Species & Dataset

Experiment

Foliar Ozone Injury

  • Phaseolus vulgaris

  • Common name: Common bean

  • Family: Fabaceae

  • Cultivar: Phaseolus vulgaris L.

  • Tissue: Shoot leaves

  • Ozone concentration: Ambient ozone (12.5 nL L−1 ± 0.96 nL L−1)

  •  Elevated ozone (151.2 nL L−1 ± 0.72 nL L−1)

  • Ozone exposure: Throughout the experiment (8 hours/day)

  • Sampling time: 11-13 days after planting

  • Platform: Hiseq 2000 (Illumina)

  • Year of study: 2015

  • Location: Urbana, USA

Phaseolus injury.jpg

Title: A comparative analysis of transcriptomic, biochemical, and physiological responses to elevated ozone identifies species-specific mechanisms of resilience in legume crop 

Summary: Current concentrations of tropospheric ozone ([O3]) pollution negatively impact plant metabolism, which can result in decreased crop yields. Interspecific variation in the physiological response of plants to elevated [O3] exists; however, the underlying cellular responses explaining species-specific differences are largely unknown. Here, a physiological screen has been performed on multiple varieties of legume species. Three varieties of garden pea (Pisum sativum L.) were resilient to elevated [O3]. Garden pea showed no change in photosynthetic capacity or leaf longevity when exposed to elevated [O3], in contrast to varieties of soybean (Glycine max (L.) Merr.) and common bean (Phaseolus vulgaris L.). Global transcriptomic and targeted biochemical analyses were then done to examine the mechanistic differences in legume responses to elevated [O3]. In all three species, there was an O3-mediated reduction in specific leaf weight and total non-structural carbohydrate content, as well as increased abundance of respiration-related transcripts. Differences specific to garden pea included a pronounced increase in the abundance of GLUTATHIONE REDUCTASE transcript, as well as greater contents of foliar glutathione, apoplastic ascorbate, and sucrose in elevated [O3]. These results suggest that garden pea may have had greater capacity for detoxification, which prevented net losses in CO2 fixation in an elevated [O3] environment

 

Data repository: NCBI [GenBank: SRP009826]

Reference: Yendrek, C.R., Koester, R.P. and Ainsworth, E.A., 2015. A comparative analysis of transcriptomic, biochemical, and physiological responses to elevated ozone identifies species-specific mechanisms of resilience in legume crops. Journal of experimental botany, 66(22), pp.7101-7112.

Gene Identifier
AGI Gene Code
Uniprot ID
Bin Code
Bin Name
log2FC
Functional Annnotation
Phvul.004G013500.1
AT5G14740
P42737
8.3
TCA / org transformation.carbonic anhydrases
-0.7
CARBONIC ANHYDRASE
Phvul.009G178900.1
AT3G01500
P27140
8.3
TCA / org transformation.carbonic anhydrases
1.09
CARBONIC ANHYDRASE
Phvul.004G013500.3
AT5G14740
P42737
8.3
TCA / org transformation.carbonic anhydrases
-0.7
CARBONIC ANHYDRASE
Phvul.006G192400.1
AT4G05020
Q94BV7
9.2.1.2
mitochondrial electron transport / ATP synthesis.NADH-DH.type II.external
2.41
NADH-DEHYDROGENASE [type II, external]
Phvul.002G223400.1
AT1G07180
Q8GWA1
9.2.1.4
mitochondrial electron transport / ATP synthesis.NADH-DH.type II.internal matrix
1.57
NADH-DEHYDROGENASE [type II, internal matrix]
Phvul.002G175300.1
AT2G29990
O80874
9.2.1.4
mitochondrial electron transport / ATP synthesis.NADH-DH.type II.internal matrix
-2.41
NADH-DEHYDROGENASE [type II, internal matrix]
Phvul.008G260300.1
AT2G29990
O80874
9.2.1.4
mitochondrial electron transport / ATP synthesis.NADH-DH.type II.internal matrix
0.7
NADH-DEHYDROGENASE [type II, internal matrix]
Phvul.011G058400.1
AT3G51790
Q96326
9.6
mitochondrial electron transport / ATP synthesis.cytochrome c
0.76
CYTOCHROME C
Phvul.004G070000.1
ATCG00830
29.2.1.1.1.2.2
protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit.L2
-1.24
CYTOCHROME C OXIDASE
Phvul.003G219400.1
AT2G22780
O82399
5.1
fermentation.LDH
0.59
Fermentation: LACTATE DEHYDROGENASE
Phvul.008G243200.1
AT2G22780
O82399
5.2
fermentation.PDC
0.6
Fermentation: PYRUVATE DECARBOXYLASE
Phvul.008G095400.1
AT5G01320
Q9M040
5.2
fermentation.PDC
-0.86
Fermentation: PYRUVATE DECARBOXYLASE
Phvul.002G072100.1
AT3G48000
Q9SU63
5.10
fermentation.aldehyde dehydrogenase
1.52
Fermentation: ALDEHYDE DEHYDROGENASE
Phvul.002G314000.1
AT3G48000
Q9SU63
5.10
fermentation.aldehyde dehydrogenase
0.7
Fermentation: ALDEHYDE DEHYDROGENASE
Phvul.004G162300.1
AT3G48000
Q9SU63
5.10
fermentation.aldehyde dehydrogenase
1.88
Fermentation: ALDEHYDE DEHYDROGENASE
Phvul.009G226700.1
AT1G79440
Q9SAK4
5.10
fermentation.aldehyde dehydrogenase
0.96
Fermentation: ALDEHYDE DEHYDROGENASE
Phvul.003G199100.2
AT1G23800
Q8S528
5.10
fermentation.aldehyde dehydrogenase
0.8
Fermentation: ALDEHYDE DEHYDROGENASE
Phvul.003G209100.1
6.2
gluconeogenesis / glyoxylate cycle.malate synthase
2.68
Gluconeogenesis / glyoxylate cycle: CITRATE SYNTHASE
Phvul.002G007700.1
35.2
not assigned.unknown
-3.37
Gluconeogenesis / glyoxylate cycle: MALATE DEHYDROGENASE
Phvul.002G139200.1
AT5G65690
B5X574
6.4
gluconeogenesis / glyoxylate cycle.PEPCK
2.19
Gluconeogenesis / glyoxylate cycle: PEPCK
Phvul.011G105500.1
AT1G77060
O49290
6.9
gluconeogenesis / glyoxylate cycle.isocitrate lyase
9.52
Gluconeogenesis / glyoxylate cycle: ISOCITRATE LYASE
Phvul.009G049200.1
AT3G49360
Q8LG70
7.1.2
OPP.oxidative PP.6-phosphogluconolactonase
-0.89
Pentose phosphate pathway, oxidative: 6-PHOSPHOGLUCONOLACTONASE
Phvul.004G150100.1
AT4G20930
Q9SUC0
35.1
not assigned.no ontology
0.81
Pentose phosphate pathway, oxidative: 6-PHOSPHOGLUCONATE DEHYDROGENASE
Phvul.006G127500.1
AT1G17650
F4I907
13.2.4.3
amino acid metabolism.degradation.branched chain group.valine
0.94
Pentose phosphate pathway, oxidative: 6-PHOSPHOGLUCONATE DEHYDROGENASE
Phvul.008G023700.2
AT5G41670
Q9FFR3
7.1.3
OPP.oxidative PP.6-phosphogluconate dehydrogenase
0.73
Pentose phosphate pathway, oxidative: 6-PHOSPHOGLUCONATE DEHYDROGENASE
Phvul.004G046100.1
AT5G41670
Q9FFR3
7.1.3
OPP.oxidative PP.6-phosphogluconate dehydrogenase
-1.99
Pentose phosphate pathway, oxidative: 6-PHOSPHOGLUCONATE DEHYDROGENASE
Phvul.002G281000.1
AT5G13420
Q9LYR4
7.2.2
OPP.non-reductive PP.transaldolase
1.94
Pentose phosphate pathway, non-reductive: TRANSALDOLASE
Phvul.008G003600.1
AT5G13420
Q9LYR4
7.2.2
OPP.non-reductive PP.transaldolase
0.64
Pentose phosphate pathway, non-reductive: TRANSALDOLASE
Phvul.006G122300.1
AT3G04790
Q9S726
1.3.10
PS.calvin cycle.Rib5P Isomerase
-0.69
Pentose phosphate pathway, non-reductive: RIBOSE 5-PHOSPHATE ISOMERASE
Phvul.002G234600.1
AT1G71100
Q9C998
7.2.4
OPP.non-reductive PP.ribose 5-phosphate isomerase
-0.62
Pentose phosphate pathway, non-reductive: RIBOSE 5-PHOSPHATE ISOMERASE
Phvul.006G011600.1
AT5G21100
Q8LPL3
21.2.1
redox.ascorbate and glutathione.ascorbate
1.11
ASCORBATE OXIDASE [cell wall]
Phvul.006G011700.1
AT5G21100
Q8LPL3
21.2.1
redox.ascorbate and glutathione.ascorbate
-1.92
ASCORBATE OXIDASE [cell wall]
Phvul.011G071300.1
AT1G07890
Q05431
21.2.1
redox.ascorbate and glutathione.ascorbate
0.19
ASCORBATE PEROXIDASE 1 [cytoplasm]
Phvul.002G107000.1
AT4G35970
Q7XZP5
21.2.1
redox.ascorbate and glutathione.ascorbate
-2.32
ASCORBATE PEROXIDASE 3 [microsome]
Phvul.011G035000.1
AT4G35970
Q7XZP5
21.2.1
redox.ascorbate and glutathione.ascorbate
0.08
ASCORBATE PEROXIDASE 3 [microsome]
Phvul.009G093000.1
AT3G09640
Q1PER6
26.12
misc.peroxidases
-0.88
ASCORBATE PEROXIDASE 6 [cytoplasm]
Phvul.009G126500.1
AT4G08390
Q42592
21.2.1
redox.ascorbate and glutathione.ascorbate
-0.65
ASCORBATE PEROXIDASE [thylakoid]
Phvul.009G126500.2
AT4G08390
Q42592
21.2.1
redox.ascorbate and glutathione.ascorbate
0.18
ASCORBATE PEROXIDASE [thylakoid]
Phvul.009G011100.1
AT1G20630
Q96528
21.6
redox.dismutases and catalases
0.07
CATALASE 2
Phvul.001G001000.1
AT1G20630
Q96528
21.6
redox.dismutases and catalases
0.07
CATALASE 2
Phvul.007G009800.1
AT1G19570
Q9FWR4
21.2.1
redox.ascorbate and glutathione.ascorbate
-0.03
DEHYDROASCORBATE REDUCTASE 2
Phvul.001G230400.1
AT1G75270
Q9FRL8
21.2.1
redox.ascorbate and glutathione.ascorbate
0.24
DEHYDROASCORBATE REDUCTASE 3 [chloroplast]
Phvul.002G322400.1
AT2G25080
P52032
21.2.2
redox.ascorbate and glutathione.glutathione
0.46
GLUTATHIONE PEROXIDASE 3
Phvul.002G288700.1
AT4G31870
Q9SZ54
21.2.2
redox.ascorbate and glutathione.glutathione
1.34
GLUTATHIONE PEROXIDASE 6
Phvul.004G083600.1
AT3G54660
P42770
21.2.2
redox.ascorbate and glutathione.glutathione
0.3
GLUTATHIONE REDUCTASE [cytoplasm]
Phvul.004G083700.1
AT3G54660
P42770
21.2.2
redox.ascorbate and glutathione.glutathione
0.21
GLUTATHIONE REDUCTASE [cytoplasm]
Phvul.007G177200.1
AT3G24170
P48641
21.2.2
redox.ascorbate and glutathione.glutathione
-0.05
GLUTATHIONE REDUCTASE [chloroplast]
Phvul.007G230300.1
AT5G03630
Q93WJ8
21.2
redox.ascorbate and glutathione
0.1
MONODEHYDROASCORBATE REDUCTASE 1
Phvul.008G155600.1
AT3G52880
Q9LFA3
21.2.1
redox.ascorbate and glutathione.ascorbate
-0.37
MONODEHYDROASCORBATE REDUCTASE 4
Phvul.006G097000.1
AT2G28190
O78310
21.6
redox.dismutases and catalases
-0.14
SUPEROXIDE DISMUTASE 1 [Cu,Zn]
Phvul.011G086300.1
AT1G08830
P24704
21.6
redox.dismutases and catalases
-0.6
SUPEROXIDE DISMUTASE 2 [Cu,Zn]
Phvul.004G081000.1
AT2G28190
O78310
21.6
redox.dismutases and catalases
-0.19
SUPEROXIDE DISMUTASE 3 [Cu,Zn]
Phvul.007G135400.1
AT4G25100
P21276
21.6
redox.dismutases and catalases
1.16
SUPEROXIDE DISMUTASE 2 [Fe; chloroplast]
Phvul.007G135400.2
AT4G25100
P21276
21.6
redox.dismutases and catalases
0.74
SUPEROXIDE DISMUTASE 2 [Fe; chloroplast]
Phvul.006G010800.1
AT5G51100
Q9LU64
21.6
redox.dismutases and catalases
-0.33
SUPEROXIDE DISMUTASE 3 [Fe; chloroplast]
Phvul.009G141600.1
AT3G56350
Q9LYK8
21.6
redox.dismutases and catalases
0.28
SUPEROXIDE DISMUTASE 1 [Mn]
Phvul.001G249200.1
AT4G39650
Q680I5
20.2
stress.abiotic
-1.34
?-GLUTAMYL TRANSPEPTIDASE
Phvul.002G289200.1
#N/A
#N/A
0.18
GLUTAMATE-CYSTEINE LIGASE
Phvul.006G094500.1
21.2.2
redox.ascorbate and glutathione.glutathione
-0.06
GLUTATHIONE SYNTHETASE
Phvul.006G145300.1
AT4G04040
F4JGR5
4.1.5
glycolysis.cytosolic branch.pyrophosphate-fructose-6-P phosphotransferase
-2.03
PHOSPHOFRUCTOKINASE [cytoplasm]
Phvul.001G259000.1
AT1G13440
Q9FX54
4.1.8
glycolysis.cytosolic branch.glyceraldehyde 3-phosphate dehydrogenase (GAP-DH)
0.65
GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE [cytoplasm]
Phvul.004G127500.1
AT1G74030
Q9C9C4
4.1.13
glycolysis.cytosolic branch.enolase
0.74
ENOLASE [cytoplasm]
Phvul.004G078400.1
AT4G26390
O65595
4.1.14
glycolysis.cytosolic branch.pyruvate kinase (PK)
-1.43
PYRUVATE KINASE [cytoplasm]
Phvul.003G024800.1
AT1G53310
Q9MAH0
4.1.15
glycolysis.cytosolic branch.phospho-enol-pyruvate carboxylase (PEPC)
-1.64
PHOSPHO-ENOL-PYRUVATE CARBOXYLASE [cytoplasm]
Phvul.005G066400.1
AT3G14940
Q84VW9
4.1.15
glycolysis.cytosolic branch.phospho-enol-pyruvate carboxylase (PEPC)
1.55
PHOSPHO-ENOL-PYRUVATE CARBOXYLASE [cytoplasm]
Phvul.002G096000.1
AT5G17530
Q8W4R0
4.2.2
glycolysis.plastid branch.phosphoglucomutase (PGM)
-1.63
PHOSPHOGLUCOMUTASE [plastid]
Phvul.008G180200.1
AT5G42740
P34795
4.2.3
glycolysis.plastid branch.glucose-6-phosphate isomerase
-0.6
GLUCOSE-6-PHOSPHATE ISOMERASE [cytoplasm]
Phvul.002G306800.1
AT5G56630
Q9C5J7
4.1.4
glycolysis.cytosolic branch.phosphofructokinase (PFK)
1.41
PHOSPHOFRUCTOKINASE [plastid]
Phvul.011G090600.1
AT3G50520
Q9SCS3
4.3.12
glycolysis.unclear/dually targeted.phosphoglycerate mutase
-0.68
PHOSPHOGLYCERATE MUTASE [localization unclear]
Phvul.003G106700.1
AT1G54220
Q5M729
13.2.4.1
amino acid metabolism.degradation.branched chain group.shared
0.9
PYRUVATE DEHYDROGENASE [E2]
Phvul.008G239900.1
AT1G54340
Q9SLK0
8.1.4
TCA / org transformation.TCA.IDH
0.58
ISOCITRATE DEHYDROGENASE
Phvul.003G253200.1
AT2G18450
Q9ZPX5
8.1.7
TCA / org transformation.TCA.succinate dehydrogenase
0.78
SUCCINATE DEHYDROGENASE
Phvul.009G111500.2
AT5G11670
Q9LYG3
8.2.10
TCA / org transformation.other organic acid transformatons.malic
2.56
MALATE OXIDOREDUCTASE
Phvul.010G094700.1
AT2G13560
Q9SIU0
8.2.10
TCA / org transformation.other organic acid transformatons.malic
0.83
MALATE OXIDOREDUCTASE
Phvul.005G166400.1
AT5G25880
Q9XGZ0
8.2.10
TCA / org transformation.other organic acid transformatons.malic
0.87
MALATE OXIDOREDUCTASE
Phvul.005G043500.1
AT1G10670
Q9SGY2
8.2.11
TCA / org transformation.other organic acid transformatons.atp-citrate lyase
-0.85
ATP-CITRATE LYASE
Phvul.005G048000.1
AT3G48000
Q9SU63
8.2.99
TCA / org transformation.other organic acid transformatons.misc
0.66
Misc. organic acid transformatons
Phvul.005G048300.1
AT3G48000
Q9SU63
8.2.99
TCA / org transformation.other organic acid transformatons.misc
0.67
Misc. organic acid transformatons
Phvul.002G071200.1
AT3G01500
P27140
8.3
TCA / org transformation.carbonic anhydrases
-1.37
CARBONIC ANHYDRASE
Phvul.008G181400.2
AT1G58180
Q9C6F5
8.3
TCA / org transformation.carbonic anhydrases
2.33
CARBONIC ANHYDRASE