. 2018 Jul 2;9:932. doi: 10.3389/fpls.2018.00932

Table 1.

Primers used in this study for probe synthesis, sequencing, qPCR and clone analysis.

Primer	Use	Template	Gene	Genomic position			Sequence (5′ → 3′)	Reference
				TYLCSV^a	TYLCV^a	TYLCMaV^a
MA14	Probe synthesis	TYLCSV	Rep	2,587–2,604^b			TGCATTTATTTGAAAACG	Navas-Castillo et al., 1999
MA15	Probe synthesis	TYLCSV	V2	162–145			AAAGGATCCCACATATTG	Navas-Castillo et al., 1999
MA20	Sequencing	TYLCV	CP		1,019–1,036		TACGCATGCCTCTAATCC	This work
MA30	Probe synthesis	TYLCV	Rep		2,564–2,584		GAGCAATTAGGATATGTGAGG	Navas-Castillo et al., 1999
MA31	Probe synthesis	TYLCV	V2		168–150		AGTGGGTCCCACATATTGC	Navas-Castillo et al., 1999
MA99	Sequencing	TYLCSV	CP	891–908			AAGGAGCAGTGTCTGTTG	Monci et al., 2002
		TYLCMaV	CP			891-908
MA863	Sequencing	TYLCSV	Rep	2,217–2,234			CGTAAGCGTCATTGGCTG
		TYLCV	Rep		2,226–2,243
		TYLCMaV	Rep			2,217–2,234
MA1197	Sequencing	TYLCMalV	V2			257–277	TGGGTCATGATCTAATTAGGG	This work
MA1198	Sequencing	TYLCSV	V2	257–277			TGGGTCACGATCTAATTAGGG	This work
MA1199	Sequencing	TYLCV	V2		263–283		TGGGCCACGATTTAATTAGGG	This work
MA1365	Sequencing	TYLCSV	Ren	1,177–1,156			AACAATGTWATYAGAGCAGTTG	This work
		TYLCV	Ren		1,186–1,165
		TYLCMaV	Ren			1,177–1,156
MA1461	Sequencing	TYLCSV	Rep	1,703–1,725			CCTGGATTGCAGAGGAAGATAGT	This work
		TYLCV	Rep		1,712-1,734
		TYLCMaV	Rep			1,703–1,725
MA1506	Real-time PCR	TYLCSV	C4/Rep	2,225–2,244			TCATTGGCTGTCTGCTGTCC	This work
MA1507	Real-time PCR	TYLCSV	C4/Rep	2,462–2,443			ATGGGCAACCTCATCTCCAC	This work
MA1508	Real-time PCR	TYLCV	C4/Rep		2,234–2,253		TCATTGGCTGACTGCTGACC	This work
		TYLCMaV	C4/Rep			2,225–2,244
MA1509	Real-time PCR	TYLCV	C4/Rep		2,403–2,384		TTCGACCTGGTATCCCCAAG	This work
		TYLCMaV	C4/Rep			2,394–2,375
25S rRNA UNIV (+)	Real-time PCR	Tomato 25S rRNA gene	-	-	-	-	ATAACCGCATCAGGTCTCCA	Mason et al., 2008
25S rRNA UNIV(-)	Real-time PCR	Tomato 25S rRNA gene	-	-	-	-	CCGAAGTTACGGATCCATTT	Mason et al., 2008
M13 UNIV (+)	Clone PCR analysis	pBSK+	-	-	-	-	CGCCAGGGTTTTCCCAGTCACGAC
M13 UNIV (-)	Clone PCR analysis /sequencing	pBSK+	-	-	-	-	TCACACAGGAAACAGCTATGAC

TYLCSV, tomato yellow leaf curl Sardinia virus; TYLCV, tomato yellow leaf curl virus and TYLCMaV, tomato yellow leaf curl Malaga virus.

Nucleotide numbers refer to the sequences of TYLCSV [ES:Mur1:92] (Z25751) (Noris et al., 1994), TYLCV [ES:72:97] (AF071228) (Navas-Castillo et al., 1999), and TYLCMaV [ES:421:99] (AF271234) (Monci et al., 2002).