Species & Dataset

Experiment

Foliar Ozone Injury

  • Viburnum lantana

  • Common name: Wayfaring tree

  • Family: Adoxaceae

  • Cultivar: Viburnum lantana L.

  • Tissue: Shoot leaves

  • Ozone concentration: ​60 ± 13 ppb           

  • Ozone exposure:45 consecutive days (5 hours/day)

  • Sampling time: 15 days after ozone fumigation

  • Platform: 454-pyrosequencing

  • Year of study: 2016

  • Location: Italy

viburnum lantanum injury.jpg

Title: Suppression substractive hybridization and NGS reveal differential transcriptome expression profiles in wayfaring tree (Viburnum lantana L.) treated with ozone

 

Summary: Tropospheric ozone (O3) is a global air pollutant that causes high economic damages by decreasing plant productivity. It enters the leaves through the stomata, generates reactive oxygen species, which subsequent decrease in photosynthesis, plant growth, and biomass accumulation. In order to identify genes that are important for conferring O3 tolerance or sensitivity to plants, a suppression subtractive hybridization analysis was performed on the very sensitive woody shrub, Viburnum lantana, exposed to chronic O3 treatment (60ppb,5hd -1 for 45 consecutive days). Transcript profiling and relative expression assessment were carried out in asymptomatic leaves, after 15 days of O3 exposure. At the end of the experiment symptoms were observed on all treated leaves and plants, with an injured leaf area per plant accounting for 16.7% of the total surface. Cloned genes were sequenced by 454 pyrosequencing and transcript profiling and relative expression assessment were carried out on sequenced reads. A total of 38,800 and 12,495 high quality reads obtained in control and O3 treated libraries, respectively (average length of 319±156.7 and 255±107.4bp). The Ensembl transcriptome yielded a total of 1241 unigenes with a total sequence length of 389,126 bp and an average length size of 389 bp (guanine cytosine content=49.9%). mRNA abundance was measured by reads per kilo base per million and 41 and 37 ensembl unigenes showed up and down regulation respectively. Unigenes functionally associated to photosynthesis and carbon utilization were repressed, demonstrating the deleterious effect of O3 exposure. Unigenes functionally associated to heat shock proteins and glutathione were concurrently induced, suggesting the role of thylakoid localized proteins and antioxidant detoxification pathways as an effective strategy for responding to O3. Gene Ontology analysis documented a differential expression of coregulated transcripts for several functional categories, including specific transcription factors (MYB and WRKY). This study demonstrates that a complex sequence of events takes place in the cells at intracellular and membrane level following O3 exposure and elucidates the effects of this oxidative stress on the transcriptional machinery of the non model plant species V.lantana, with the final aim to provide the molecular supportive knowledge for the use of this plant as O3-bioindicator.

 

Data repository: European Nucleotide Archive (ENA) (Project number PRJEB9317)

Reference: Gottardini, E., Cristofori, A., Pellegrini, E., La Porta, N., Nali, C., Baldi, P. and Sablok, G., 2016. Suppression substractive hybridization and NGS reveal differential transcriptome expression profiles in wayfaring tree (Viburnum lantana L.) treated with ozone. Frontiers in plant science, 7, p.713.

Gene identifier
Bin Code
Bin Name
FoldChange
Log2FC
Functional annotation
EnsVib0421
#N/A
#N/A
2.576288256
1.365
Protein of unknown function CP12
EnsVib0435
21.99
redox.misc
0.579665226
-0.787
NAD(P)-binding domain
EnsVib0445
#N/A
#N/A
0.014638106
-6.094
Photosystem I PsaO
EnsVib0462
27.4
RNA.RNA binding
0.215870335
-2.212
Ribosomal protein S4e, central
EnsVib0469
21.4
redox.glutaredoxins
1.932217321
0.95
Thioredoxin fold
EnsVib0476
27.4
RNA.RNA binding
0.483053306
-1.05
Ribosomal protein S5 domain 2-type fold
EnsVib0492
#N/A
#N/A
10.62718527
3.41
Tetratricopeptide-like helical
EnsVib0499
#N/A
#N/A
0.391043808
-1.355
#N/A
EnsVib0501
#N/A
#N/A
0.044418723
-4.493
Bax inhibitor-1-related
EnsVib0505
23
nucleotide metabolism
35.10192313
5.133
ATPase, AAA-type, core
EnsVib0509
#N/A
#N/A
0.029275961
-5.094
#N/A
EnsVib0512
#N/A
#N/A
0.002683607
-8.542
Translation protein SH3-like
EnsVib0516
21.2
redox.ascorbate and glutathione
38.32229988
5.26
Thioredoxin fold
EnsVib0518
2.2.1.3.30
major CHO metabolism.degradation.sucrose.invertases.inhibitors
0.006851881
-7.189
Pectin lyase fold
EnsVib0535
#N/A
#N/A
1.449160908
0.535
PapD-like
EnsVib0638
23.3
nucleotide metabolism.salvage
0.429381762
-1.22
Phosphoribulokinase
EnsVib0688
15
metal handling
0.644074168
-0.635
Zinc finger, C3HC4 RING-type
EnsVib0735
#N/A
#N/A
0.161017506
-2.635
Heat shock protein DnaJ
EnsVib0746
17.5.1.2
hormone metabolism.ethylene.synthesis-degradation.1-aminocyclopropane-1-carboxylate oxidase
0.161017056
-2.635
Oxoglutarate/iron-dependent oxygenase
EnsVib0765
#N/A
#N/A
11.27126561
3.495
Protein of unknown function DUF1817
EnsVib0767
#N/A
#N/A
9.661092729
3.272
#N/A
EnsVib0792
#N/A
#N/A
0.161018352
-2.635
#N/A
EnsVib0812
8.2.10
TCA / org transformation.other organic acid transformatons.malic
2.737305381
1.453
NAD(P)-binding domain
EnsVib0830
17.7.1
hormone metabolism.jasmonate.synthesis-degradation
29.94934696
4.904
Myb, DNA-binding
EnsVib0869
23.3
nucleotide metabolism.salvage
2.898322417
1.535
ABC-2 type transporter
EnsVib0899
#N/A
#N/A
0.644072125
-0.635
#N/A
EnsVib0984
#N/A
#N/A
0.402545073
-1.313
#N/A
EnsVib1062
#N/A
#N/A
0.322035516
-1.635
#N/A
EnsVib0002
17.7.1.2
hormone metabolism.jasmonate.synthesis-degradation.lipoxygenase
133.6448453
7.062
Lipoxygenase, LH2
EnsVib0016
#N/A
#N/A
0.04025452
-4.635
Ribosomal protein S5 domain 2-type fold
EnsVib0022
10.2
cell wall.cellulose synthesis
5.152580748
2.365
GOLD
EnsVib0032
#N/A
#N/A
0.402545043
-1.313
Cold acclimation WCOR413
EnsVib0035
17.7.1.2
hormone metabolism.jasmonate.synthesis-degradation.lipoxygenase
0.21636803
-2.208
Lipoxygenase, LH2
EnsVib0036
17.7.1.3
hormone metabolism.jasmonate.synthesis-degradation.allene oxidase synthase
0.002385474
-8.712
Lipoxygenase, LH2
EnsVib0039
15
metal handling
0.912435453
-0.132
GroES-like
EnsVib0041
#N/A
#N/A
58.93246407
5.881
HSP20-like chaperone
EnsVib0046
#N/A
#N/A
1.932209923
0.95
Cold acclimation WCOR413
EnsVib0071
#N/A
#N/A
0.322036585
-1.635
#N/A
EnsVib0080
15
metal handling
0.01951731
-5.679
Twin-arginine translocation pathway, signal sequence
EnsVib0083
27.4
RNA.RNA binding
0.107345516
-3.22
A.T hook-like
EnsVib0085
23
nucleotide metabolism
0.414046106
-1.272
ATPase, AAA-type, core
EnsVib0120
#N/A
#N/A
1.610182059
0.687
#N/A
EnsVib0128
13
amino acid metabolism
11.91532739
3.575
Amino acid-binding ACT
EnsVib0139
15
metal handling
0.966109102
-0.05
Zinc finger, C3HC4 RING-type
EnsVib0140
29.5
protein.degradation
4.669526862
2.223
Peptidase C1A, papain
EnsVib0148
21.99
redox.misc
0.64407236
-0.635
Aldo/keto reductase
EnsVib0155
29.5
protein.degradation
2.65679815
1.41
Peptidase C1A, papain
EnsVib0159
6.1
gluconeogenesis / glyoxylate cycle.citrate synthase
46.05117033
5.525
Citrate synthase-like
EnsVib0162
1.1.5
PS.lightreaction.other electron carrier (ox/red)
0.015335006
-6.027
Cytochrome P450
EnsVib0178
15
metal handling
0.032203665
-4.957
Lipoxygenase, LH2
EnsVib0185
21.99
redox.misc
1.288141109
0.365
Thioredoxin-like
EnsVib0199
23
nucleotide metabolism
0.02408931
-5.375
ATPase, AAA-type, core
EnsVib0212
15
metal handling
0.073446926
-3.767
Twin-arginine translocation pathway, signal sequence
EnsVib0217
#N/A
#N/A
0.885599372
-0.175
#N/A
EnsVib0225
#N/A
#N/A
5.79665016
2.535
#N/A
EnsVib0241
23
nucleotide metabolism
33.59908965
5.07
Nucleotide-binding, alpha-beta plait
EnsVib0243
23
nucleotide metabolism
89.52600184
6.484
Nucleotide-binding, alpha-beta plait
EnsVib0244
1.3.6
PS.calvin cycle.aldolase
0.080785699
-3.63
Aldolase-type TIM barrel
EnsVib0251
#N/A
#N/A
47.98334977
5.584
#N/A
EnsVib0266
23
nucleotide metabolism
0.046005222
-4.442
ATPase, AAA-type, core
EnsVib0267
#N/A
#N/A
38.96635677
5.284
Ricin B lectin
EnsVib0271
#N/A
#N/A
2.25425171
1.173
#N/A
EnsVib0273
#N/A
#N/A
15.77975582
3.98
Aquaporin
EnsVib0283
#N/A
#N/A
5.658635322
2.5
#N/A
EnsVib0284
#N/A
#N/A
0.322036177
-1.635
GRIM-19
EnsVib0308
23
nucleotide metabolism
22.22051024
4.474
#N/A
EnsVib0313
1.3.1
PS.calvin cycle.rubisco large subunit
0.025762992
-5.279
Ribulose bisphosphate carboxylase, small chain
EnsVib0314
20.1.4
stress.biotic.kinases
12.39837581
3.632
Acetylglutamate kinase
EnsVib0316
#N/A
#N/A
1.974221465
0.981
#N/A
EnsVib0332
#N/A
#N/A
19.10747634
4.256
#N/A
EnsVib0341
#N/A
#N/A
30.91548061
4.95
Oligopeptide transporter
EnsVib0359
#N/A
#N/A
25.44081614
4.669
#N/A
EnsVib0376
26.2
misc.UDP glucosyl and glucoronyl transferases
59.89866134
5.904
UDP-glucuronosyl/UDP-glucosyltransferase
EnsVib0383
#N/A
#N/A
22.22049289
4.474
Protein of unknown function DUF584
EnsVib0387
#N/A
#N/A
26.40693734
4.723
Protein of unknown function DUF862, eukaryotic
EnsVib0402
#N/A
#N/A
58.28857672
5.865
#N/A
EnsVib0416
#N/A
#N/A
415.4266668
8.698
HSP20-like chaperone
EnsVib0419
#N/A
#N/A
29.62732089
4.889
TMS membrane protein/tumour differentially expressed protein