Two-step genomic sequence comparison strategy to design Trichoderma strain-specific primers for quantitative PCR

Table 1 Primer characteristics

Genome location or reference	Code	Primer set	Sequence (5′–3′)	Fragment size (bp)
>T37_S00003:2560926-2576741	P1	T-1F	GTGGCGAAAACTCTCATACTCGT	127
	P1	T-1R	CTATAAATCAAGTTTGCCGTGCT	127
	P2	T-2F	GCCCACTCAAATTGCGAACATA	143
	P2	T-2R	CGACGACGACATACTCATCAATC	143
	P3	T-3F	TGGTCTAACGGCTCTTCAACAT	136
	P3	T-3R	AGGCACTGACACTTTATCTGGT	136
	P4	T-4F	CGACGGAACTACATGATAAGCAA	102
	P4	T-4R	CCTAAATGAATGAGCCTCGTCT	102
>T37_S00005:2001401-2006364	P5	T-5F	TGTCTACCAATCACCAGTTTACG	134
	P5	T-5R	CACCATTGTTCCATCCATTACCA	134
	P6	T-6F	TGGTAATGGATGGAACAATGGT	126
	P6	T-6R	CCTCGCTTCACTGACTGGA	126
>T37_S00007:2096560-2099766	P7	T-7F	GTGGCGTCCTTGGTCATTG	128
	P7	T-7R	ACACAGAGCGTAGGCATAGAT	128
	P8	T-8F	TATGCTGGTGGTGGTCTTAGTG	136
	P8	T-8R	GTAATGGCTGAATAGGTGCGATAA	136
>T37_S00017:678513-681994	P9	T-9F	TCTCTACAAGCTCCAAGACCAC	114
	P9	T-9R	ATTGTCATTGTGCATTTATCGAG	114
	P10	T-10F	CTCCATCACCTGCATTTAGTGT	143
	P10	T-10R	TCGACAGTGATTCATAAGGCATC	143
GFP fragment	P11	gfp-F	AGAAGAACGGCATCAAGGTG	171
GFP fragment	P11	gfp-R	TCTCGTTGGGGTCTTTGCT	171
HYG fragment	P12	hyg-F	CATTGACTGGAGCGAGGC	99
HYG fragment	P12	hyg-R	CGTCTGCTGCTCCATACAA	99
GFP-HYG fragment	P13	gfphyg-F	GCCGATAGTGGAAACCGA	140
GFP-HYG fragment	P13	gfphyg-R	CTTGTGGCCGTTTACGTCG	140
López-Mondéjar et al. (2010) and Beaulieu et al. (2011)	ITS1	ITS1-S	ACAACTCCCAAACCCAATGTGA	207
López-Mondéjar et al. (2010) and Beaulieu et al. (2011)	ITS1	ITS1-R	CGTTGTTGAAAGTTTTGATTCATTT	207