 -1.6 -1.84 2.45 Hl3793
ES437785     -2.52 -2.27 2.02 Hl2561
ES437735    -1.65    2.01 Hl1860
ES437731    7.52 11.15 5   Hlct397
ES437686    5.78 12.48 7.98 2.59 Hlct182
ES437728      2.19   Hl3941
ES437725    1.76 1.81 2.15   Hl1453
ES437714    -2.05 -2.15 -2.15 2.94 Hl2078
ES437671    -2.61 -2.13 -2.46   Hl393
ES437743    1.58 1.96 1.84   Hl109
  1. A total of 133 differentially expressed unigenes during different phases of nodule formation were sorted into groups according to their putative physiological role estimated according to TAIR. Clones obtained by a reverse transcriptase–PCR based cloning approach appear in italic. Negative and positive values indicate down- and up-regulation respectively. Values presented in bold format represent those meeting the criteria of a FDR < 0.05 and a fold change ≥ 1.87 or ≤ -1.87. Values without bold format represent a fold change ≥ 1.41 or ≤ -1.41. Note that for the time point T24h versus T0 there are less values in bold format since only two replicates were carried out. NA stands for not available data due to their removal from analysis before normalization.