Unraveling the early molecular and physiological mechanisms involved in response to phenanthrene exposure

Anne-Sophie Dumas; Ludivine Taconnat; Evangelos Barbas; Guillem Rigaill; Olivier Catrice; Delphine Bernard; Abdelilah Benamar; David Macherel; Abdelhak El Amrani; Richard Berthomé

doi:10.1186/s12864-016-3133-0

BMC Genomics

Table 1 The most differentially expressed genes (DEGs) during the time course in PHN-treated plants

From: Unraveling the early molecular and physiological mechanisms involved in response to phenanthrene exposure

AGI identifier	Gene annotation	30 min		2 h		4 h		8 h		24 h
AGI identifier	Gene annotation	Ratio	p-value	Ratio	p-value	Ratio	p-value	Ratio	p-value	Ratio	p-value
*Genes rapidly upregulated after 30 min of treatmentwhose levles remained high throughout the time course*
AT1G70800	EHB1__Calcium-dependent lipid-binding (CaLB domain) family protein	0.64	4 . *88E-02*	1.23	*2.80E-09*	1.91	*0.00E + 00*	1.97	*0.00E + 00*	1.19	*0.00E + 00*
AT4G38620^a	ATMYB4_MYB4_myb domain protein 4	3.51	*0.00E + 00*	2.19	*0. 00E + 00*	2.30	*0.00E + 00*	2.18	*0.00E + 00*	1.94	*0.00E + 00*
AT2G47950	unknown protein	1.49	*0.00E + 00*	2.27	*0.00E + 00*	2.27	*0.00E + 00*	2.65	*0.00E + 00*	1.91	*0.00E + 00*
AT5G48540^a	receptor-like protein kinase-related family protein	1.42	*0.00E + 00*	2.44	*0.00E + 00*	3.27	*0.00E + 00*	3.48	*0.00E + 00*	3.51	*0.00E + 00*
AT5G59820^a	RHL41_ZAT12__C2H2-type zinc finger family protein	1.19	*0.00E + 00*	1.63	*0.00E + 00*	2.14	*0.00E + 00*	2.70	*0.00E + 00*	2.50	*0.00E + 00*
AT2G16900	Arabidopsis p hosp holip ase-like protein (PEARLI 4) family	0.98	*3.61E-09*	1.68	*0.00E + 00*	1.67	*3.06E-11*	1.61	*0.00E + 00*	2.16	*0.00E + 00*
AT1G68620 ^b	alpha/beta-Hydrolases superfamily protein	0.93	*6. 02E-08*	2.18	*0.00E + 00*	1.68	*2.29E-11*	2.77	*0.00E + 00*	2.70	*0.00E + 00*
AT5G56630^b	PFK7__phosphofructokinase 7	0.91	*2.45E-07*	1.59	*0.00E + 00*	2.41	*0.00E + 00*	1.54	*0.00E + 00*	2.53	*0.00E + 00*
AT3G22840^a	ELIP_ELIP1__Chlorophyll A-B binding family protein	0.89	*6.36E-07*	1.40	*0.00E + 00*	2.19	*0.00E + 00*	1.70	*0.00E + 00*	2.38	*0.00E + 00*
AT1G63840	RING/U-box superfamily protein	0.83	*1.31E-05*	1.80	*0.00E + 00*	1.64	*1.22E-10*	2.10	*0.00E + 00*	2.16	*0.00E + 00*
AT2G36590	ATPROT3_ProT3__proline transporter 3	0.79	*7. 54E-05*	1.42	*0.00E + 00*	1.93	*0.00E + 00*	1.80	*0.00E + 00*	2.24	*0.00E + 00*
AT4G39670	Glycolipid transfer protein (GLTP) family protein	0.73	*1.16E-03*	1.26	*9.30E-10*	1.01	*4.52E-02*	1.42	*0.00E + 00*	2.13	*0.00E + 00*
AT4G27657	unknown protein	0.70	*4.31E-03*	1.26	*6.61E-10*	1.10	*4.30E-03*	1.75	*0.00E + 00*	0.74	*2.19E-03*
AT4G15248^a	B-box type zinc fnger family protein	1.39	*0.00E + 00*	1.75	*0.00E + 00*	1.04	*1.93E-02*	0.35	1.00E + 00	1.63	*0.00E + 00*
*Genes differentially upregulated after 2 h whose levels remained high*
AT2G35980	ATNHL10_NHL10_YLS9__Late embryogenesis abundant (LEA) hydroxyproline-rich glycoprotein family	0.56	7.20E-01	1.72	0.00E + 00	1.96	*0.00E + 00*	1.81	*0.00E + 00*	2.34	*0.00E + 00*
AT3G22600	Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein	0.16	1.00E + 00	1.68	*0.00E + 00*	1.96	*0.00E + 00*	1.36	*0.00E + 00*	1.96	*0.00E + 00*
AT4G25640	ATDTX35_DTX35_FFT__detoxifying efflux carrier 35	0.27	1.00E + 00	1.66	*0.00E + 00*	1.40	*6.73E-07*	1.98	*0.00E + 00*	2.11	*0.00E + 00*
AT3G21560	UGT84A2__UDP-Glycosyltransferase superfamily protein	0.52	1.00E + 00	1.48	*0.00E + 00*	2.21	*0.00E + 00*	1.60	*0.00E + 00*	1.93	*0.00E + 00*
AT1G74010^b	Calcium-dependent phosphotriesterase superfamily protein	0.46	1.00E + 00	1.39	*0.00E + 00*	1.68	*3.06E-11*	1.32	*0.00E + 00*	2.50	*0.00E + 00*
AT1G75040	PR-5_PR5__pathogenesis-related gene 5	0.21	1.00E + 00	1.32	*3.84E-11*	1.50	*2.24E-08*	1.71	*0.00E + 00*	1.75	*0.00E + 00*
AT1G30700	FAD-binding Berberine family protein	0.48	1.00E + 00	1.26	*9. 30E-10*	1.06	*1.24E-02*	1.56	*0.00E + 00*	2.28	*0.00E + 00*
AT3G04300	RmlC-like cupins superfamily protein	0.37	1.00E + 00	1.25	*1.14E-09*	1.73	*0.00E + 00*	2.08	*0.00E + 00*	2.25	*0.00E + 00*
AT1G18980	RmlC-like cupins superfamily protein	0.2	1.00E + 00	1.16	*6.26E-08*	1.55	*3.16E-09*	1.57	*0.00E + 00*	1.59	*0.00E + 00*
AT1G76980	unknown protein	0.51	1.00E + 00	1.15	*9.70E-08*	1.67	*4.59E-11*	1.78	*0.00E + 00*	1.85	*0.00E + 00*
AT5G54500^b	FQR1__flavodoxin-like quinone reductase 1	0.47	1.00E + 00	1.12	*3.41E-07*	1.14	*1.72E-03*	1.50	*0.00E + 00*	1.79	*0.00E + 00*
AT1G74450	Protein of unknown function (DUF793)	0.41	1.00E + 00	1.09	*1.17E-06*	1.16	*9.83E-04*	1.06	*3.11E-09*	1.10	*2.24E-11*
AT3G04000^b	NAD(P)-binding Rossmann-fold superfamily protein	0.06	1.00E + 00	0.95	*3.38E-04*	1.16	*1.01E-03*	1.53	*0.00E + 00*	1.23	*0.00E + 00*
AT1G27120	Galactosyltransferase family protein	0.00	1.00E + 00	0.91	*1.33E-03*	2.00	*0.00E + 00*	2.30	*0.00E + 00*	2.45	*0.00E + 00*
AT2G17500	Auxin efflux carrier family protein	−0.20	1.00E + 00	0.80	*4.29E-02*	1.19	*3.99E-04*	1.79	*0.00E + 00*	1.20	*0.00E + 00*
*Genes differentially upregulated after 4 h of treatment*
AT1G78340	ATGSTU22_GSTU22__glutathione S-transferase TAU 22	0.04	1.00E + 00	0.56	1.00E + 00	1.62	*2.45E-10*	1.75	*0.00E + 00*	1.69	*0.00E + 00*
*AT1G17170*	ATGSTU24_GST_GSTU24__glutathione S-transferase TAU 24	0.06	1. 00E + 00	0.39	1. 00E + 00	1.57	*1.98E-09*	2.00	*0.00E + 00*	2.05	*0.00E + 00*
AT3G51660	Tautomerase/MIF superfamily protein	0.10	1. 00E + 00	0.75	1.85E-01	1.47	*5.93E-08*	1.8	*0.00E + 00*	2.27	*0.00E + 00*
AT5G36270 ^b	similar to DHAR2, glutathione dehydrogenase (ascorbate)	0.00	1. 00E + 00	0.55	1.00E + 00	1.38	*1.16E-06*	1.56	*0.00E + 00*	1.74	*0.00E + 00*
AT4G15480	UGT84A1__UDP-Glycosyltransferase superfamily protein	0.18	1.00E + 00	0.47	1.00E + 00	1.27	*4.29E-05*	1.02	*2.61E-08*	1.40	*0.00E + 00*
AT1G78380	ATGSTU19_GST8_GSTU19__glutathione S-transferase TAU 19	0.1	1. 00E + 00	0.69	1.00E + 00	1.23	*1.42E-04*	1.45	*0.00E + 00*	1.49	*0.00E + 00*
*AT2G29500*	HSP20-like chaperones superfamily protein	0.16	1. 00E + 00	0.29	1.00E + 00	1.15	*1.22E-03*	1.11	*1.94E-10*	1.53	*0.00E + 00*
*AT1G75030*	ATLP-3_TLP-3__thaumatin-like protein 3	0.19	1.00E + 00	0.59	1.00E + 00	1.13	*1.98E-03*	1.45	*0.00E + 00*	1.35	*0.00E + 00*
AT1G75270 ^b	DHAR2__dehydroascorbate reductase 2	0.36	1.00E + 00	0.78	8.04E-02	1.09	*5.83E-03*	1.60	*0.00E + 00*	1.49	*0.00E + 00*
AT1G64900	CYP89_CYP89A2__cytochrome P450, family 89, subfamly A, polypeptide 2	−0.03	1. 00E + 00	0.33	1.00E + 00	1.08	*6.73E-03*	1.16	*1.49E-11*	1.19	*0.00E + 00*
AT3G13520^b	AGP12_ATAGP12__arabinogalactan protein 12	0.17	1. 00E + 00	0.57	1.00E + 00	1.08	*6.96E-03*	1.39	*0.00E + 00*	0.88	*4.96E-06*
AT2G12190	Cytochrome P450 superfamily protein	−0.04	1.00E + 00	0.43	1.00E + 00	1.04	*1.98E-02*	0.97	*3.77E-07*	0.96	*6.31E-08*
AT4G13180^b	NAD(P)-binding Rossmann-fold superfamily protein	0.28	1.00E + 00	0.29	1.00E + 00	1.03	*2.87E-02*	1.07	*1.53E-09*	1.39	*0.00E + 00*
AT1G05680	UGT74E2__Uridine diphosphate glycosyltransferase 74E2	0.14	1.00E + 00	−0.05	1.00E + 00	1.01	*4.09E-02*	1.8	*0.00E + 00*	0.83	*3.77E-05*
AT2G48140	EDA4 Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein	0.02	1. 00E + 00	0.74	2.24E-01	1.20	*2.82E-04*	0.73	*9.70E-03*	0.40	1.00E + 00
AT3G09270	ATGSTU8_GSTU8__glutathione S-transferase TAU 8	−0.12	1. 00E + 00	0.41	1.00E + 00	1.15	*1.12E-03*	0.26	1.00E + 00	1.09	*5.98E-11*
AT1G23490	ARF 1_ATARF_ATARF 1_ATARFA1A__ADP-ribosylation fictor 1	0.48	1.00E + 00	0.76	1 49E-01	1.04	*1.99E-02*	0.64	2.29E-01	1.32	*0.00E + 00*
ATI G58370 ^b	ATXYN1_RXF12_glycosyl hydrolase famly 10 protein/carbohydrate-binding domain-containing	0.17	1.00E + 00	0.64	1.00E + 00	1.13	*2.13E-03*	0.08	1.00E + 00	−0.86	*1.10E-05*
*Genes differentially upregulated after 8 h of treatment*
AT5G22140	FAD/NAD(P)-binding oxidoreductase family protein	0.3	1. 00E + 00	0.02	1.00E + 00	0.76	1.00E + 00	2.15	*0.00E + 00*	1.97	*0.00E + 00*
AT3G44190	FAD/NAD(P)-binding oxidoreductase family protein	0.03	1. 00E + 00	0.21	1.00E + 00	0.95	1.78E-01	2.05	*0.00E + 00*	2.01	*0.00E + 00*
AT2G23110	Late embryogenesis abundant protein, group 6	0.45	1.00E + 00	0.78	8.62E-02	0.51	1.00E + 00	1.87	*0.00E + 00*	2.04	*0.00E + 00*
AT5G64250	Aldolase-type TIM barrel family protein	−0.01	1.00E + 00	0.35	1.00E + 00	0.59	1.00E + 00	1.62	*0.00E + 00*	1.55	*0.00E + 00*
AT3G28210^a	PMZ_SAP12__zinc finger (AN1-like) family protein	0.36	1. 00E + 00	0.52	1.00E + 00	0.98	8.17E-02	1.60	*0.00E + 00*	2.09	*0.00E + 00*
AT1G75280^b	NmrA-like negative transcriptional regulator family protein	0.15	1. 00E + 00	0.62	1.00E + 00	0.86	1.00E + 00	1.56	*0.00E + 00*	1.37	*0.00E + 00*
AT4G24160	alpha/beta-Hydrolases superfamily protein	−0.01	1.00E + 00	0.40	1.00E + 00	0.59	1.00E + 00	1.52	*0.00E + 00*	1.25	*0.00E + 00*
AT3G10500	anac053_NAC053__NAC domain containing protein 53	0.12	1.00E + 00	0.77	1.19E-01	0.66	1.00E + 00	1.48	*0.00E + 00*	1.16	*0.00E + 00*
AT2G01180^a	ATLPP1_ATPAP1_LPP1_PAP1__phosphatidic acid phosphatase 1	0.20	1. 00E + 00	0.33	1.00E + 00	0.95	1.92E-01	1.44	*0.00E + 00*	1.97	*0.00E + 00*
AT5G54206	similar to 12-oxophytodienoate reductase OPR1	0.17	1. 00E + 00	0.15	1.00E + 00	0.29	1.00E + 00	1.41	*0.00E + 00*	2.04	*0.00E + 00*
AT2G29460 ^b	ATGSTU4_GST22_GSTU4__glutathione S-transferase tau 4	0.12	1.00E + 00	0.52	1.00E + 00	1.00	5.79E-02	1.37	*0.00E + 00*	0.95	*1.12E-07*
AT4G34131	UGT73B3__UDP-glucosyl transferase 73B3	0.33	1.00E + 00	0.38	1.00E + 00	0.89	7.10E-01	1.31	*0.00E + 00*	1.38	*0.00E + 00*
AT1G05670	Pentatricopeptide repeat (PPR-like) superfamily protein	0.20	1. 00E + 00	0.02	1.00E + 00	0.71	1.00E + 00	1.30	*0.00E + 00*	0.69	*1.70E-02*
AT1G77120^b	ADH_ADH1_ATADH_ATADH1__alcohol dehydrogenase 1	−0.18	1. 00E + 00	0.54	1.00E + 00	0.25	1.00E + 00	1.30	*0.00E + 00*	1.02	*3.44E-09*
AT2G21620	RD2__Adenine nucleotide alpha hydrolases-like superfamily protein	−0.01	1.00E + 00	0.75	1.73E-01	0.94	2.14E-01	1.28	*0.00E + 00*	1.82	*0.00E + 00*
AT1G66580	RPL10C_SAG24__senescence associated gene 24	0.32	1.00E + 00	0.45	1.00E + 00	0.63	1.00E + 00	1.26	*0.00E + 00*	1.44	*0.00E + 00*
AT2G36950	Heavy metal transport/detoxification superfamily protein	0.21	1. 00E + 00	0.45	1.00E + 00	−0.10	1.00E + 00	1.26	*0.00E + 00*	1.01	*4.60E-09*
AT1G72490	unknown protein	−0.09	1. 00E + 00	0.20	1.00E + 00	0.02	1.00E + 00	1.25	*0.00E + 00*	1.10	*2.24E-11*
AT1G67600^a	Acid phosphatase/vanadium-dependent haloperoxidase-related protein	0.01	1.00E + 00	0.45	1.00E + 00	0.5	1.00E + 00	1.25	*0.00E + 00*	1.07	*1.94E-10*
AT5G27760	Hypoxia-responsive family protein	0.14	1.00E + 00	0.47	1.00E + 00	0.83	1.00E + 00	1.19	*0.00E + 00*	1.43	*0.00E + 00*
*Genes differentially upregulated after 24 h of treatment*
AT1G65290b	mtACP2__mitochondrial acyl carrier protein 2	0.13	1.00E + 00	0.06	1.00E + 00	0.13	1.00E + 00	0.34	1.00E + 00	2.63	*0.00E + 00*
AT4G3 7990^b	ATCAD8_CAD-B2_ELI3_ELI3-2__elicitor-activated gene 3-2	0.07	1.00E + 00	0.3	1.00E + 00	0.34	1.00E + 00	0.00	1.00E + 00	2.43	*0.00E + 00*
AT5G25260	SPFH/Band 7/PHB domain-containing membrane-associated protein family	−0.1	1.00E + 00	−0.06	1.00E + 00	0.30	1.00E + 00	0.04	1.00E + 00	2.07	*0. 00E + 00*
AT2G18690	unknown protein	0.11	1.00E + 00	0.70	7.28E-01	0.54	1.00E + 00	0.66	1.32E-01	1.98	*0. 00E + 00*
AT4G12490	Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein	0.22	1.00E + 00	0.07	1.00E + 00	0.66	1.00E + 00	0.28	1.00E + 00	1.90	*0.00E + 00*
AT1G14870	AtPCR2_PCR2_PLANT CADMIUM RESISTANCE 2	−0.03	1.00E + 00	0.51	1.00E + 00	0.03	1.00E + 00	0.48	1.00E + 00	1.76	*0 00E + 00*
AT2G23150	ATNRAMP3_NRAMP3__natural resistance-associated macrophage protein 3	−0.17	1.00E + 00	−0.16	1.00E + 00	0.01	1.00E + 00	0.59	1.00E + 00	1.69	*0 00E + 00*
AT2G17740	Cysteine/Histidine-rich C1 domain family protein	−0.03	1.00E + 00	−0.15	1.00E + 00	0.66	1.00E + 00	0.20	1.00E + 00	1.67	*0 00E + 00*
AT1G66090	Disease resistance protein (TIR-NBS class)	0.36	1.00E + 00	0.29	1.00E + 00	0.66	1.00E + 00	0.55	1.00E + 00	1.67	*0 00E + 00*
AT5G06320	NHL3_NDR1/HN1-Ike 3	−0.28	1.00E + 00	0.11	1.00E + 00	−0.08	1.00E + 00	0.31	1.00E + 00	1.60	*0 00E + 00*
AT2G29350	SAG13__senescence-associated gene 13	−0.17	1.00E + 00	0.17	1.00E + 00	0.82	1.00E + 00	0.59	1.00E + 00	1.55	*0 00E + 00*
AT1G13330	AHP2__Arabidopsis Hop2 homolog	0.00	1.00E + 00	−0.09	1.00E + 00	0.69	1.00E + 00	0.36	1.00E + 00	1.55	*0 00E + 00*
AT5G13320	GDG1_GH3.12_PBS3_WIN3__Auxin-responsive GH3 family protein	−0.1	1.00E + 00	−0.25	1.00E + 00	0.11	1.00E + 00	−0.07	1.00E + 00	1.54	*0 00E + 00*
AT5G17380^b	Thiamine pyrophosphate dependent pyruvate decarboxylase family protein	0.04	1.00E + 00	0.03	1.00E + 00	0.35	1.00E + 00	0.65	1.76E-01	1.48	*0 00E + 00*
AT2G20142^a	Toll-Interleukin-Resistance (TIR) domain family protein	0.06	1.00E + 00	0.05	1.00E + 00	0.21	1.00E + 00	0.23	1.00E + 00	1.47	*0 00E + 00*
AT4G26200	ACS7_ATACS7__1-amino-cyclopropane-1-carboxylate synthase 7	0.22	1.00E + 00	−0.01	1.00E + 00	0.18	1.00E + 00	0.26	1.00E + 00	1.44	*0 00E + 00*
AT1G74710	ATICS1_EDS16_ICS1_SID2__ADC synthase superfamily protein	0.05	1.00E + 00	−0.19	1.00E + 00	0.14	1.00E + 00	−0.09	1.00E + 00	1.41	*0 00E + 00*
AT4G11890	Protein kinase superfamily protein	0.10	1.00E + 00	0.19	1.00E + 00	−0.04	1.00E + 00	0.56	1.00E + 00	1.38	*0 00E + 00*
AT5G25250	SPFH/Band 7/PHB domain-containing membrane-associated protein family	0.07	1.00E + 00	0.00	1.00E + 00	0.28	1.00E + 00	0.40	1.00E + 00	1.38	*0.00E + 00*
AT1G26380	FAD-binding Berberine family protein	0.24	1.00E + 00	0.24	1.00E + 00	0.34	1.00E + 00	0.43	1.00E + 00	1.38	*0 00E + 00*
*Genes differentially down-regulated after 2 h of treatment whose levels remained low*
AT1G26810	GALT1__galactosyltransferase1	−0.13	1.00E + 00	−1.16	*7.36E-08*	−1.71	*7.64E-12*	−1.65	*0.00E + 00*	−1.79	*0 00E + 00*
AT3G19450^b	ATCAD4_CAD_CAD-C_CAD4__GroES-like zinc-binding alcohol dehydrogenase family protein	0.03	1.00E + 00	−0.82	*2.57E-02*	−1.22	*1.62E-04*	−1.74	*0.00E + 00*	−1.74	*0.00E + 00*
AT5G48930^b	HCT__hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase	−0.20	1.00E + 00	−1.17	*5.58E-08*	−1.11	*3.21E-03*	−1.50	*0.00E + 00*	−1.18	*0 00E + 00*
*Genes differentially downregulated after 4 h of treatment whose levels remained low*
AT1G08630b	THA1__threonine aldolase 1	0.06	1.00E + 00	−0.54	1.00E + 00	*−1.81*	*0.00E + 00*	*−0.92*	*3.97E-06*	−1.62	*0 00E + 00*
AT1G43160^a	RAP2.6__related to AP2 6	0.02	1.00E + 00	−0.57	1.00E + 00	*−1.57*	*1.81E-09*	*−1.16*	*7.45E-12*	−0.99	*1.74E-08*
AT5G49730	ATFRO6_FRO6_FRO6__ferric reduction oxidase 6	−0.05	1.00E + 00	−0.27	1.00E + 00	*−1.35*	*3.59E-06*	*−0.79*	*9.47E-04*	−1.46	*0 00E + 00*
AT5G25460	Protein of unknown function, DUF642	−0.03	1.00E + 00	−0.55	1.00E + 00	*−1.30*	*1.38E-05*	*−1.72*	*0.00E + 00*	−1.41	*0 00E + 00*
AT4G29905	unknown protein	0.00	1.00E + 00	0.29	1.00E + 00	*−1.16*	*9.80E-04*	*−0.76*	*3.17E-03*	−1.83	*0 00E + 00*
AT1G05240	Peroxidase superfamily protein	0.08	1.00E + 00	0.19	1.00E + 00	*−1.07*	*9. 14E-03*	*−1.48*	*0.00E + 00*	−0.91	*8 55E-07*
AT4G23400	PIP1;5_PIP1D__plasma membrane intrinsic protein 1;5	−0.29	1.00E + 00	−0.16	1.00E + 00	*−1.06*	*1.23E-02*	*−0.99*	*1.06E-07*	−1.50	*0 00E + 00*
AT1G69100	Eukaryotic aspartyl protease family protein	0.13	1.00E + 00	−0.04	1.00E + 00	*−1.06*	*1.39E-02*	*−1.21*	*0.00E + 00*	−1.03	*2 08E-09*
AT5G01210^b	HXXXD-type acyl-transferase famiy protein	0.05	1.00E + 00	−0.78	8.20E-02	*−1.65*	*7.64E-11*	*−1.37*	*0.00E + 00*	−0.38	1.00E + 00
AT2G45960	ATHH2_PIP1;2_PIP1B_TMP-A__plasma membrane intrinsic protein 1B	−0.17	1.00E + 00	−0.11	1.00E + 00	*−1.14*	*1.71E-03*	*−0.77*	*2.47E-03*	−0.37	1.00E + 00
AT1G65930^b	cICDH__cytosolic NADP + −dependent isocitrate dehydrogenase	−0.03	1.00E + 00	−0.29	1.00E + 00	*−1.13*	*2.23E-03*	*−0.96*	*5.06E-07*	−0.56	1.00E + 00
AT4G14040	EDA38_SBP2__selenium-binding protein 2	0.21	1.00E + 00	−0.31	1.00E + 00	*−1.01*	*3. 90E-02*	*−0.70*	*3.08E-02*	−0.60	4.43E-01
AT1G64370	unknown protein	−0.15	1.00E + 00	−0.22	1.00E + 00	*−1.01*	*3. 93E-02*	*−0.77*	*1.80E-03*	−0.16	1.00E + 00
*Genes differentially downregulated afteer 8 h of treatment whose levels remained low*
AT3G03780^b	ATMS2_MS2__methionine synthase 2	0.15	1.00E + 00	−0.55	1.00E + 00	−0.50	1.00E + 00	−1.66	*0.00E + 00*	−2.22	*0 00E + 00*
AT4G22210	LCR85__low-molecular-weight cysteine-rich 85	−0.16	1.00E + 00	−0.27	1.00E + 00	−0.69	1^+00	−1.56	*0.00E + 00*	−1.27	*0 00E + 00*
AT4G15390	HXXXD-type acyl-transferase famiy protein	0.08	1.00E + 00	−0.44	1.00E + 00	−0.70	1.00E + 00	−1.39	*0.00E + 00*	−1.54	*0 00E + 00*
AT3G59970^b	MTHFR1__methylenetetrahydrofolate reductase 1	0.02	1.00E + 00	−0.54	1.00E + 00	−0.40	1.^+0	−1.30	*0.00E + 00*	−1.06	*2.69E-10*
AT2G44160^b	MTHFR2__methylenetetrahydrofolate reductase 2	0.20	1.00E + 00	−0.28	1.00E + 00	−0.52	1.00E + 00	−1.28	*0.00E + 00*	−0.95	*1 38E-07*
AT5G39210	CRR7__chlororespiratory reduction 7	−0.09	1.00E + 00	0.14	1.00E + 00	−0.58	1.^+0	−1.27	*0.00E + 00*	−0.89	*2 07E-06*
AT3G19820	CBB1_DIM_DIM1_DWF1_EVE1__cell elongation protein/DWARF1 / DIMINUTO (DIM)	0.07	1.00E + 00	−0.11	1.00E + 00	−0.45	1.00E + 00	−1.27	*0.00E + 00*	−1.15	*0 00E + 00*
AT1G29600^a	Zinc finger C-x8-C-x5-C-x3-H type family protein	−0.10	1.00E + 00	−0.15	1.00E + 00	−0.19	1.00E + 00	−1.22	*0.00E + 00*	−1.02	*2.45E-09*
AT4G12545	Bifunctional mhbitor/lpkl-transfer protein/seed storage 2S albumin superfamily protein	−0.03	1.00E + 00	0.28	1.00E + 00	−0.70	1.00E + 00	−1.20	*0.00E + 00*	−1.66	*0 00E + 00*
AT1G11860^b	Glycine cleavage T-protein family	0.00	1.00E + 00	−0.16	1.00E + 00	−0.32	1.00E + 00	−1.17	*7.45E-12*	−1.14	*0.00E + 00*
AT3G60320	Protein of unknown function (DUF630 and DUF632)	0.03	1.00E + 00	−0.18	1.00E + 00	−0.72	1.00E + 00	−1.10	*3.72E-10*	−0.77	*6.14E-04*
AT5G24760	GroES-like zinc-binding dehydrogenase family protein	−0.04	1.00E + 00	−0.50	1.00E + 00	−0.34	1.00E + 00	−1.08	*1.44E-09*	−1.19	*0.00E + 00*
AT5G17920^b	ATCIMS_ATMETS_ATMS1__Cobalamin-independent synthase family protein	0.13	1.00E + 00	−0.26	1.00E + 00	−0.41	1.00E + 00	−1.06	*3.43E-09*	−0.99	*1.51E-08*
AT3G06350b	EMB3004_MEE32__dehydroquinate dehydratase, putative/shikimate dehydrogenase, putative	−0.11	1.00E + 00	−0.25	1.00E + 00	−0.62	1.00E + 00	−1.03	*1.42E-08*	−0.85	*1.91E-05*
AT3G16390^b	NSP3__nitrile specifier protein 3	0.06	1.00E + 00	0.20	1.00E + 00	0.30	1.00E + 00	−1.03	*1.88E-08*	−1.02	*2.19E-09*
AT1G29560^a	Zinc finger C-x8-C-x5-C-x3-H type family protein	0.15	1.00E + 00	−0.38	1.00E + 00	−0.45	1.00E + 00	−1.00	*8.83E-08*	−0.93	*2.64E-07*
AT5G03300^b	ADK2__adenosine kinase 2	0.16	1.00E + 00	−0.30	1.00E + 00	0.03	1.00E + 00	−0.99	*1.40E-07*	−0.94	*1.98E-07*
AT1G80830	ATNRAMP1_NRAMP1_PMIT1__natural resistance-associated macrophage protein 1	−0.02	1.00E + 00	−0.46	1.00E + 00	−0.93	2.79E-01	−0.99	*1.54E-07*	−0.75	*1.16E-03*
AT4G14890	FdC2__2Fe-2S ferredoxin-like superfamily protein	−0.10	1.00E + 00	−0.19	1.00E + 00	−0.48	1.00E + 00	−0.97	*2.69E-07*	−1.01	*4.56E-09*
AT5G65010^b	ASN2__asparagine synthetase 2	−0.03	1.00E + 00	0.07	1.00E + 00	−0.15	1.00E + 00	−0.97	*2.79E-07*	−0.84	*3.11E-05*
Genes differentially downregulated only after 24 h of treatment
AT5G36910^a	THI2.2__thionin 2.2	−0.16	1.00E + 00	0.04	1.00E + 00	−0.38	1.00E + 00	0.21	1.00E + 00	−1.73	*0.00E + 00*
AT2G25510	unknown protein	−0.09	1.00E + 00	0.23	1.00E + 00	0.11	1.00E + 00	−0.40	1.00E + 00	−1.52	*0.00E + 00*
AT1G17190	ATGSTU26_GSTU26__glutathione S-transferase tau 26	−0.01	1.00E + 00	−0.19	1.00E + 00	0.32	1.00E + 00	−0.31	1.00E + 00	−1.41	*0.00E + 00*
AT3G16450	JAL33__Mannose-binding lectin superfamily protein	0.00	1.00E + 00	0.28	1.00E + 00	−0.51	1.00E + 00	−0.67	9.73E-02	−1.30	*0.00E + 00*
AT4G35100	PIP2;7_PIP3_PIP3A_SIMIP__plasma membrane intrinsic protein 3	0.01	1.00E + 00	0.10	1.00E + 00	−0.81	1.00E + 00	−0.67	7.65E-02	−1.26	*0.00E + 00*
AT3G28270	Protein ofunknown function (DUF677)	−0.26	1.00E + 00	0.46	1.00E + 00	0.25	1.00E + 00	−0.57	1.00E + 00	−1.26	*0.00E + 00*
AT5G51720	2 iron, 2 sulfur cluster binding	−0.06	1.00E + 00	−0.25	1.00E + 00	−0.17	1.00E + 00	−0.38	1.00E + 00	−1.24	*0.00E + 00*
AT5G24420^b	PGL5__6-phosphogluconolactonase 5	0.00	1.00E + 00	0.05	1.00E + 00	−0.32	1.00E + 00	−0.02	1.00E + 00	−1.20	*0.00E + 00*
AT4G13870^a	ATWEX_ATWRNEXO_WEX_WRNEXO__Werner syndrome-like exonuclease	−0.02	1.00E + 00	0.10	1.00E + 00	0.61	1.00E + 00	−0.34	1.00E + 00	−1.19	*0.00E + 00*
AT3G02380b	ATCOL2_COL2__CONSTANS-like 2	−0.11	1.00E + 00	−0.60	1.00E + 00	−0.41	1.00E + 00	0.04	1.00E + 00	−1.15	*0.00E + 00*
AT4G16980^b	arab inogalactan-p rotein family	0.07	1.00E + 00	−0.10	1.00E + 00	−0.84	1.00E + 00	−0.54	1.00E + 00	−1.14	*0.00E + 00*
AT3G45140	ATLOX2_LOX2__lipoxygenase 2	−0.12	1.00E + 00	0.51	1.00E + 00	0.51	1.00E + 00	−0.24	1.00E + 00	−1.11	*1.50E-11*
AT1G12090	ELP__extensin-like protein	−0.06	1.00E + 00	−0.04	1.00E + 00	−0.52	1.00E + 00	−0.33	1.00E + 00	−1.08	*8.97E-11*
AT1G54000	GLL22__GDSL-like Lipase/Acylhydrolase superfamily protein	0.03	1.00E + 00	−0.28	1.00E + 00	−0.77	1.00E + 00	−0.55	1.00E + 00	−1.06	*3.59E-10*
AT5G58260^b	NdhN__oxidoreductases, acting on NADH or NADPH, quinone or similar compound as acceptor	0.04	1.00E + 00	−0.01	1.00E + 00	−0.14	1.00E + 00	−0.58	1.00E + 00	−1.05	*6.51E-10*
AT3G16420	JAL30_PBP1__PYK10-binding protein 1	−0.04	1.00E + 00	0.07	1.00E + 00	0.01	1.00E + 00	−0.64	2.36E-01	−1.02	*2.91E-09*
AT3G16440	ATMLP-300B_MEE36_MLP-300B__myrosinase-binding protein-like protein-300B	−0.24	1.00E + 00	0.21	1.00E + 00	−0.37	1.00E + 00	−0.38	1.00E + 00	−0.91	*9.46E-07*
AT3G15850^b	ADS3_FAD5_FADB_JB67__fatty acid desaturase 5	−0.21	1.00E + 00	−0.01	1.00E + 00	−0.68	1.00E + 00	−0.06	1.00E + 00	−0.91	*9.94E-07*
AT3G01480	ATCYP38_CYP38__cyclophilin 38	0.07	1.00E + 00	0.01	1.00E + 00	−0.76	1.00E + 00	−0.54	1.00E + 00	−0.88	*4.47E-06*
AT3G11170^b	AtFAD7_FAD7_FADD__fatty acid desaturase 7	0.03	1.00E + 00	−0.12	1.00E + 00	−0.30	1.00E + 00	−0.63	2.78E −01	−0.87	*7 28E-06*

Of all the DEGs, a maximum of 20 genes for each different response pattern are listed. AGI identifiers and gene annotation in bold correspond to genes involved in the xenome. Expression changes are given as log2. Expression changes in bold correspond to genes differentially expressed at the significant threshold of Bonferroni p-value <0.05 in our study. ^aregulatory genes. ^bmetabolic genes identified using either the MapMan pathway analysis tool choosing Metabolism-overview or the AraGEM tool [84]

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