Species & Dataset
Experiment
Foliar Ozone Injury
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Phaseolus vulgaris
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Common name: Common bean
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Family: Fabaceae
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Cultivar: Phaseolus vulgaris L.
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Tissue: Shoot leaves
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Ozone concentration: Ambient ozone (12.5 nL L−1 ± 0.96 nL L−1)
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Elevated ozone (151.2 nL L−1 ± 0.72 nL L−1)
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Ozone exposure: Throughout the experiment (8 hours/day)
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Sampling time: 11-13 days after planting
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Platform: Hiseq 2000 (Illumina)
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Year of study: 2015
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Location: Urbana, USA
Title: A comparative analysis of transcriptomic, biochemical, and physiological responses to elevated ozone identifies species-specific mechanisms of resilience in legume crop
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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]
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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 |