Table II.

Differentially down-regulated genes upon infection of Arabidopsis with R. fascians D188

Gene	Function	Codea	Fold Change
			7 dpi	14 dpi	24 dpi
Biotic/abiotic stress
At1g23130	Bet v I allergen family protein	d131	2.42	0.67	0.20
At1g54040	Kelch repeat-containing protein	d129	0.98	0.63	0.46
At1g70850	Bet v I allergen family protein	d94	0.96	0.59	0.25
At1g70880	Bet v I allergen family protein	d61	1.09	0.73	0.48
At2g15490	UDP-glucoronosyl/UDP-glucosyl transferase family protein	d31	1.27	0.98	0.48
At2g18420	Gibberellin-responsive protein (putative)	d73	1.10	0.79	0.27
At2g35980	HIN1 family protein	d85	1.39	1.00	0.45
At2g45210	Auxin-responsive protein-related	d109	0.97	0.74	0.42
At3g28930	avrRpt2-induced AIG2 protein (AIG2)	d70	1.13	0.90	0.47
At5g14920	Gibberellin-regulated family protein	d133	1.45	0.99	0.49
At5g53160	Expressed protein	d110	0.87	1.02	0.42
Cell organization and biogenesis
At4g36380	Cytochrome P450 90C1 (CYP90C1)/rotundifolia3 (ROT3)	d107	0.92	0.81	0.44
At5g66540	Expressed protein	d36	1.31	0.72	0.41
Development
At1g02820	Late embryogenesis abundant 3 (LEA3) family protein	d145	1.74	0.76	0.26
At4g02380	Late embryogenesis abundant 3 (LEA3) family protein	d140	1.72	0.78	0.26
DNA and RNA metabolism
At5g64200	Arg/Ser-rich splicing factor SC35	d91	1.41	0.64	0.45
Electron transport or energy pathway
At1g26410	FAD-binding domain-containing protein	d144	1.48	0.98	0.40
At2g44790	Uclacyanin II	d86	0.84	0.91	0.35
At3g22370	Alternative oxidase 1a, mitochondrial (AOX1A)	d84	1.13	0.90	0.43
At3g56060	Glc-methanol-choline (GMC) oxidoreductase family protein	d87	0.81	0.67	0.32
At4g15760	Monooxygenase (putative; MO1)		1.03	0.82	0.50
At4g15765	Monooxygenase family protein		0.85	0.75	0.40
At4g38540	Monooxygenase (putative; MO2)	d46	1.16	0.87	0.47
At5g36220	Cytochrome P450 81D1 (CYP81D1; CYP91A1)	d138	1.12	0.97	0.48
Metabolism
At1g05010	Ethylene-forming enzyme (ACO; EAT1)	d111	1.02	1.15	0.48
At1g21440	Mutase family protein	d5	0.44	0.50	0.77
At1g24100	UDP-glucoronosyl/UDP-glucosyl transferase family protein	d34	0.45	0.69	0.83
At1g64660	Cys/Met metabolism pyridoxal-phosphate-dependent enzyme	d113	1.30	0.83	0.28
At2g25450	2-Oxoglutarate-dependent dioxygenase (putative)	d55	0.54	0.44	0.22
At2g26560	Patatin (putative)	d108	1.40	0.66	0.41
At3g08860	β-Ala-pyruvate aminotransferase (putative)/AGT (putative)	d142	1.01	0.69	0.43
At3g09260	Glycosyl hydrolase family 1 protein	d96	1.14	1.16	0.48
At3g09270	Glutathione S-transferase (putative)	d77	1.02	0.96	0.50
At3g13450	Branched chain α-keto acid dehydrogenase E1 β-subunit (DIN4)	d143	1.01	0.83	0.47
At3g14990	4-Methyl-5(β-hydroxyethyl)-thiazole-monophosphate bios (putative)	d75	0.96	0.83	0.44
At3g19710	Branched chain amino acid aminotransferase (putative; BCAT4)	d16	0.46	0.57	1.25
At3g29250	Short-chain dehydrogenase/reductase (SDR) family protein	d83	1.06	0.89	0.46
At3g44300	Nitrilase 2 (NIT2)	d150	1.43	0.72	0.10
At3g48990	AMP-dependent synthetase and ligase family protein	d25	0.93	0.73	0.47
At3g58990	Aconitase C-terminal domain-containing protein	d20	0.40	0.53	1.45
At3g60130	Glycosyl hydrolase family 1/β-glucosidase (putative; YLS1)	d28	1.02	0.87	0.36
At4g13250	Short-chain dehydrogenase/reductase (SDR) family protein	d54	0.37	0.48	0.31
At4g13430	Aconitase family protein/aconitate hydratase family protein	d130	0.40	0.49	0.72
At4g15530	Pyruvate phosphate dikinase family protein	d63	0.87	0.78	0.47
At4g28780	GDSL-motif lipase/hydrolase family protein	d103	1.04	0.71	0.30
At5g07440	Glu dehydrogenase 2 (GDH2)	d148	1.13	0.95	0.38
At5g02780	In2-1 protein (putative)	d73	1.89	0.91	0.31
At5g09440	Phosphate-responsive protein (putative)	d56	1.32	0.50	0.32
At5g09530	Hyp-rich glycoprotein family protein	d22	1.25	0.88	0.46
At5g17380	Pyruvate decarboxylase family protein	d53	0.78	0.91	0.49
At5g23020	2-Isopropylmalate synthase 2 (IMS2)	d11	0.64	0.66	0.34
At5g23660	Nodulin MtN3 family protein	d68	1.86	0.63	0.47
At5g44020	Acid phosphatase class B family protein	d122	1.50	0.81	0.27
At5g44930	Exostosin family protein	d127	1.06	0.64	0.36
At5g49360	Glycosyl hydrolase family 3 protein	d152	1.04	0.53	0.38
At5g51970	Sorbitol dehydrogenase (putative)/l-iditol 2-dehydrogenase (putative)	d39	0.98	0.70	0.48
At5g59530	2-Oxoglutarate-dependent dioxygenase (putative)	d37	1.23	0.99	0.47
At5g65010	Asn synthetase 2 (ASN2)	d88	1.03	0.91	0.44
Protein modification
At1g72070	DNAJ heat shock N-terminal domain-containing protein	d80	1.86	0.65	0.32
At3g01290	Band 7 family protein	d134	1.18	0.91	0.45
At4g16563	Aspartyl protease family protein	d93	1.31	0.67	0.48
At4g38690	1-Phosphatidylinositol phosphodiesterase-related	d2	1.06	0.64	0.50
At5g23210	Ser carboxypeptidase S10 family protein	d146	1.26	0.71	0.48
AtCg00670	ATP-dependent Clp protease proteolytic subunit		1.05	0.86	0.47
Response to stress
At1g07890	l-Ascorbate peroxidase 1, cytosolic (APX1)	d42	0.59	0.66	0.40
At1g08830	Copper/zinc superoxide dismutase (CSD1)	d92	0.38	1.43	0.86
At1g09560	Germin-like protein (GLP4; GLP5)	d44	1.23	0.78	0.36
At1g45145	Thioredoxin H-type 5 (TRX-h5; TOUL)	d102	1.37	0.69	0.41
At1g73330	Protease inhibitor (putative; DR4)	d69	2.06	0.65	0.13
At2g23680	Stress-responsive protein (putative)	d71	1.36	0.76	0.37
At2g28190	Copper/zinc superoxide dismutase (CSD2)	d106	0.44	1.18	1.12
At2g37130	Peroxidase 21 (PER21; P21; PRXR5)	d8	0.74	0.52	0.31
At2g37180	Water stress-induced tonoplast intrinsic protein (RD28)	d49	0.84	0.84	0.46
At2g38870	Protease inhibitor (putative)	d45	2.62	1.61	0.50
At2g39800	Δ1-Pyrroline-5-carboxylate synthetase A/P5CS A (P5CS1)	d95	0.48	0.70	1.94
At3g50970	Dehydrin xero2 (XERO2)/low-temperature-induced protein LTI30	d67	1.27	0.47	0.45
At4g02520	Glutathione S-transferase (putative)	d119	1.10	0.73	0.21
At4g08390	l-Ascorbate peroxidase, stromal (sAPX)	d149	0.43	0.68	0.38
At4g25100	Superoxide dismutase (Fe), chloroplast (SODB; FSD1)	d120	0.67	0.41	0.24
At4g35770	Senescence-associated protein (SEN1)	d38	1.37	0.81	0.42
At4g37530	Peroxidase 50 (PER50; PRXR50)	d132	0.68	0.75	0.42
At5g14780	Formate dehydrogenase (FDH)	d79	0.74	0.80	0.45
Signal transduction
At1g02340	Reduced phytochrome signaling (REP1; BHLH26)	d29	0.86	0.55	0.27
At4g30270	MERI-5 protein (MERI-5; MERI5B)	d116	1.66	0.48	0.28
At5g15410	Cyclic nucleotide-gated channel (CNGC2)	d3	0.97	0.84	0.48
Transcription factor
At2g36890	Myb family transcription factor (MYB38)	d51	0.99	0.90	0.48
At2g43060	Expressed protein	d59	1.17	0.72	0.39
At2g46970	Basic helix-loop-helix (bHLH) protein (putative)		1.18	0.68	0.23
At3g05690	CCAAT-binding transcription factor (CBF-B/NF-YA) family protein	d32	0.87	0.69	0.43
At3g51910	Heat shock transcription factor family protein	d24	1.13	0.87	0.45
At3g56400	WRKY family transcription factor	d105	0.46	1.20	1.62
At3g60530	Zinc finger (GATA type) family protein	d26	1.35	0.93	0.37
At5g07690	Myb family transcription factor (MYB29)	d7	0.33	0.53	1.05
At5g07700	Myb family transcription factor (MYB76)	d125	0.35	0.51	1.28
At5g23000	Myb family transcription factor (MYB37)	d114	1.04	0.81	0.49
At5g53980	Homeobox-Leu zipper family protein	d136	0.87	1.07	0.49
At5g63790	No apical meristem (NAM) family protein	d43	0.62	0.97	0.41
Transport
At1g08230	Amino acid transporter family protein	d115	1.02	0.79	0.46
At1g66760	MATE efflux family protein	d101	1.16	0.85	0.47
At1g78000	Sulfate transporter (Sultr1;2)	d76	1.54	0.57	0.47
At1g80830	NRAMP metal ion transporter 1 (NRAMP1)	d82	0.68	0.67	0.37
At2g10940	Protease inhibitor/seed storage/lipid transfer protein (LTP)	d153	0.85	0.91	0.37
At2g26650	Potassium channel protein 1 (AKT1)	d104	1.15	0.74	0.44
At2g40300	Ferritin (putative)	d123	0.78	0.79	0.42
At2g45180	Protease inhibitor/seed storage/lipid transfer protein (LTP)	d17	2.20	0.95	0.38
At3g48970	Copper-binding family protein	d97	1.15	0.85	0.48
At3g53980	Protease inhibitor/seed storage/lipid transfer protein (LTP)	d30	1.68	0.48	1.18
At3g56090	Ferritin (putative)	d14	1.03	1.07	0.48
At3g56200	Amino acid transporter family protein	d52	1.90	0.69	0.44
At4g00370	Sugar transporter family protein	d12	1.22	0.77	0.43
At4g04770	ATP-binding cassette transporter (ABC1)	d9	0.36	0.46	0.40
At4g12030	Bile acid:sodium symporter family protein	d1	0.38	0.48	1.26
At4g30110	ATPase E1-E2-type family protein	d6	0.77	0.54	0.41
At5g10180	Sulfate transporter	d10	0.46	0.42	0.14
At5g61520	Hexose transporter (putative)	d60	1.23	0.81	0.45
At5g62670	ATPase, plasma membrane-type (putative)/proton pump (putative)	d128	0.82	0.84	0.46
Others
At1g02850	Glycosyl hydrolase family 1 protein	d126	1.11	1.01	0.43
At1g04660	Gly-rich protein	d117	0.99	0.61	0.47
At1g18590	Sulfotransferase family protein	d4	0.40	0.56	1.66
At1g49320	BURP domain-containing protein	d78	0.57	0.48	0.33
At1g76590	Zinc-binding family protein	d58	1.00	0.65	0.36
At1g76800	Nodulin (putative)	d13	0.88	0.63	0.30
At1g78830	Curculin-like (Man-binding) lectin family protein	d48	1.24	0.72	0.34
At2g03890	Phosphatidylinositol 3- and 4-kinase family protein	d139	1.22	0.96	0.45
At2g05440	Gly-rich protein	d135	1.39	0.54	0.09
At2g05540	Gly-rich protein	d74	0.84	0.78	0.39
At2g32870	MATH domain-containing protein	d141	0.77	0.48	0.62
At2g39030	GCN5-related N-acetyltransferase (GNAT) family protein	d50	1.32	0.81	0.37
At2g39310	Jacalin lectin family protein	d100	1.05	0.80	0.48
At2g39330	Jacalin lectin family protein	d35	0.78	0.46	0.41
At2g41380	Embryo-abundant protein-related	d147	1.33	0.90	0.47
At2g43530	Trypsin inhibitor (putative)	d65	2.20	0.60	0.45
At3g04720	Hevein-like protein (HEL)	d90	1.50	0.73	0.13
At3g15356	Legume lectin family protein		1.16	0.71	0.21
At3g22740	Homocysteine S-methyltransferase 3 (HMT-3)	d18	0.34	0.60	1.09
At3g48390	MA3 domain-containing protein		1.01	0.77	0.47
At3g50440	Hydrolase, α/β-fold family protein	d15	1.00	0.61	0.35
At3g50440	Hydrolase, α/β-fold family protein		0.99	0.70	0.45
At3g54600	DJ-1 family protein		0.46	0.58	1.02
At4g00780	MATH domain-containing protein	d64	0.84	0.49	0.97
At4g01440	Nodulin MtN21 family protein	d121	0.93	0.83	0.50
At4g04810	SeIR domain-containing protein		2.40	0.62	0.38
At4g04830	SeIR domain-containing protein	d21	2.94	0.65	0.30
At4g15610	Integral membrane family protein	d137	1.48	0.74	0.24
At4g28050	Senescence-associated protein (putative)	d99	1.10	0.57	0.25
At4g36850	PQ-loop repeat family protein/transmembrane family protein		0.99	0.65	0.46
At4g38080	Hyp-rich glycoprotein family protein	d98	1.58	0.80	0.33
At4g39940	Adenylylsulfate kinase 2 (AKN2)	d112	0.39	0.59	1.13
Unknown
At1g01430	Expressed protein	d72	0.96	0.78	0.49
At1g07090	Expressed protein	d40	1.26	0.85	0.46
At1g10090	Expressed protein	d27	0.92	0.60	0.37
At1g29050	Expressed protein	d41	1.18	0.66	0.45
At1g49310	Expressed protein	d89	0.85	0.66	0.45
At1g54740	Expressed protein	d62	0.78	0.66	0.48
At1g73810	Expressed protein		1.05	0.65	0.44
At2g04795	Expressed protein	d19	1.24	0.63	0.42
At3g19030	Expressed protein	d124	1.61	0.71	0.49
At3g28320	Hypothetical protein	d66	0.78	0.83	0.34
At4g31330	Expressed protein	d118	1.01	0.70	0.49
At4g32480	Expressed protein		0.93	0.62	0.36
At5g01740	Expressed protein	d23	1.43	0.75	0.28
At5g03545	Expressed protein	d47	3.21	1.07	0.25
At5g40450	Expressed protein		0.87	0.88	0.49
At5g40450	Expressed protein	d151	1.46	0.86	0.47
At5g45410	Expressed protein	d81	0.62	0.74	0.47
At5g64090	Expressed protein	d57	1.49	0.49	0.52

^aRefers to genes in the right panel of Figure 4.