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Table 1 Capillary electrophoresis Universal-tailed Mismatch Amplification mutation assays for genotyping single nucleotide polymorphisms in Brucella isolates

From: Genotyping of Brucella species using clade specific SNPs

SNP assay

Allelic Primer1

Allelic Primer2

Consensus Primer

Amplicon Size

Dye Set

Allele

SNP position in 16 M

Branch

2366

CACGGCCTATCTGCTGGGCT

CACGGCCTATCTGCTGGGAC

GAGCGTCGTGAAGTCGGTTAC

151

NED/PET

T/C

1173417

A

4748

ACAGTCAGACAAGGACCGGA

AACAGTCAGACAAGGACCGAC

GTAACAAGAACACGGCCTTTACGC

155

FAM/VIC

C/A

1744207

B

1562

CACGCAAAATAGCTAAATGAAATATAC

ACGCAAAATAGCTAAATGAAATATTG

GATGGCTTTCCGGGGCTATC

189

NED/PET

C/G

1405281

B

2922

TAAAGACGGCGATTACCGAG

GTAAAGACGGCGATTACCGTA

GACAACGCCAACGGCATTCTT

179-180

NED/PET

G/A

413931

C

991

CAGTATGAAGCTTATTTTAAGCCA

GCAGTATGAAGCTTATTTTAAGCAG

GTATGCTCAAGCGCCAAGCTG

195

FAM/VIC

G/A

1601481

C

3740

CGGAATACGAAAACTCACATTATAG

CGGAATACGAAAACTCACATTATTA

GCGGGGCCATAGGGAAATAC

133

VIC/FAM

G/A

675905

D

1344

ACACGGTTGGAATTATCCACT

ACACGGTTGGAATTATCCATC

GACCGGCAAGCTTGAATCG

171

FAM/VIC

C/T

1392400

D

5754

GCTGGAACATATAGAAAAGATCATAAAAG

GCTGGAACATATAGAAAAGATCATAAATA

GCAGCCTTCCAAGGAAAAGAACG

117

VIC/FAM

G/A

1083478

E

1522

GGTGAACATTTCGCCATCAG

GGTGAACATTTCGCCATCTA

GTTCGATGAACCTCGTGGCATT

123-124

NED/PET

G/A

497534

E

6214

ATTGAATGATGAGCGATATTGTG

TGAATGATGAGCGATATTGCA

GAGCGCTTGTCGGAGGTTGTT

110-112

PET/NED

A/G

242224

F

2995

CGAAACAGCTGAGAAGATCGAG

AAACAGCTGAGAAGATCGGC

GTTAGAAGCCTGGCCCGTTCTC

101

VIC/FAM

G/C

478183

G

8872

GCATCGAACTCATTCTCGCT

GCATCGAACTCATTCTCGTC

GCGAAATCAAGGCCCCATTTG

160

PET/NED

C/T

1170581

G

1688

CGATCTGCCAGTTGACGAGA

CGATCTGCCAGTTGACGATT

GTGCAACGCCTCACGCATAAT

181

FAM/VIC

T/A

1348434

H

5362

ATTACCACGCACCGATGAGA

ATTACCACGCACCGATGAAG

GCATCCATGACGGCGTGAAAC

240

FAM/VIC

G/A

507275

I

8306

CACGGTTGCATGGTTTGTATATA

ACGGTTGCATGGTTTGTATAAG

GAGCACCAAACCGGGTGATGT

259

FAM/VIC

G/A

1876820

I

10621

TATGCAATTCGTGTCGCATG

TATGCAATTCGTGTCGCAGA

GTTTCAGGACTTTTGGGAACTGACC

233

NED/PET

G/A

1207543

J

10621R

GGTAATTTTTCCGCTTGCGT

CGGTAATTTTTCCGCTTGCTC

GCACGGGCGCAGGCTCTTAT

250

PET/NED

C/T

1207539

J

  1. First allele is the ancestral SNP state and has a VIC or NED dye; second allele is derived and has a FAM or PET dye. Universal tails were added to the 5' end of the allelic primers during primer synthesis. See Figures 1 and S1 for branch location of SNPs in phylogeny. SNP positions are given for B. melitensis 16 M genome and all are on chromosome I except assays 6214 and 2995 are on chromosome II.
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BMC Microbiology

ISSN: 1471-2180

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