TABLE 3.

Primers and PCR conditions used in this study

Gene	Primer name	Primer sequence	Product size (bp)	PCR conditions
				MgCl2 concn (mM)	Amplification conditions
rrla (copies no. 1, 2, and 3)	F2	5′-AAGGCATAGACAGCCAGGAG-3′
rrla (copy no. 1)	R1.3	5′-GCTTGCTAACTCACACCAAC-3′	2,573	1.5	1 cycle of 5 min at 95°C; 35 cycles of 15 s at 94°C, 30 s at 62°C, and 150 s at 72°C; 1 cycle of 5 min at 72°C
rrla (copy no. 2)	R2''.2	5′-CAAGGAATCACGGTAGG-3′	2,566	1.5	1 cycle of 5 min at 95°C; 35 cycles of 15 s at 94°C, 30 s at 55°C, and 150 s at 72°C; 1 cycle of 5 min at 72°C
rrla (copy no. 3)	R3.2	5′-GAACCAACAAGCATTCTC-3′	2,274	1.5	1 cycle of 5 min at 95°C; 35 cycles of 15 s at 94°C, 30 s at 55°C, and 150 s at 72°C; 1 cycle of 5 min at 72°C
rrlb (copies no. 1, 2, and 3)	23S F	5′-AAGTTCCGACCTGCACGAAT-3′	859
	23S R	5′-GTAGTCTTCAACGGGCTTCA-3′
rplDa,b	L4_F	5′-AAAGGTGCAATTCCTGGTG-3′	897	3	1 cycle of 5 min at 95°C; 35 cycles of 15 s at 94°C, 35 s at 50°C, and 50 s at 72°C; 1 cycle of 5 min at 72°C
	L4_R	5′-CTGGTTTGTTTGAAGCGTTTAG-3′
rplVa,b	L22_F	5′-GCATAACGCAAAGACCAC-3′	834	3	1 cycle of 5 min at 95°C; 35 cycles of 15 s at 94°C, 35 s at 50°C, and 50 s at 72°C; 1 cycle of 5 min at 72°C
	L22_R	5′-AGCAATACCTTCAGCCACCA-3′
rrlc (copies no. 1, 2, and 3)	F1	5′-GGAAAGTTGGCCGTAGAGG-3′
rrlc (copy no. 1)	R1.2	5′-TCCTTCGCCATCGGAAAGTC-3′	3,440	1.5	1 cycle of 1 min at 98°C; 35 cycles of 15 s at 98°C, 30 s at 58°C, and 120 s at 72°C; 1 cycle of 8 min at 72°C
rrlc (copy no. 2)	R2.2	5′-AGGGCAAGGAATCACGGTAG-3′	3,302	1.5	1 cycle of 1 min at 98°C; 35 cycles of 15 s at 98°C, 30 s at 58°C, and 120 s at 72°C; 1 cycle of 8 min at 72°C
rrlc (copy no. 3)	R3.5	5′-AGTGTTCTGCAAGTGGACAACTC-3′	3,505	1.5	1 cycle of 1 min at 98°C; 35 cycles of 15 s at 98°C, 30 s at 58°C, and 120 s at 72°C; 1 cycle of 8 min at 72°C
rplDc	L4_MF	5′-CAGCAGCTATTACAACGA-3′	4,855	3	1 cycle of 1 min at 98°C; 35 cycles of 15 s at 98°C, 30 s at 58°C, and 150 s at 72°C; 1 cycle of 8 min at 72°C
	L22_R	5′-AGCAATACCTTCAGCCACCA-3′
rplVc	L22_MF	5′-CACGAGGTGAGTGATGGA-3′	4,674	3	1 cycle of 1 min at 98°C; 35 cycles of 15 s at 98°C, 30 s at 58°C, and 150 s at 72°C; 1 cycle of 8 min at 72°C
	L22_MR	5′-AACACCATTACTCTCAAGA-3′

^aPrimers used for DNA amplification.

^bPrimers used for DNA sequencing (dynamics of substitutions).

^cPrimers used for natural transformation.