MLSSR Typing Method

SSR used on typing method

Marker locus	Locus name	SSR	Genome ORF^a	No. of alleles^b	D value^c
1	1793091	GGGGGGGGGGGGGGGGGGGG	GI: 13881617 phosphatidylethanolamine-binding protein (Mycobacterium tuberculosis CDC 1551)	5	0.700
2	2719085	GGGGGGGGGG	No hit^d (210_MAP.128)	3	0.616
3^e	607784	CG CG CG CG CG C	IGI: RMMR05031 6-aminohexanoate-cyclic dimer hydrolase (Mycobacterium marinum)	2	0.189
			GI: 13883430 hydrolase, alpha/beta-hydrolase fold family (M. tuberculosis CDC1551)
4	3406364	GC GC GC GC GC	GI: 2791627 fixA (M. tuberculosis H37Rv)	2	0.100
5	3735342	GC GC GC GC GC	GI: 13092881 putative S-adenosyl-l-homocysteine hydrolase (Mycobacterium leprae)	4	0.363
6	4286068	GCG GCG GCG GCG GCG GC	IGI: RMMR06009 heat shock protein 70 (M. marinum)	2	0.395
7	4310932	CCG CCG CCG CCG CCG CC	GI: 10579910 phytoene dehydrogenase (Halobacterium spp.)	2	0.100
8	1028129	GGT GGT GGT GGT GGT GG	GI: 3261715 mfd (M. tuberculosis H37Rv)	4	0.668
9	2955362	TGC TGC TGC TGC TGC TG	GI: 2117199 narG (M. tuberculosis H37Rv)	4	0.553
10	3558075	GCC GCC GCC GCC GCC G	GI: 1781217 nuoG (M. tuberculosis H37Rv)	3	0.279
11	1536798	CCG CCG CCG CCG CCG	GI: 5524340 PstA (Mycobacterium avium)	4	0.363

^aGI, NCBI gene identification number; IGI, Integrated Genomics gene identification number.

^bThe average number of alleles was 3.20.

^cD was calculated by using the equation 1 − ∑(allele frequency)² (22). The average D value was 0.393.

^dNo hit, no nucleotide match with any sequences in the GenBank database.

^eLocus 3 is located in an intergenic region of two ORFs (6-aminohexanoate-cyclic dimer and hydrolase [the alpha/beta-hydrolase fold]).

Repeat and locus	Position in genome^a	SSR	Forward primer	Forward primer size (bp)	Reverse primer	Reverse primer size (bp)
1793091	1793091-1793109	GGGGGGGGGGGG GGGGGGGG	TCAGACTGTGCGGTATGGAA	20	GTGTTCGGCAAAGTCGTTGT	20
2719085	2719085-2719094	GGGGGGGGGG	GTGACCAGTGTTTCCGTGTG	20	TGCACTTGCACGACTCTAGG	20
607784	607784-607794	CG CG CG CG CG C	ATCCAACGCCATGTACTCGT	20	GAGCAGCATCGAGGTGAAAC	20
3406364	3406364-3406373	GC GC GC GC GC	GTTCTCGATGGACAGCTTGC	20	GGAGGACGAACCACACTCAT	20
3735342	3735342-3735351	GC GC GC GC GC	TGTCGAACTTGCTCTTGGTG	20	CGTCCTGCAACATCTTCTCC	20
4286068	4286068-4286084	GCG GCG GCG GCG GCG GC	GAATCGTCTTGCCTCACTGG	20	TCGAGCAACTGATCTCCACA	20
4310932	4310932-4310948	CCG CCG CCG CCG CCG CC	CGGCAATACCTCGAACAGAT	20	GCTGAAGAGGTCGTGCAGAT	20
1028129	1028129-1028145	GGT GGT GGT GGT GGT GG	AGATGTCGACCATCCTGACC	20	AAGTAGGCGTAACCCCGTTC	20
2955362	2955362-2955378	TGC TGC TGC TGC TGC TG	GACAAGTTCGGGTTGACCAC	20	AGTTCCTCGACCCAGTCGT	19
3558075	3558075-3558090	GCC GCC GCC GCC GCC G	CTGGAACGTGTCCGAATTG	19	GTATTCGGTGCGGATCTCCT	20
1536798	1536798-1536812	CCG CCG CCG CCG CCG	CTGGAGTGGAAGAGCAGTCC	20	GCTGCGTTACCTCAACACC	19

^aThe position in the genome is the coordinate of the SSR locus in the M. paratuberculosis strain K10 genome (GenBank accession number AE016958).