Table 3.

Selection of P. graminis f. sp. tritici (Pgt) genes strongly up-regulated during wheat infection

		Best BLAST hit		Expression levels		Wheat/urediniospores
Pgt ID	Function	Mlp ID	GenBank accession no.	Wheat	Urediniospores	Fold-change	P value
PGTG_12502	Amino acid permease	113062	No hit	31,670	68*	467.2	0.004
PGTG_15174	Differentiation-related protein Infp	No hit	AAD38996	23,002	50*	466.3	0.002
PGTG_07532	Amino acid permease	113062	No hit	13,666	47*	293.8	0.005
PGTG_07938	Invertase	44167	CAG26671	18,901	70*	271	3.63 × 10−4
PGTG_17720	Zinc finger, C2H2 type	No hit	No hit	31,604	175	180.9	0.004
PGTG_16569	Multicopper oxidase, secreted	112024	BAG50320	18,825	114*	166.6	0.012
PGTG_15026	Lipase	96073	XP_001273241	21,088	229	92.4	1.22 × 10−6
PGTG_10570	Aspartic protease, secreted	89871	No hit	3,493	46*	76.1	0.04
PGTG_05667	Cu/Zn SOD, secreted	73483	XP_002418001	10,257	138*	74.7	0.004
PGTG_11683	Major intrinsic protein	106246	No hit	8,738	118*	74.6	4.73 × 10−4
PGTG_19191	Serine carboxypeptidase, secreted	49959	EEY14780	6,156	86*	71.8	0.017
PGTG_11725	Endo-1,4-β-glucanase, secreted, GH5	47207	AAR29981	6,503	100*	65.3	0.038
PGTG_08842	Thiamine monophosphate synthase/TENI	63716	No hit	7,343	117*	63.1	7.47 × 10−4
PGTG_10915	Major intrinsic protein	89561	No hit	41,747	686	61	0.006
PGTG_05491	MFS sugar transporter, putative	86594	XP_002480590	28,494	478	59.8	0.006
PGTG_15162	Endo-β-mannanase, GH5	86044	ABR27262	6,992	123*	57.3	0.009
PGTG_02527	Chitin synthase N-terminal, GT2	73345	ABB70409	33,954	766	44.4	8.40 × 10−4
PGTG_06309	Plasma membrane (H+) ATPase	44104	CAA05841	10,443	272	38.5	0.003
PGTG_01889	Lipase, secreted	91294	No hit	13,249	348	38.2	9.55 × 10−4
PGTG_15889	Aspartic peptidase A1	34644	XP_001880663	4,880	128*	38.2	0.019
PGTG_15122	Chitinase, GH18	75188	CAQ51152	15,175	415	36.6	2.63 × 10−4
PGTG_12200	MFS monocarboxylate transporter	86626	XP_001267950	1,636	49*	34	0.012
PGTG_15888	Aspartic peptidase A1	34644	XP_001880663	2,159	77*	28.2	0.021
PGTG_18584	Hexose transporter HXT1	38418	CAC41332	8,629	378	22.9	0.006

Up-regulation in infected wheat is assessed by comparing transcripts profiles to those from resting urediniospores. Wheat leaves were infected by P. graminis f. sp. tritici urediniospores and left for 8 d after inoculation under controled conditions. At this stage, wheat rust pathogen has started to sporulate and macroscopic flecking are visible. Expression values are the means of three biological replicates for 8 dpi and urediniospores. Based on statistical analysis of normalized fluorescence levels, a gene was considered significantly regulated if it met two criteria (1): t test P value, 0.05 (using mattes in Matlab); infected wheat at 8 dpi versus urediniospores fold-change > 10. Genes were selected on the basis of homology to a function, and hypothetical proteins or genes without homology of unknown function were discarded. The complete list of significantly regulated genes is detailed in Dataset S1, Table S16.

*Below background expression level.