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Table 2 VNTR loci on the genome of S. Enteritidis

From: Allele distribution and genetic diversity of VNTR loci in Salmonella entericaserotype Enteritidis isolates from different sources

Locus (alias)

Dye labeled

Primer sequences (5'-3')

PCR set

Conc. (uM)

Location (size)b; gene

Repeats size (bp)

No. repeatsc

Reference

SE1

D3

F – AGACGTGGCAAGGAACAGTAG

  

LK5 Contig 1680_10.15

   
  

R – CCAGCCATCCATACCAAGAC

A

0.10

283–549 (267 bp)

7

5

[15]

SE3

D2

F – CAACAAAACAACAGCAGCAT

  

LK5 Contig 1921_10.15

   
  

R – GGGAAACGGTAATCAGAAAGT

A

0.10

537–856 (320 bp)

12

4

[15]

SE8

D2

F – TTGCCGCATAGCAGCAGAAGT

  

PT4

   
  

R – GCCTGAACACGCTTTTTAATAGGCT

A

0.15

2812703–2813171 (469 bp)

87

1

[15]

SE10a(STTR1)

D4

F – GCTGAAGAAGCGGCAAAAC

  

PT4

   
  

R – GTACCGCTATCTTTCGATGGC

A

0.05

774231–774760 (530 bp); SEN0697

45

8

[15, 27]

SE2

D4

F – CTTCGGATTATACCTGGATTG

  

LK5 Contig 1930_10.15

   
  

R – TGGACGGAGGCGATAG

B

0.05

906–1106 (201 bp)

7

5

[15]

SE5 (STTR5, Sal16)

D2

F – CGGGAAACCACCATCAC

  

PT4

   
  

R – CAGGCCGAACAGCAGGAT

B

0.10

3073216–3073427 (212 bp); SEN2867

6

12

[15, 27, 28]

SE6a(STTR3, 3629542)

D3

F – CGGTGGCGGAGATTCTAATCA

  

PT4

   
  

R – ACGCCGTTGCTGAAGGTAAT

B

0.10

3510975–3511412 (438 bp); SEN3305

33

11

[15, 27, 29]

SE7

D4

F – CCGACCCAATAAGGAG

  

LK5 Contig 1168_10.15

   
  

R – CTTACCGTTGGTAGTTTGTTA

B

0.03

323–867 (545 bp)

61

8

[13, 15]

SE9

D2

F – CGTAGCCAATCAGATTCATCCCGCG

  

PT4

   
  

R – TTTGAAACGGGGTGTGGCGCTG

B

0.10

533132–533460 (329 bp); SEN0475

9

3

[15]

  1. a: Primer sets were redesigned in this study to remove non-specific PCR amplicons when multiplex PCR is applied.
  2. Repeats sequences for locus SE6: TCGTCATCGCCGCTATCGTCGGGCGGGGTTACA
  3. Repeats sequences for locus SE10: TTCGGCATCCGCTTTCTTCTTCGCGTCCGCCGCCGCTTTCGCCGC
  4. b: The locations were based on the genome sequences of Salmonella enterica serovar Enteritidis LK5 http://www.salmonella.org/genomics/sen.dbs and PT4 http://xbase.bham.ac.uk/colibase strains
  5. c: Alignment parameters chosen to weight for match, mismatch and indels were 2.3.5 or 2.5.5 which is more permissive than other options http://tandem.bu.edu/trf/trf.html. Repeat numbers for locus SE7 were counted manually due to imperfect repeat sequences. Repeat numbers for all loci are rounded to the nearest integer. For example, repeat number at locus SE7 in LK5 strain was rounded from 7.5 to 8.