Table 2.

Overview of the distribution of upregulated genes compared to liquid cultures across infection stages, according to the identification of conserved domains. *: those with one candidate effector.

Functional Class	Family	24 hpi	48 hpi	60 hpi	72 hpi	84 hpi	Total
Carbohydrate active enzyme	Auxiliary Activities *	0	1	5	7	13	13
	Glycoside hydrolases	0	6	11	22	33	37
	Carbohydrate binding modules	0	0	0	0	2	2
	Glycosyl Transferases	0	0	1	3	6	6
	Carbohydrate Esterases	0	3	6	6	6	6
	Polysaccharide Lyases	0	0	1	1	1	1
	Total of CAZyme domains	0	10	24	39	61	65
	Total of genes encoding CAZymes	0	9	23	38	59	63
Transcription factor	Fungal Zn(2)-Cys(6) binuclear cluster domain	0	0	2	2	4	4
	Fungal specific transcription factor	0	0	2	4	6	6
	Helix-loop-helix DNA-binding domain	0	0	0	0	1	1
	Zinc finger, C2H2 type	1	1	2	3	2	4
	bZIP transcription factor	0	0	0	1	2	2
	Spt20 family	1	0	0	0	0	1
	CP2 transcription factor	0	0	0	1	0	1
	Total of transcription factor domain	2	1	6	11	15	19
	Total of genes encoding transcription factors	2	1	4	9	12	16
Secondary metabolism	Polyketide synthase dehydratase	0	0	1	2	2	2
	Condensation domain	0	0	1	2	2	2
	Phosphopantetheine attachment site	0	0	1	2	2	2
	Ketoreductase domain (KR)	0	0	1	2	2	2
	Total of secondary metabolism domains	0	0	4	8	8	8
	Total of secondary metabolism associated genes	0	0	2	2	2	2
Candidate effector		1	11	19	26	24	27
Peptidase	Serine peptidase	1	2	3	6	9	10
	Metallopeptidase	0	1	2	3	6	6
	Cystein peptidase	2	1	1	0	3	3
	Peptidase inhibitor	0	0	0	0	1	1
	Total of genes encoding peptidases	3	4	6	9	19	20
Transmembrane transporter	The Ca2+:Cation Antiporter (CaCA) Family	0	0	1	4	0	4
	The Amino Acid/Auxin Permease (AAAP) Family	0	0	0	3	2	3
	The ATP-binding Cassette (ABC) Superfamily	0	1	2	4	4	5
	The Major Facilitator Superfamily (MFS)	0	0	3	7	13	14
	The Amino Acid-Polyamine-Organocation (APC) Family	0	0	3	2	3	4
	The Proton-dependent Oligopeptide Transporter (POT) Family	0	0	0	0	1	1
	The Small Conductance Mechanosensitive Ion Channel (MscS) Family	0	0	0	1	1	1
	The P-type ATPase (P-ATPase) Superfamily	0	0	1	3	2	4
	The Mitochondrial Carrier (MC) Family	0	0	1	1	1	1
	The Oligopeptide Transporter (OPT) Family	0	0	0	0	1	1
	The Transient Receptor Potential Ca2+ Channel (TRP-CC) Family	0	0	0	1	1	1
	Threonine/serine exporter	0	0	0	1	1	1
	Mitochondrial calcium uniporter	0	0	0	0	1	1
	Total of transmembrane transporter genes	0	1	11	27	31	41
Other pathogenicity related-factors	Nudix	0	0	1	1	2	2
	Necrosis and ethylene-inducing peptide *	0	3	6	6	6	6
	Stress response	0	0	3	12	13	16
	Pathogenicity	0	2	3	4	8	9
Oxydoreduction	Cytochrome P450	0	0	2	7	10	11
	NAD/FAD binding and other oxydo-reductase	3	8	17	37	53	58
Cellular process	AAA family	0	0	0	0	2	2
	Binding	6	7	14	15	10	24
	Cell differentiation	1	1	1	1	0	1
	DNA repair	1	1	1	1	1	1
	Intracellular transport	1	1	3	10	8	13
	Methyltransferase	1	1	3	6	10	13
	Mitochondria	1	1	2	2	1	2
	Protein kinase	1	1	2	3	6	7
	Transcription	4	3	3	6	4	8
	Translation	3	5	9	10	5	12
	Ubiquitinilation	1	1	1	2	4	4
Metabolic process	Alpha/beta hydrolase	0	0	1	1	2	2
	AMP-binding enzyme	0	0	1	1	2	2
	Carbohydrate metabolism	1	1	2	2	6	6
	Coenzyme A metabolism	0	0	0	0	1	1
	Lipid metabolism	0	0	0	4	5	6
Cell structure		4	4	6	9	6	11
Hypothetical protein		27	33	60	93	120	144
Others		2	3	18	40	51	63