Table 1.

Mapping of RNA-seq reads using Cronartium ribicola reference transcriptome (17,880 contigs)

Sample	cDNA Library	Mapped reads (n)	Total reads (n)	Mapped reads (%)	Expressed transcript/unigene (n)
Aeciospore	AB4	28,674,922	33,449,754	85.73 %	10,462/7,375
	AB3	41,873,710	48,161,514	86.94 %	10,886/7,622
	AB6	28,037,995	33,065,836	84.79 %	12,100/8,766
	Sub-total	98,586,627	114,677,104	85.97 %	13,589/9,884
Urediniospore	AA3	32,359,165	38,025,520	85.10 %	12,533/8,971
	AA8	18,171,226	20,924,558	86.84 %	11,497/8,149
	AAF	27,678,509	32,977,432	83.93 %	12,620/9,019
	Sub-total	78,208,900	91,927,510	85.08 %	14,022/10,191
Infected WWP stem	F3	13,325,832	59,693,634	22.32 %	12,292/8,966
	F5	18,449,393	75,975,818	24.28 %	12,325/8,977
	F8	23,381,136	89,845,810	26.02 %	12,582/9,175
	Sub-total	55,156,361	225,515,262	24.46 %	13,799/10,119
Infected WWP needle (4 dpi)	SUS (cr2/cr2)	6,033,538	116,335,954	5.19 %	1,722/1,542
	RES (Cr2/-)	11,018,625	141,232,768	7.80 %	818/770
	Sub-total	17,052,163	257,568,722	6.62 %	1,878/1,674