. 2016 Nov 3;17:860. doi: 10.1186/s12864-016-3192-2

Table 4.

Differentially expressed Fom genes significantly up-regulated in planta during infection of DZA315 or A17 at 2 and 7 dpi. DEGs are ranked by DZA315 fold change (FC) over in vitro at 2 dpi. Bold FC indicates DZA315 fold changes greater than A17

Protein ID	Chrom./scaffold^a	Sec. pred.^b	SSP^c	Eff.P pred.^d	AA^e	Potential role^f	DZA315 FC^g		A17 FC^g		IV ^h
Protein ID	Chrom./scaffold^a	Sec. pred.^b	SSP^c	Eff.P pred.^d	AA^e	Potential role^f	2dpi	7dpi	2dpi	7dpi
Fom_SIX13	CDC	+	SSP	-	292	SIX effector	397336	1290948	280959	1123836	-
Fom_16257	CDC	+	SSP	+	91	uncharacterised	172951	741455	150562	301124	-
Fom_16301	CDC	+	SSP	+	144	LysM	161369	912838	114105	425854	-
Fom_16235	CDC	+	SSP	+	264	uncharacterised	37641	172951	35120	131072	+
Fom_15517	CDC	-			567	abhydrolase/peptidase	12417	7132	7643	8780	+
Fom_16729	core	-			54	Protease (partial)	11585	212927	23170	114105	-
Fom_16326	CDC	+	SSP	+	111	uncharacterised	11585	106464	7132	57052	+
Fom_SIX1	CDC	+	SSP	-	279	SIX effector	11585	61147	10809	40342	+
Fom_SIX8	CDC	+	SSP	+	141	SIX effector	8780	106464	8192	70240	+
Fom_16154	CDC	+		-	610	GMC_oxidoreductase	4390	20171	3566	12417	+
Fom_16208	core	-			185	peptidase	2896	37641	2048	15287	+
Fom_12303	core	+	SSP	+	169	uncharacterised	2195	61147	2353	23170	-
Fom_16263	CDC	-			235	uncharacterised	2195	14263	1911	6208	+
Fom_15948	CDC	+	SSP	+	215	peroxidase	1911	16384	1097	6654	+
Fom_10610	core	+		-	478	oxidoreductase	1552	5793	1448	2896	+
Fom_16592	CDC	-			87	uncharacterised	1261	5043	630	3566	+
Fom_15730	CDC	-			199	GST	776	891	315	588	+
Fom_15949	CDC	-			373	peroxidase	776	8192	776	4096	+
Fom_09820	core	-			545	p450	512	239	388	239	+
Fom_09550	core	-			87	uncharacterised	446	3566	1097	3822	+
Fom_SIX9	CDC	+	SSP	+	122	SIX effector	239	1552	208	1024	+
Fom_15614	CDC	+	SSP	-	221	glyco_hydrolase	223	478	181	274	+
Fom_06101	core	-			420	uncharacterised	194	239	181	128	+
Fom_14503	core	-			138	SnoaL	169	119	223	45	+
Fom_07856	core	-			533	MFS	147	169	97	84	+
Fom_16718	core	-			79	protease	111	2702	208	1176	+
Fom_07866	core	-			123	uncharacterised	79	69	60	34	+
Fom_16085	CDC	-			403	2OG-FeII_Oxy	60	446	52	315	+
Fom_10284	core	-			112	ligase	60	239	49	338	+
Fom_02574	core	+	SSP	+	87	uncharacterised	49	32	32	24	+
Fom_04867	core	-			300	NAD_binding	39	23	32	9	+
Fom_07859	core	-			292	LigB, dioxyenase	37	17	11	11	+
Fom_01704	core	-			398	methionine synth.	24	26	32	23	+
Fom_13701	core	-			391	oxidoreductase	24	24	20	11	+
Fom_12076	core	+		-	324	uncharacterised	21	45	26	20	+
Fom_02353	core	+	SSP	-	295	endoglucanase	21	39	23	23	+
Fom_15788	CDC	+	SSP	+	199	uncharacterised	18	69	11	49	+
Fom_04087	core	+	SSP	+	158	uncharacterised	16	91	13	42	+
Fom_10931	core	+		-	330	pectinesterase	11	60	20	26	+
Fom_08395	core	+	SSP	-	291	abhydrolase	9	17	6	5	+
Fom_16385	CDC	-			195	glyco_hydrolase	9	39	10	30	+
Fom_07662	core	-			438	aminotransferase	9	34	4	16	+
Fom_08559	core	+		-	433	glyco_hydrolase	8	64	9	37	+
Fom_04883	core	-			514	p450	7	9	7	5	+
Fom_15521	CDC	-			660	AMP-binding	6	5	5	5	+
Fom_05481	core	+	SSP	-	292	uncharacterised	6	5	5	3	+
Fom_01040	core	-			124	uncharacterised	6	7	12	8	+
Fom_16221	CDC	-			83	glyco_hydrolase	5	37	6	23	+
Fom_16350	core	-			174	abhydrolase	5	2	5	4	+
Fom_10260	core	-			255	flavodoxin	5	10	3	5	+
Fom_09704	core	+		-	418	glyco_hydrolase	4	32	4	17	+

^apredicted core or CD chromosome (CDC) location

^bpredicted secreted based on SignalP

^cpredicted small secreted protein (SSP) based on ≤ 300 amino acids, SignalP, and ≤1 transmembrane domains

^dEffectorP prediction (performed if predicted to be secreted): + effector, - non-effector

^eBold font: protein length ≤ 300 amino acids

^fPotential role based on Pfam domain, best BlastP match or other characteristics

^gFold change in planta gene expression over in vitro conditions

^hexpression in vitro, –: 0-10 % RNA-Seq read coverage over all replicates, +: >10 % RNA-Seq read coverage over all replicates