Species & Dataset

  • Brassica campestris

  • Common name: Mustard, Pak choi

  • Family: Brassicaceae

Experiment

  • Cultivar: Pak Choi (‘Jingguan’)

  • Tissue: Second leaves from the top

  • Ozone concentration: ​251.71 ± 8.15 ppb

  • Ozone exposure: 2 days (8 hours/day)

  • Sampling time: End of exposure period

  • Platform: Illumina Hiseq 2500

  • Year of study: 2017

  • Location: China

Title: Transcriptomic analysis of Pak Choi under acute ozone exposure revealed regulatory mechanism against ozone stress

 

Summary: Ground-level ozone (O3) is one of the major air pollutants, which cause oxidative injury to plants. The physiological and biochemical mechanisms underlying the responses of plants to O3 stress have been well investigated. However, there are limited reports about the molecular basis of plant responses to O3. In this study, a comparative transcriptomic analysis of Pak Choi (Brassica campestris ssp. chinensis) exposed to different O3 concentrations was conducted for the first time. Seedlings of Pak Choi with five leaves were exposed to non-filtered air (NF, 31 ppb) or elevated O3 (E-O3, 252 ppb) for 2 days (8 h per day, from 9:00–17:00). Compared with plants in the NF, a total of 675 differentially expressed genes (DEGs) were identified in plants under E-O3, including 219 DEGs with decreasedexpressions and 456 DEGs with increased expressions. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that O3 stress invoked multiple cellular defense pathways to mitigate the impaired cellular integrity and metabolism, including ‘glutathione metabolism’, ‘phenylpropanoid biosynthesis’, ‘sulfur metabolism’, ‘glucosinolate biosynthesis’, ‘cutin, suberine and wax biosynthesis’ and others. Transcription factors potentially involved in this cellular regulation were also found, such as AP2-ERF, WRKY, JAZ, MYB etc. Based on the RNA-Seq data and previous studies, a working model was proposed integrating O3 caused reactive oxygen burst, oxidation-reduction regulation, jasmonic acid and downstream functional genes for the regulation of cellular homeostasis after acute O3 stress. The present results provide a valuable insight into the molecular responses of Pak Choi to acute O3 stress and the specific DEGs revealed in this study could be used for further functional identification of key allelic genes determining the O3 sensitivity of Pak Choi.

 

Data repository: NCBI Sequence Read Archive (SRA) repository (Accession number SRP100739)

Reference: Zhang, L., Xu, B., Wu, T., Wen, M.X., Fan, L.X., Feng, Z.Z. and Paoletti, E., 2017. Transcriptomic analysis of Pak Choi under acute ozone exposure revealed regulatory mechanism against ozone stress. BMC plant biology, 17(1), pp.1-15.

Gene Id
log2FoldChange
P value
p adjusted
Blast swiss prot
Novel00198
2.3796
0.031331
1
PREDICTED: LOW QUALITY PROTEIN: zinc finger protein ZAT12 [Brassica rapa]
Novel00239
1.8391
0.0016367
0.65326
BnaA05g36040D [Brassica napus]
Novel00281
3.6393
0.014608
1
-//-
Novel00301
-2.0001
0.0095875
1
BnaA03g36250D [Brassica napus]
Novel00394
2.9789
0.0042837
1
PREDICTED: probable sulfate transporter 4.2 [Brassica rapa]
Novel00474
-0.83744
0.034275
1
PREDICTED: nitrile-specifier protein 2-like [Brassica rapa]
Novel00479
-1.4541
0.043806
1
-//-
Novel00652
5.007
0.00047641
0.31186
BnaA06g16030D [Brassica napus]
Novel00655
1.3495
0.033791
1
-//-
Novel00725
-0.86713
0.043063
1
PREDICTED: CBL-interacting serine/threonine-protein kinase 25 [Brassica rapa]
Novel00906
-1.8961
0.0092292
1
PREDICTED: putative ribonuclease H protein At1g65750 [Brassica rapa]
Novel00939
-2.0826
0.037074
1
PREDICTED: uncharacterized protein LOC103868993 [Brassica rapa]
Novel00940
-1.5896
0.036736
1
PREDICTED: uncharacterized protein LOC103833987 isoform X1 [Brassica rapa]
Novel00971
1.6485
0.008162
1
BnaA08g28890D [Brassica napus]
Novel00975
#NAME?
0.0029021
0.88649
PREDICTED: U-box domain-containing protein 52-like [Brassica rapa]
Novel01038
0.9736
0.037561
1
PREDICTED: folylpolyglutamate synthase isoform X2 [Brassica rapa]
Novel01073
1.3997
0.021953
1
-//-
Novel01075
-2.3961
0.048293
1
BnaA09g11270D [Brassica napus]
Novel01115
1.3046
0.027175
1
PREDICTED: protein HOTHEAD-like isoform X1 [Brassica rapa]
Novel01116
4.2131
0.00025504
0.19908
BnaC04g24690D [Brassica napus]
Novel01134
Inf
0.0010695
0.51479
PREDICTED: uncharacterized protein LOC103843858 [Brassica rapa]
Novel01217
0.87443
0.049064
1
BnaA10g26410D [Brassica napus]
Novel01263
7.5698
0.010222
1
PREDICTED: uncharacterized protein LOC103849967 isoform X2 [Brassica rapa]
Novel01294
6.1354
0.018327
1
-//-
Bra038089
6.7475
0.029491
1
-//-
Bra038101
-1.9568
0.018394
1
-//-
Bra038267
2.004
0.01617
1
-//-
Bra038426
1.0841
0.033567
1
-//-
Bra038451
1.4115
0.0033201
0.89808
-//-
Bra038460
1.5492
0.012005
1
sp|B9SA89|CSPLB_RICCO CASP-like protein 2B1 OS=Ricinus communis GN=RCOM_0864260 PE=2 SV=1//5.62967e-61
Bra038521
1.4647
0.0019759
0.7239
-//-
Bra038663
1.2266
0.0043657
1
-//-
Bra038677
3.7944
0.0021981
0.78408
-//-
Bra038734
-1.5347
0.00012353
0.13043
-//-
Bra038756
-2.063
0.022561
1
-//-
Bra038935
-1.3402
0.012921
1
-//-
Bra038952
0.94855
0.041898
1
-//-
Bra038965
1.3336
0.010564
1
-//-
Bra038967
1.2732
0.0031005
0.89374
-//-
Bra038999
-1.316
0.020495
1
-//-
Bra039047
5.2091
0.0000109
0.025587
sp|Q9LHA1|C8D11_ARATH Cytochrome P450 81D11 OS=Arabidopsis thaliana GN=CYP81D11 PE=2 SV=1//0
Bra039112
1.7879
0.0049156
1
-//-
Bra039150
0.92323
0.047011
1
sp|Q9SGA6|RS191_ARATH 40S ribosomal protein S19-1 OS=Arabidopsis thaliana GN=RPS19A PE=2 SV=1//4.6349e-100
Bra039217
1.9679
0.0096431
1
sp|Q8S8Q6|TET8_ARATH Tetraspanin-8 OS=Arabidopsis thaliana GN=TET8 PE=2 SV=1//1.85291e-145
Bra039304
-1.1401
0.007898
1
-//-
Bra039368
-0.85512
0.04252
1
sp|Q9LK64|AB3C_ARATH ABC transporter C family member 3 OS=Arabidopsis thaliana GN=ABCC3 PE=1 SV=1//0
Bra039379
-1.1151
0.010635
1
-//-
Bra039531
3.1432
0.01538
1
sp|C0LGP4|Y3475_ARATH Probable LRR receptor-like serine/threonine-protein kinase At3g47570 OS=Arabidopsis thaliana GN=At3g47570 PE=2 SV=1//1.60956e-173
Bra039556
3.137
0.019321
1
-//-
Bra039680
1.0377
0.038753
1
-//-
Bra039707
1.1101
0.013542
1
-//-
Bra039752
1.4812
0.015192
1
sp|Q9C8D1|PUB20_ARATH U-box domain-containing protein 20 OS=Arabidopsis thaliana GN=PUB20 PE=2 SV=1//0
Bra039800
1.2463
0.046185
1
-//-
Bra039818
0.9976
0.044618
1
-//-
Bra039948
-1.0384
0.015708
1
-//-
Bra039980
2.259
0.011042
1
sp|Q9ZW24|GSTU7_ARATH Glutathione S-transferase U7 OS=Arabidopsis thaliana GN=GSTU7 PE=2 SV=1//7.65853e-123
Bra039982
1.9586
0.046515
1
-//-
Bra039984
4.166
0.0039897
0.98925
sp|Q9ZW29|GSTU2_ARATH Glutathione S-transferase U2 OS=Arabidopsis thaliana GN=GSTU2 PE=2 SV=1//9.34868e-142
Bra040158
2.8051
0.046743
1
-//-
Bra040287
1.2607
0.022025
1
-//-
Bra040363
1.7841
0.015917
1
sp|Q9SFU3|PPA15_ARATH Purple acid phosphatase 15 OS=Arabidopsis thaliana GN=PAP15 PE=1 SV=1//0
Bra040554
-1.387
0.02779
1
-//-
Bra040577
2.0264
0.0094337
1
-//-
Bra040588
-1.4728
0.023764
1
-//-
Bra040628
2.233
0.0016165
0.65326
-//-
Bra040777
1.7053
0.024067
1
sp|Q949Y5|EGY1_ARATH Probable zinc metalloprotease EGY1, chloroplastic OS=Arabidopsis thaliana GN=EGY1 PE=2 SV=1//1.7978e-34
Bra040903
-0.8354
0.035363
1
-//-
Bra040926
4.7836
0.00015791
0.13601
sp|Q8VWJ2|WRK28_ARATH Probable WRKY transcription factor 28 OS=Arabidopsis thaliana GN=WRKY28 PE=2 SV=1//1.09585e-140
Bra040939
1.0448
0.046869
1
sp|Q9FH05|SCP42_ARATH Serine carboxypeptidase-like 42 OS=Arabidopsis thaliana GN=SCPL42 PE=2 SV=1//0
Bra040972
-1.6996
0.039601
1
-//-
Bra041032
-0.89792
0.037099
1
-//-
Bra041035
2.93
0.0035443
0.92804
-//-
Bra041046
5.3692
0.003465
0.91459
-//-
Bra041142
2.2467
0.036314
1
-//-
Bra033811
5.08
0.00025295
0.19908
-//-
Bra033869
-1.2186
0.016453
1
-//-
Bra034049
1.754
0.0079979
1
-//-
Bra034061
4.5045
0.0019253
0.7239
sp|Q9SR36|GSTU8_ARATH Glutathione S-transferase U8 OS=Arabidopsis thaliana GN=GSTU8 PE=2 SV=1//2.25462e-132
Bra034100
2.3972
0.02569
1
-//-
Bra034162
-1.3233
0.010417
1
sp|Q9SRL4|ENAS2_ARATH Cytosolic endo-beta-N-acetylglucosaminidase 2 OS=Arabidopsis thaliana GN=ENGASE2 PE=1 SV=1//1.46064e-06
Bra034201
-1.3222
0.026577
1
sp|Q9ZQZ9|TI204_ARATH Protein TIC 20-IV, chloroplastic OS=Arabidopsis thaliana GN=TIC20-IV PE=2 SV=1//1.10318e-167
Bra034206
3.5366
0.0013619
0.58653
-//-
Bra034313
-1.5178
0.0064742
1
sp|O81020|NPC2_ARATH Non-specific phospholipase C2 OS=Arabidopsis thaliana GN=NPC2 PE=2 SV=1//0
Bra034350
3.7621
0.0045295
1
-//-
Bra034424
3.6806
0.023453
1
-//-
Bra034429
1.0486
0.037801
1
sp|Q0VD42|TM136_BOVIN Transmembrane protein 136 OS=Bos taurus GN=TMEM136 PE=2 SV=1//5.87969e-12
Bra034433
0.94927
0.046824
1
-//-
Bra034557
2.9198
0.038462
1
-//-
Bra034611
1.7083
0.01066
1
-//-
Bra034806
-1.4718
0.0029781
0.88649
-//-
Bra035002
3.093
0.036625
1
-//-
Bra035029
Inf
0.041356
1
-//-
Bra035348
1.2489
0.01625
1
-//-
Bra035413
-0.88737
0.040513
1
sp|Q944S1|RH22_ARATH DEAD-box ATP-dependent RNA helicase 22 OS=Arabidopsis thaliana GN=RH22 PE=2 SV=1//0
Bra035505
2.2915
0.046534
1
-//-
Bra035640
1.3865
0.0095042
1
sp|Q9LTS3|CKX3_ARATH Cytokinin dehydrogenase 3 OS=Arabidopsis thaliana GN=CKX3 PE=1 SV=1//0
Bra035732
3.8447
0.040549
1
-//-
Bra035942
0.82099
0.048593
1
-//-
Bra035945
2.7534
0.048783
1
-//-
Bra035956
-0.90949
0.046802
1
-//-
Bra035966
-1.2525
0.028692
1
-//-
Bra035973
3.9977
0.047185
1
-//-
Bra036138
4.4573
1.77e-9
0.0000193
sp|Q9FGZ4|WRK48_ARATH Probable WRKY transcription factor 48 OS=Arabidopsis thaliana GN=WRKY48 PE=2 SV=1//4.92091e-129
Bra036151
4.8354
0.021864
1
-//-
Bra036293
-1.1381
0.010145
1
-//-
Bra036306
3.0907
0.023875
1
-//-
Bra036782
1.0857
0.013571
1
-//-
Bra036841
-1.9196
0.0034382
0.91459
-//-
Bra036881
1.9968
0.027727
1
-//-
Bra037007
3.7488
0.01194
1
-//-
Bra037039
-2.8673
0.036802
1
-//-
Bra037124
-1.5104
0.021469
1
-//-
Bra037161
2.2692
0.00000822
0.020696
-//-
Bra037170
-0.90891
0.047222
1
sp|Q6NQL6|LPPE2_ARATH Lipid phosphate phosphatase epsilon 2, chloroplastic OS=Arabidopsis thaliana GN=LPPE2 PE=1 SV=1//1.76404e-103
Bra037191
-0.81318
0.036978
1
sp|Q39129|STR16_ARATH Thiosulfate sulfurtransferase 16, chloroplastic OS=Arabidopsis thaliana GN=STR16 PE=1 SV=2//3.61344e-62
Bra037295
1.1895
0.011638
1
-//-
Bra037358
-1.2764
0.0030386
0.88914
sp|Q84WU2|UBP13_ARATH Ubiquitin carboxyl-terminal hydrolase 13 OS=Arabidopsis thaliana GN=UBP13 PE=1 SV=1//6.93248e-09
Bra037386
1.5525
0.00015641
0.13601
-//-
Bra037422
2.1404
0.00000389
0.010623
-//-
Bra037456
1.1519
0.042505
1
-//-
Bra037465
-1.0579
0.024548
1
-//-
Bra037480
1.102
0.0098159
1
-//-
Bra037715
-0.85595
0.040244
1
-//-
Bra038031
3.8324
0.001802
0.69386
-//-
Bra030032
-1.3001
0.047371
1
sp|O04067|AGL9_SINAL Agamous-like MADS-box protein AGL9 homolog OS=Sinapis alba GN=AGL9 PE=2 SV=1//1.55905e-179
Bra030177
1.2096
0.022665
1
sp|P56812|PDCD5_MOUSE Programmed cell death protein 5 OS=Mus musculus GN=Pdcd5 PE=1 SV=3//3.57267e-26
Bra030178
1.7468
0.0081106
1
-//-
Bra030223
-2.1767
0.021634
1
-//-
Bra030241
1.1905
0.047807
1
-//-
Bra030284
-1.8986
0.0082314
1
-//-
Bra030334
-2.6289
0.00091937
0.47764
sp|Q9GZR2|REXO4_HUMAN RNA exonuclease 4 OS=Homo sapiens GN=REXO4 PE=1 SV=2//5.27345e-25
Bra030337
-1.3541
0.0058576
1
-//-
Bra030386
2.9583
0.0011706
0.55404
sp|Q9SE50|BGL18_ARATH Beta-D-glucopyranosyl abscisate beta-glucosidase OS=Arabidopsis thaliana GN=BGLU18 PE=1 SV=2//0
Bra030389
1.3018
0.025705
1
-//-
Bra030402
-3.9227
0.030183
1
-//-
Bra030589
1.6322
0.040212
1
-//-
Bra030903
4.7344
0.036299
1
-//-
Bra030940
-1.3255
0.042704
1
sp|Q5UPH8|YR106_MIMIV Uncharacterized protein R106 OS=Acanthamoeba polyphaga mimivirus GN=MIMI_R106 PE=4 SV=1//1.03058e-10
Bra031012
1.4071
0.023245
1
-//-
Bra031069
3.5983
0.03248
1
-//-
Bra031393
-1.3569
0.033852
1
-//-
Bra031433
2.0175
0.040952
1
-//-
Bra031485
5.7413
0.0000582
0.09518
sp|F4HPY8|ALKR6_ARATH Probable aldo-keto reductase 6 OS=Arabidopsis thaliana GN=At1g60750 PE=3 SV=1//0
Bra031572
1.1938
0.028645
1
-//-
Bra031603
2.6173
0.0030426
0.88914
-//-
Bra031627
-0.83956
0.031925
1
sp|O04153|CALR3_ARATH Calreticulin-3 OS=Arabidopsis thaliana GN=CRT3 PE=1 SV=2//0
Bra031727
3.46
0.00011741
0.13043
-//-
Bra031747
1.5881
0.036882
1
-//-
Bra031757
3.0079
0.0014521
0.60204
-//-
Bra031878
-1.2824
0.032281
1
-//-
Bra031918
1.7391
0.014016
1
-//-
Bra031940
-1.2042
0.0038556
0.97824
sp|O49623|DPNP2_ARATH SAL2 phosphatase OS=Arabidopsis thaliana GN=SAL2 PE=2 SV=1//0
Bra031975
1.1257
0.012406
1
-//-
Bra031977
1.9073
0.0069081
1
sp|Q8W4K3|CAAT4_ARATH Cationic amino acid transporter 4, vacuolar OS=Arabidopsis thaliana GN=CAT4 PE=2 SV=1//0
Bra032010
0.88638
0.033553
1
sp|Q96324|GSTFB_ARATH Glutathione S-transferase F11 OS=Arabidopsis thaliana GN=GSTF11 PE=2 SV=1//1.88419e-115
Bra032019
1.6002
0.011951
1
-//-
Bra032030
1.135
0.049432
1
-//-
Bra032058
2.3325
0.049842
1
-//-
Bra032171
-1.0369
0.020077
1
-//-
Bra032303
-0.93395
0.02522
1
-//-
Bra032386
-1.3087
0.048212
1
-//-
Bra032624
-3.4412
0.034496
1
-//-
Bra032670
2.5691
0.0003453
0.24046
sp|F4HVY0|CER1_ARATH Protein ECERIFERUM 1 OS=Arabidopsis thaliana GN=CER1 PE=1 SV=1//0
Bra032693
2.1737
0.00088008
0.4646
-//-
Bra032762
-1.4815
0.0279
1
-//-
Bra032956
0.95989
0.044547
1
sp|Q9LW26|Y3684_ARATH Acyltransferase-like protein At3g26840, chloroplastic OS=Arabidopsis thaliana GN=At3g26840 PE=2 SV=1//0
Bra033077
3.0821
0.040949
1
-//-
Bra033117
2.0785
0.04317
1
-//-
Bra033249
1.2855
0.0022519
0.78408
-//-
Bra033436
2.2488
0.047789
1
-//-
Bra033482
3.2228
0.045008
1
-//-
Bra033532
2.662
0.024849
1
-//-
Bra033736
-1.082
0.046943
1
-//-
Bra033805
Inf
0.02699
1
-//-
Bra027042
1.3038
0.0092904
1
-//-
Bra027094
-1.1741
0.0058955
1
-//-
Bra027134
2.4943
0.032591
1
-//-
Bra027210
2.9506
0.00044797
0.29923
-//-
Bra027237
-1.8702
0.00021132
0.17734
-//-
Bra027257
-0.94936
0.024237
1
sp|Q9LK72|LECT5_ARATH Lectin-like protein At3g16530 OS=Arabidopsis thaliana GN=At3g16530 PE=1 SV=1//8.49046e-164
Bra027286
1.6245
0.031261
1
-//-
Bra027316
Inf
0.016217
1
-//-
Bra027353
1.0991
0.025465
1
-//-
Bra027432
-0.88762
0.029127
1
-//-
Bra027529
#NAME?
0.044303
1
-//-
Bra027547
3.4742
0.0062913
1
-//-
Bra027611
-0.99072
0.027948
1
sp|Q9LQ02|NRPD1_ARATH DNA-directed RNA polymerase IV subunit 1 OS=Arabidopsis thaliana GN=NRPD1 PE=1 SV=1//0
Bra027700
-2.7589
0.0029302
0.88649
-//-
Bra027724
-1.2284
0.0090418
1
-//-
Bra027782
3.8983
0.0000619
0.096436
sp|Q9SUS5|RHA1B_ARATH E3 ubiquitin-protein ligase RHA1B OS=Arabidopsis thaliana GN=RHA1B PE=2 SV=1//2.35232e-32
Bra027871
-1.3361
0.041266
1
sp|Q96FL8|S47A1_HUMAN Multidrug and toxin extrusion protein 1 OS=Homo sapiens GN=SLC47A1 PE=1 SV=1//2.97342e-44
Bra027987
4.418
0.0032489
0.89374
-//-
Bra027990
2.2413
0.0014531
0.60204
-//-
Bra028220
-1.1956
0.026872
1
sp|Q9FID8|Y5900_ARATH Putative receptor-like protein kinase At5g39000 OS=Arabidopsis thaliana GN=At5g39000 PE=3 SV=1//0
Bra028290
5.4137
0.0032598
0.89374
-//-
Bra028425
-1.3438
0.0055043
1
-//-
Bra028485
-0.79689
0.048893
1
-//-
Bra028503
1.559
0.016258
1
-//-
Bra028564
1.1805
0.018106
1
-//-
Bra028568
1.1859
0.025565
1
-//-