Species & Dataset

  • Viburnum lantana

  • Common name: Wayfaring tree

  • Family: Adoxaceae

Foliar Ozone Injury

viburnum lantanum injury.jpg

Experiment

  • 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

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 ID
RPKM (Induced)
(RPKM(Repressed)
LOG2(RPKMinduced/RPKMrepressed)
EnsVib0421
1079.506
419.016
1.365
EnsVib0435
1104.566
1905.524
-0.787
EnsVib0445
45.536
3110.785
-6.094
EnsVib0462
2802.433
12982.02
-2.212
EnsVib0469
672.344
347.965
0.95
EnsVib0476
181.501
375.737
-1.05
EnsVib0492
4698.98
442.166
3.41
EnsVib0499
2592.57
6629.871
-1.355
EnsVib0501
160.831
3620.793
-4.493
EnsVib0505
10482.382
298.627
5.133
EnsVib0509
124.508
4252.909
-5.094
EnsVib0512
48.905
18223.608
-8.542
EnsVib0516
11980.509
312.625
5.26
EnsVib0518
53.141
7755.68
-7.189
EnsVib0535
672.344
463.954
0.535
EnsVib0638
505.357
1176.941
-1.22
EnsVib0688
114.803
178.245
-0.635
EnsVib0735
88.264
548.164
-2.635
EnsVib0746
64.112
398.169
-2.635
EnsVib0765
2996.883
265.887
3.495
EnsVib0767
2502.252
259.003
3.272
EnsVib0792
213.002
1322.843
-2.635
EnsVib0812
1810.514
661.422
1.453
EnsVib0830
12167.042
406.254
4.904
EnsVib0869
1405.811
485.043
1.535
EnsVib0899
1472.754
2286.629
-0.635
EnsVib0984
660.851
1641.682
-1.313
EnsVib1062
192.337
597.254
-1.635
EnsVib0002
47466.907
355.172
7.062
EnsVib0016
80.041
1988.373
-4.635
EnsVib0022
1276.691
247.777
2.365
EnsVib0032
1528.918
3798.129
-1.313
EnsVib0035
2409.234
11134.889
-2.208
EnsVib0036
51.858
21739.078
-8.712
EnsVib0039
3028.647
3319.3
-0.132
EnsVib0041
12510.596
212.287
5.881
EnsVib0046
320.828
166.042
0.95
EnsVib0071
211.256
656
-1.635
EnsVib0080
95.811
4909.027
-5.679
EnsVib0083
71.394
665.086
-3.22
EnsVib0085
1004.15
2425.213
-1.272
EnsVib0120
560.287
347.965
0.687
EnsVib0128
4314.969
362.136
3.575
EnsVib0139
590.226
610.931
-0.05
EnsVib0140
2014.616
431.439
2.223
EnsVib0148
258.378
401.163
-0.635
EnsVib0155
1764.555
664.166
1.41
EnsVib0159
21181.42
459.954
5.525
EnsVib0162
161.082
10504.202
-6.027
EnsVib0178
79.67
2473.942
-4.957
EnsVib0185
241.435
187.429
0.365
EnsVib0199
787.284
32681.883
-5.375
EnsVib0212
368.189
5012.994
-3.767
EnsVib0217
1030.928
1164.102
-0.175
EnsVib0225
2761.414
476.381
2.535
EnsVib0241
30441.548
906.023
5.07
EnsVib0243
32567.948
363.782
6.484
EnsVib0244
2515.299
31135.449
-3.63
EnsVib0251
12308.353
256.513
5.584
EnsVib0266
74.061
1609.839
-4.442
EnsVib0267
13500.245
346.459
5.284
EnsVib0271
1589.536
705.128
1.173
EnsVib0273
4073.828
258.168
3.98
EnsVib0283
12530.052
2214.324
2.5
EnsVib0284
122.148
379.299
-1.635
EnsVib0308
4244.273
191.007
4.474
EnsVib0313
122.73
4763.81
-5.279
EnsVib0314
4625.958
373.11
3.632
EnsVib0316
7848.857
3975.672
0.981
EnsVib0332
17510.034
916.397
4.256
EnsVib0341
12309.586
398.169
4.95
EnsVib0359
7683.33
302.008
4.669
EnsVib0376
12886.598
215.14
5.904
EnsVib0383
7632.406
343.485
4.474
EnsVib0387
11362.377
430.28
4.723
EnsVib0402
16311.009
279.832
5.865
EnsVib0416
58328.812
140.407
8.698
EnsVib0419
25025.161
844.665
4.889