TABLE 2.

Primer sequences used in MLST analysis of pSymA and pSMED02 of Medicago-nodulating rhizobia

Locus and primer typeaPrimer sequencebLength (bp)cLocation on pSymAdLocus location on pSMED02
PCR primers
    adeC3F: 5′-CGGCAGGTGGGTGAACGTCTA-3′1,088965405-967192236432-238219
R: 5′-TGCCGAGTTTCACCGTGTTTT-3′
    fixKF: 5′-GCGCCGMYCAGCAGCTTCGTT-3′515350925-351560139026-139661
R: 5′-CCGCGAGCGCCATGCAACT-3′
    napBF: 5′-CCGGGCGGCGTCGAAGCACTT-3′441676725-677228134395-136899
R: 5′-GCGGGCATTGGGATCGAGATT-3′
    nifDF: 5′-GCGCCGTAAAAAGCACCTGAG-3′1,370454549-4560511191216-1192484
R: 5′-GCGCGTCGTAGAGGTCCCAGA-3′ (MLST)
    nifDF: 5′-GCCAAGGAAGCCAAGGTAATA-3′1,765
R: 5′-GGGGAGCATGGTCGAGCACTT-3′ (full)
    nodCF: 5′-CGCRATTGTTGATGCAGTGCT-3′1,958479009-4802891144475-1145977
R: 5′-CGCGCGTGCTCATCCKGAAGT-3′
    SMa0198F: 5′-CCKCGSGCSATGAGCTAT-3′647108822-109769275441-276388
R: 5′-ACGCCGGCGATCGACAGCAG-3′
Sequence primers
    adeC3F: 5′-CACGGCACGACGACCATGTT-3′401313-332
R: 5′-GTGCCGGAGTGGCTGTCAT-3′851-869
    fixKF: 5′-ACGCGCCGATCAAGTCTAT-3′389126-144
R: 5′- GCCCCTGTGCTTCAGCTT-3′547-564
    napBF: 5′-CGGCGTCGAAGCACTTCAGA-3′329108-127
R: 5′-GCATTGGGATCGAGATTGTTG-3′519-539
    nifDF: 5′-CGGCTTGATTGGTGACGACAT-3′457e496-516e
R: 5′-CAAGCCGCCGACGTAAAGCAT-3′1175-1195e
    nifDF: 5′-GCGCCGTAAAAAGCACCTGAG-3′Full87-107f
F: 5′-ACCGGCTATGAACTCGAAAA-3′1237-1256f
R: 5′-ACCGGGCCGTGCGAAATGTG-3′268-286f
R: 5′-GCGCGTCGTAGAGGTCCCAGA-3′1436-1456f
    nodCF: 5′-CGCGCGATCCGAGGTTCA-3′349e311-328e
R: 5′-GAGGCCGCGCAACAGAG-3′897-881e
F: 5′-GCGCGATCCGAGGTTCAGCTT-3′Full312-332f
F: 5′-GCGGCCCTTGTGCTATGT-3′623-640f
R: 5′-TCCGCTTTCCGACGTTCT-3′347-364f
R: 5′-GGCGGTGCTGGTTGTGTC-3′13-30f
    SMa0198F: 5′-GGGCRCMTTCGTCAGCTTCGT-3′429207-227
R: 5′-CCGGCGATCGACAGCAGCGTG-3′714-734
  • a The genes listed code for the following products: adeC3, adenine deaminase; fixK, transcriptional regulator FixK; napB, nitrate reductase cytochrome c-type subunit; nifD, nitrogenase molybdenum-iron protein alpha chain; nodC, N-acetylglucosaminyltransferase; SMa0198, ABC transporter, permease.

  • b F, forward; R, reverse.

  • c The lengths shown represent the product length for the PCR primers and the sequence length for the sequence primers.

  • d The locations shown represent the locus location on pSymA for the PCR primers and the primer location on pSymA for the sequence primers.

  • e Primers used for both the allele and complete sequence determinations.

  • f Primers used for complete sequence determinations.