Species & Dataset

  • Quercus ilex

  • Common name: Holm oak, Evergreen oak

  • Family: Fagaceae

Foliar Ozone Injury

quercus injury.JPG

Experiment

  • Cultivar: Quecus ilex L.

  • Tissue: Shoot leaves

  • Ozone concentration: 80 ± 3 nL L-1          

  • Ozone exposure: Single pulse of 5 hours

  • Sampling time: ​ Immediately after ozone fumigation

  • Platform: HiSeq 2000 (Illumina)

  • Year of study: 2018

  • Location: Italy

Title: How Quercus ilex L. saplings face combined salt and ozone stress: a transcriptome analysis

 

Summary: Similar to other urban trees, holm oaks (Quercus ilex L.) provide a physiological, ecological and social service in the urban environment, since they remove atmospheric pollution. However, the urban environment has several abiotic factors that negatively influence plant life, which are further exacerbated due to climate change, especially in the Mediterranean area. Among these abiotic factors, increased uptake of Na+ and Cl− usually occurs in trees in the urban ecosystem; moreover, an excess of the tropospheric ozone concentration in Mediterranean cities further affects plant growth and survival. Here, we produced and annotated a de novo leaf transcriptome of Q.ilex as well as transcripts over- or under expressed after a single episode of O3 (80 nl l-1, 5 h), a salt treatment (150 mM for 15 days) or a combination of these treatments, mimicking a situation that plants commonly face, especially in urban environments. Salinity dramatically changed the profile of expressed transcripts, while the short O3 pulse had less effect on the transcript profile. However, the short O3 pulse had a very strong effect in inducing over- or under-expression of some genes in plants coping with soil salinity. Many differentially regulated genes were related to stress sensing and signalling, cell wall remodelling, ROS sensing and scavenging, photosynthesis and to sugar and lipid metabolism. Most differentially expressed transcripts revealed here are in accordance with a previous report on Q.ilex at the physiological and biochemical levels, even though the expression profiles were overall more striking than those found at the biochemical and physiological levels. We produced for the first time a reference transcriptome for Q.ilex, and performed gene expression analysis for this species when subjected to salt, ozone and a combination of the two. The comparison of gene expression between the combined salt + ozone treatment and salt or ozone alone showed that even though many differentially expressed genes overlap all treatments, combined stress triggered a unique response in terms of gene expression modification. The obtained results represent a useful tool for studies aiming to investigate the effects of environmental stresses in urban-adapted tree species.

 

Data repository: SRA (Bioproject accession PRJNA490658)

Reference: Natali, L., Vangelisti, A., Guidi, L., Remorini, D., Cotrozzi, L., Lorenzini, G., Nali, C., Pellegrini, E., Trivellini, A., Vernieri, P. and Landi, M., 2018. How Quercus ilex L. saplings face combined salt and ozone stress: a transcriptome analysis. BMC genomics, 19(1), pp.1-18.

Gene
logFC
FDR
Functional annotation
Regulation
contig_81324
-1.40724902
0.035180012
---NA---
DOWN
contig_13068
-1.406242075
0.000154862
chaperonin 60 subunit beta chloroplastic
DOWN
contig_51498
-1.403543435
0.037138252
---NA---
DOWN
contig_31708
-1.398227855
0.006582261
ABC transporter F family member 4
DOWN
contig_3051
-1.373227377
0.001051416
PREDICTED: uncharacterized protein LOC103495620
DOWN
contig_56626
-1.358206885
0.045879131
---NA---
DOWN
contig_27620
-1.32665753
0.032279798
---NA---
DOWN
contig_35482
-1.325654528
0.011067019
---NA---
DOWN
contig_72417
-1.315590013
0.009069119
---NA---
DOWN
contig_56952
-1.300796766
0.012807877
---NA---
DOWN
contig_20977
-1.300156394
0.046524281
---NA---
DOWN
contig_161945
-1.297393577
0.002158088
chaperonin 60 subunit alpha chloroplastic-like
DOWN
contig_12686
-1.285805275
0.004972696
Leucine-rich repeat kinase family isoform 1
DOWN
contig_38136
-1.270663894
0.016349931
---NA---
DOWN
contig_16492
-1.265182733
0.032279798
xylose isomerase
DOWN
contig_13477
-1.244287765
0.000385088
ru large subunit-binding subunit chloroplastic
DOWN
contig_74929
-1.234147415
0.049514328
---NA---
DOWN
contig_29405
-1.219040924
0.031870124
TMV resistance N-like isoform X5
DOWN
contig_83784
-1.211941565
0.020155373
transposon TX1 uncharacterized 149 kDa
DOWN
contig_26006
-1.172701176
0.020155373
40S ribosomal S13-like
DOWN
contig_47146
-1.169834585
0.004886975
---NA---
DOWN
contig_10520
-1.161883649
0.019141173
chaperonin 60 subunit alpha chloroplastic-like
DOWN
contig_18337
-1.161800867
0.048615035
universal stress A
DOWN
contig_31854
-1.150964516
0.03238076
DNA replication licensing factor MCM4
DOWN
contig_33745
-1.144809874
0.020155373
PREDICTED: uncharacterized protein LOC105178863
DOWN
contig_44120
-1.141236189
0.013234383
---NA---
DOWN
contig_11516
-1.13750213
0.029621639
pentatricopeptide repeat-containing At3g08820
DOWN
contig_20387
-1.129378441
0.004974027
nuclear pore complex NUP85
DOWN
contig_12757
-1.119495154
0.049654652
---NA---
DOWN
contig_64655
-1.117066773
0.000424833
---NA---
DOWN
contig_75950
-1.097690332
0.041389897
---NA---
DOWN
contig_18021
-1.082119591
0.017997811
---NA---
DOWN
contig_50370
-1.081047453
0.012298762
chaperonin 60 subunit alpha chloroplastic isoform X2
DOWN
contig_48138
-1.060997754
0.001489122
---NA---
DOWN
contig_19737
-1.057232044
0.00000129
CD99 antigen 2
DOWN
contig_64618
-1.041489907
0.033318787
---NA---
DOWN
contig_37596
-1.034274225
0.016484164
2,4-dichlorophenol 6-monooxygenase isoform X2
DOWN
contig_61208
-3.537751139
0.029507263
ribonuclease H At1g65750
DOWN
contig_75056
-3.334593773
0.02796222
---NA---
DOWN
contig_128148
-3.152229772
0.017997811
---NA---
DOWN
contig_100601
-3.15059704
0.000303495
---NA---
DOWN
contig_77721
-3.051577273
0.037221775
probable cytokinin riboside 5 -monophosphate phosphoribohydrolase LOGL10 isoform X1
DOWN
contig_75880
-3.041712895
0.046330472
---NA---
DOWN
contig_125031
-3.01301048
0.020155373
---NA---
DOWN
contig_46400
-2.969945135
0.04351202
PREDICTED: uncharacterized protein LOC107935794
DOWN
contig_21487
-2.872022307
0.039732779
PREDICTED: uncharacterized protein LOC103502279 isoform X1
DOWN
contig_150295
-2.858270078
0.049930658
---NA---
DOWN
contig_38207
-2.759485485
0.000240276
---NA---
DOWN
contig_112391
-2.598913379
0.032533234
---NA---
DOWN
contig_108666
-2.59653459
0.022816701
---NA---
DOWN
contig_77736
-2.525183301
0.028625864
cytochrome P450 87A3
DOWN
contig_60740
-2.426551507
0.041389897
---NA---
DOWN
contig_69562
-2.413768391
0.007818813
disease resistance RPP13 1
DOWN
contig_73799
-2.373918888
0.039732779
endonuclease V isoform X1
DOWN
contig_178634
-2.320967964
0.029677537
chlorophyll a-b binding chloroplastic
DOWN
contig_82034
-2.280019521
0.004974027
---NA---
DOWN
contig_3721
-2.1298742
0.013079514
TMV resistance N-like
DOWN
contig_133179
-2.011168711
0.034710103
---NA---
DOWN
contig_41169
-1.960812636
2.86e-7
---NA---
DOWN
contig_94464
-1.951704722
0.03157712
---NA---
DOWN
contig_165558
-1.909651677
0.010762993
argonaute 16-like
DOWN
contig_86194
-1.869492162
0.008540977
---NA---
DOWN
contig_76287
-1.865210936
0.003489736
---NA---
DOWN
contig_34965
-1.827390372
0.047533976
proteasome subunit beta type-7-A-like
DOWN
contig_93438
-1.815398555
0.003235894
---NA---
DOWN
contig_42644
-1.761934621
0.038352742
---NA---
DOWN
contig_35539
-1.752500104
0.005429945
---NA---
DOWN
contig_68520
-1.741540952
0.036175192
---NA---
DOWN
contig_51960
-1.716456487
0.015762073
---NA---
DOWN
contig_109679
-1.689123775
0.031326543
---NA---
DOWN
contig_95775
-1.664683569
0.037240837
---NA---
DOWN
contig_90187
-1.655167393
0.034172252
---NA---
DOWN
contig_99923
-1.64658135
0.001390571
---NA---
DOWN
contig_47634
-1.630728366
0.00748348
---NA---
DOWN
contig_97070
-1.609908844
0.002728471
---NA---
DOWN
contig_30617
-1.579027561
0.0000299
---NA---
DOWN
contig_59462
-1.535173382
0.023570163
---NA---
DOWN
contig_101356
-1.531848335
0.009771479
---NA---
DOWN
contig_48228
-1.529626694
0.00000211
TMV resistance N-like isoform X2
DOWN
contig_29012
-1.529052049
0.041017016
probable leucine-rich repeat receptor kinase At5g49770 isoform X2
DOWN
contig_67831
-1.526893342
0.048453735
---NA---
DOWN
contig_63539
-1.513980247
0.000296859
---NA---
DOWN
contig_62721
-1.483191698
0.021517416
chaperonin 60 subunit alpha chloroplastic
DOWN
contig_31544
-1.472893521
0.0000428
---NA---
DOWN
contig_47540
-1.466987147
0.00000591
Embryo defective
DOWN
contig_127362
-1.455307788
0.007628936
---NA---
DOWN
contig_37075
-1.412331824
0.037221775
---NA---
DOWN
contig_50634
1.067171055
0.037240837
PREDICTED: uncharacterized protein LOC103323735
UP
contig_12260
1.04865049
0.019953556
disease resistance RGA1
UP
contig_16231
1.043664901
0.001390571
disease resistance RGA4 isoform X1
UP
contig_43279
1.031672902
0.028529316
---NA---
UP
contig_173545
1.024696133
0.001089514
sorbin and SH3 domain-containing 2-like
UP
contig_13641
1.024136989
0.001051416
Ankyrin repeat family regulator of chromosome condensation (RCC1) family isoform 2
UP
contig_3803
1.009946507
0.007628936
cysteine-rich receptor kinase 15
UP
contig_176124
-9.282961064
0.032279798
hypothetical protein POPTR_0013s12970g
DOWN
contig_121714
-8.667942676
0.008540977
ribonuclease H At1g65750
DOWN
contig_157081
-7.65332784
0.023730309
serine threonine- phosphatase 7 long form homolog
DOWN
contig_159368
-7.653319911
0.025994617
PREDICTED: uncharacterized protein LOC102626455
DOWN
contig_177010
-7.555812838
0.048615035
---NA---
DOWN
contig_105277
-7.422547458
0.024585808
---NA---
DOWN
contig_165817
-6.913018714
0.032279798
ELAV 3 isoform X1
DOWN
contig_136125
-6.819507637
0.048229677
---NA---
DOWN
contig_96511
-6.8093373
0.011342536
---NA---
DOWN
contig_52918
-6.654198986
0.005687969
---NA---
DOWN
contig_3883
-6.622056137
0.038352742
probable disease resistance At5g66900
DOWN
contig_2748
-6.503888512
0.007336444
PREDICTED: uncharacterized protein LOC103329708
DOWN
contig_71929
-6.384529067
0.034172252
probable fructokinase-7
DOWN
contig_89129
-6.357186299
0.041389897
---NA---
DOWN
contig_120433
-6.281619711
0.038352742
---NA---
DOWN
contig_142185
-6.095238775
0.04861487
F-box kelch-repeat SKIP6-like
DOWN
contig_35102
-6.071973593
0.000472146
maf DDB_G0281937 isoform X1
DOWN
contig_160192
-5.531950726
0.009747335
---NA---
DOWN
contig_108939
-5.436858161
0.032372281
---NA---
DOWN
contig_162245
-5.420923808
0.049058321
TMV resistance N-like
DOWN
contig_157368
-5.338495286
0.016184615
---NA---
DOWN
contig_125089
-5.265751014
0.040133136
Gpr1 family (ISS)
DOWN
contig_29359
-5.238972582
0.032279798
TMV resistance N-like
DOWN
contig_125985
-5.235398665
0.006582261
---NA---
DOWN
contig_68599
-5.05154175
0.033051592
---NA---
DOWN
contig_66891
-4.997449817
0.041389897
PREDICTED: uncharacterized protein LOC105157126
DOWN
contig_177491
-4.922978793
0.023639713
---NA---
DOWN
contig_73205
-4.913113387
0.048229677
hypothetical protein POPTR_0004s11480g
DOWN
contig_12866
-4.644749887
0.004957325
60S acidic ribosomal P0
DOWN
contig_168082
-4.569073775
0.038694774
---NA---
DOWN
contig_73983
-4.501962635
0.033051592
---NA---
DOWN
contig_103006
-4.479060829
0.00095943
---NA---
DOWN
contig_79388
-4.452317855
0.015558506
disease resistance RGA1
DOWN
contig_137968
-4.390154
0.008860442
---NA---
DOWN
contig_177895
-4.383765926
0.027027446
---NA---
DOWN
contig_150576
-4.33690677
0.001051416
---NA---
DOWN
contig_134924
-4.217898256
0.009747335
---NA---
DOWN
contig_17392
-4.203158214
0.001042563
---NA---
DOWN
contig_83977
-4.083831635
0.012270109
zinc finger BED domain-containing RICESLEEPER 2-like
DOWN
contig_86768
-4.018722814
0.041017016
---NA---
DOWN
contig_74093
-3.94653451
0.030757549
endochitinase-like
DOWN
contig_158281
-3.831745835
0.000888939
---NA---
DOWN
contig_103561
-3.730979326
0.019953556
---NA---
DOWN
contig_26172
2.101365784
0.038352742
---NA---
UP
contig_14983
2.081150489
0.006582261
disease resistance RPP13 1
UP
contig_10248
2.050671481
0.004545465
G-type lectin S-receptor-like serine threonine- kinase SD2-5
UP
contig_92848
2.020219535
0.038352742
---NA---
UP
contig_28909
1.899149823
0.00322927
hypothetical protein PRUPE_ppa010997mg
UP
contig_22570
1.83599339
0.032792879
disease resistance RGA3
UP
contig_16832
1.809923222
0.009854882
Formin 18
UP
contig_67530
1.809292998
0.013577416
hypothetical protein PRUPE_ppa1027140mg
UP
contig_30911
1.806339618
0.004974027
WVD2-like 7
UP
contig_15872
1.805883634
0.001051416
TMV resistance N-like
UP
contig_15389
1.801334087
0.01901902
disease resistance RGA3
UP
contig_85305
1.784218283
0.04351202
---NA---
UP
contig_7264
1.780923741
0.041230867
EXORDIUM-like 2
UP
contig_31333
1.77477308
0.00000431
TMV resistance N-like
UP
contig_58094
1.769061992
0.02242356
TMV resistance N-like
UP
contig_55194
1.768320584
0.011135951
PREDICTED: uncharacterized protein LOC104881798
UP
contig_9521
1.759662992
0.048229677
disease resistance RGA3
UP
contig_95245
1.733813343
0.014923338
---NA---
UP
contig_46232
1.700994246
0.038352742
---NA---
UP
contig_5297
1.673760843
0.029060902
---NA---
UP
contig_20832
1.652576714
0.00733328
disease resistance RGA3
UP
contig_4492
1.567224453
0.005348009
TMV resistance N-like
UP
contig_44125
1.515865589
0.009771763
---NA---
UP
contig_38460
1.500431201
0.003399315
---NA---
UP
contig_23466
1.499028556
0.034172252
TMV resistance N-like
UP
contig_75283
1.483532422
0.049058321
---NA---
UP
contig_44108
1.457842496
0.013437811
---NA---
UP
contig_38030
1.448752334
0.04346192
serine threonine- kinase At3g07070-like
UP
contig_5922
1.447460127
0.041389897
REVEILLE 8-like isoform X2
UP
contig_35703
1.404041998
0.030416699
receptor 12
UP
contig_11644
1.373105599
0.030757549
UDP-glycosyltransferase 71K1-like
UP
contig_15865
1.367785049
0.001012921
TMV resistance N-like
UP
contig_42297
1.357003841
0.024585808
UDP-glycosyltransferase 71K1-like
UP
contig_24341
1.340828343
0.019141173
F-box kelch-repeat At3g23880-like
UP
contig_54042
1.315978303
0.048974417
bifunctional UDP-glucose 4-epimerase and UDP-xylose 4-epimerase 1-like
UP
contig_18275
1.276649606
0.011985245
DNA RNA polymerases superfamily
UP
contig_26427
1.263923671
0.045879131
---NA---
UP
contig_24311
1.260154302
0.002696619
sulfate transporter -like
UP
contig_72885
1.256830926
0.003598938
disease resistance RGA1
UP
contig_22588
1.231933915
0.0491471
CLP protease regulatory subunit X isoform 3
UP
contig_53674
1.231439251
0.041389897
glycine oxidase isoform X1
UP
contig_82056
1.21785701
0.029677537
acetylajmalan esterase-like
UP
contig_1254
1.204565236
0.010567151
---NA---
UP
contig_31917
1.195275057
0.027540972
---NA---
UP
contig_107676
1.153398041
0.01034946
sphingolipid delta(4)-desaturase DES1-like
UP
contig_42296
1.143284939
0.000888939
anthocyanidin 3-O-glucosyltransferase 2-like
UP
contig_27112
1.136735543
0.034172252
---NA---
UP
contig_21218
1.133733887
0.01659874
LNK3 isoform X1
UP
contig_28609
1.087662329
0.041389897
---NA---
UP
contig_14559
1.072321305
0.048229677
receptor kinase HERK 1
UP
contig_77149
4.806199307
0.040133136
LRR receptor-like serine threonine- kinase EFR
UP
contig_72065
4.780617487
0.009771763
---NA---
UP
contig_39861
4.766694971
0.000888939
Disease resistance RPM1
UP
contig_74452
4.706862556
0.029677537
SPIRAL1-like 1
UP
contig_169727
4.706677719
0.030553216
---NA---
UP
contig_23425
4.696424487
0.012807877
DUF3511 domain
UP
contig_60908
4.562045455
0.039912761
auxin-induced 15A
UP
contig_58723
4.49696967
0.034273191
---NA---
UP
contig_11303
4.423765879
0.041389897
receptor 12
UP
contig_80330
4.386132477
0.00152679
---NA---
UP
contig_64526
4.37889033
0.021920166
TMV resistance N-like
UP
contig_87876
4.36742034
0.044866923
Calcineurin subunit B
UP
contig_32791
4.222321283
0.032259956
receptor 12
UP