Skip to main content

Table 1 Primers and probes used in this study

From: Intragenomic diversity of Rhizobium leguminosarum bv. trifolii clover nodule isolates

RtTA1 replicon name Probe name Probe description Primers GenBank accession no
cha pssL
(Pss-I)
1300 bp of Pss-I region encoding part of putative flippase PssL pssLFw
5'-TCTTATCCGCCACGAATCTCC-3'
pssLRw
5'-GCCAGGTGAAGGGCCAGCGCCAACT-3'
DQ384110
  rfbADBC
(Pss-V)
2956 bp of Pss-V region encoding lipopolysaccharide biosynthesis proteins rfbAFw
5'-TCGAGATAGGTGCGGTTGACGTCG-3'
rfbCRw
5'-GCAGGGCAACGCTGGTGCGCTGC-3'
DQ679959
  bioA 445 bp fragment encoding adenosylmethionine-8-amino-7-oxononanoate aminotransferase bioA3
5'-CCTCGTCGAAGATCAGAAGG-3'
bioA5
5'-TCTACACCAACTCCGGTTCC-3'
DQ535896
  rpoH2 487 bp fragment encoding RNA polymerase sigma factor rpoH2Fw
5'-TGGTGCAGGAGGGCTATGTT-3'
rpoH2Rw
5'-TCGCGTTCGTTGAGATGTTTC-3'
DQ366597
  dnaC 624 bp fragment encoding DNA helicase dnaCFw
5'-CAGCCCGGCATTTTCACC-3'
dnaCRw
5'-CTGCGGCCGTTTATCGTC-3'
DQ855524
  dnaK 645 bp fragment encoding heat shock protein 70 family dnaKFw1
5'-CGTCATCACCGTTCCCGCCTACTT-3'
dnaKRw1
5'-TTGCCGAACAGCTGCTTGACGACT-3'
DQ535895
  exoR 416 bp fragment encoding negative regulator of exopolysaccharide synthesis exoRFw
5'-GTTGCCGCCTGCCTGAGATGAAC-3'
exoRRw
5'-GAGAGCAGCGCGTTGACGAAGAAG-3'
DQ347956
  rrl 1135 bp fragment comprising rRNA genes rrl and rrs-rrl intergenic spacer FGPS1490
5'-TGCGGCTGGATCACCTCCTT-3'
FGPL132
5'-CCGGGTTTCCCCATTCGG-3'
DQ639765
  lpxQ 850 bp fragment encoding lipid A oxidase lpxQFw
5'-GACGGCAAATTTCAGCGGCACATA-3'
lpxQRw
5'-GGCGGCTGAGCAACACTTACCAA-3'
DQ836933
  stbB 423 bp fragment encoding plasmid stability protein stbBFw1
5'-ATGATCGTTCTCGATACGAATGTGATTTC-3'
stbBRw1
5'-TCAGCCGTCTTCAAACGGGTTT-3'
FJ230890
  fixGH 539 bp fragment encoding nitrogen fixation cation transport proteins fix2Fw
5'-GCGGATTTCGTGCCCCTTTATGGA-3'
fix2Rw
5'-TCTCTGCGGAATGGCTACACG-3'
DQ314612
pRleTA1d prc 442 bp fragment encoding C-terminal tail-specific protease precursor prcFw
5'-CGGCTTGCGCTTTTGTAATCCTG-3'
prcRw
5'-CGCTGTTTGGTATCGGTGCTGTGC-3'
EF107512
  hlyD 620 bp fragment encoding type I secretion membrane fusion hlyDFw
5'-CGAAGTCCGCGCCCGTGTG-3'
hlyDRw
5'-TCGCGACCTTGACCTTGATGG-3'
EF123039
  repAd 1467 bp fragment encoding putative replication/partition protein of pRleTA1d repAdFw
5'-CGCCGTGCCGCCATTTGA-3'
repAdRw
5'-GGACTCCAGAGCCCGATCGTAGGTTC-3'
FJ592234
  repCd 578 bp fragment encoding putative replication protein of pRleTA1d repCdFw
5'-CCGGACGAGCAAAGACTGAAACAA-3'
repCdRw
5'-GACCGAGAGCCCGAATTTTTGTGT-3'
FJ592234
pRleTA1c lpsB2 740 bp fragment encoding dTDP-glucose 4,6-dehydratase, O-antigen biosynthesis protein lpsBFw
5'-GCACATCCGTAAAGCCAGGGTCAA-3'
lpsBRw
5'-GCGGGTTATATCAGGATGTGTCAG-3'
DQ677348
  orf16, orf17, otsB 2191 bp fragment encoding component of ABC transporter Orf16 of AraC family, transcriptional regulator Orf17, trehalose-phosphatase OtsB orf16Fw
5'-AAGCTTCTTCATTTCCGCGACGAAGCCC-3'
ostBRw
5'-AAGCTTGGCGGTGCCTTGGCACTG-3'
FJ237527
  tauA-orf14 5 kb fragment encoding taurine uptake protein TauA and flavin monooxygenase/reductase Orf14 protein tauAFw
5'-CCCGAGATGGAGGCGAGGTAAAAG-3'
orf14Rw
5'-TTGGCAAGGCAGACGAGGAGAAG-3'
ED797712 ED797713
  repAc 433 bp fragment encoding replication/partition protein of pRleTA1c repAcFw
5'-GATTTGCGTGAAYGYCGACCA-3'
repAcRw
5'-AGGTGGATTGATGTCGTCGTCTTG-3'
EU555187
  repCc 1417 bp fragment encoding replication protein of pRleTA1c repCcFw
5'-AGTTTTTGGCGCCGTTTTGGTGAG-3'
repCcRw
5'-TATCTGACCGAGGCTGCTAACCAC-3'
EU555187
pRleTA1b pssM
(Pss-III)
440 bp fragment encoding surface polysaccharide biosynthesis protein of Pss-III region MnewFw
5'-CGCAACACCGGGATTTCTG-3'
MnewRw
5'-TCGGCGGGTATGGCGTGAT-3'
DQ417329
  nadA 582 bp fragment encoding quinolinate synthetase nadAFw
5'-GCGCACAACTATCAGACACCGGAGAT-3'
nadARw
5'-GCGACATTGTCGCTCATCGAGCATT-3'
DQ521662
  minD 589 bp fragment encoding septum site-determining protein minDFw
5'-ATGATGGGGAAAGTGATCGTCGTCACGTC-3'
minDRw
5'-CGAGCAGCGGGATGGACAGG-3'
JF920043
  hutI 577 bp fragment encoding imidazolonepropionase protein hutIFw
5'-CGGCGGCGGCATCGTCTCCT-3'
hutIRw
5'-CCACCGGCGGCTTCTGCTTTTCAT-3'
JF920044
  pcaG 344 bp fragment encoding protocatechuate 3,4-dioxygenase protein pcaGFw
5'-CGGCGTCGCGATGGTCAA-3'
pcaGRw
5'-CGGCGTTGGCCTCCGTCTC-3'
JF920045
  repAb 1309 bp fragment encoding replication/partition protein of pRleTA1b repAbFw
5'-ATGCGGATCGTGCTGTCGTAGA-3'
repAbRw
5'-GCCGCGGCCAACTCCTG-3'
FJ592235
  repCb 932 bp fragment encoding putative replication protein of pRleTA1b repCbFw
5'-GGGAGCGCCTGACACTTTGCC-3'
repCbRw
5'-GGAAGCAGGGTTTGAAGCATCGTA-3'
FJ592235
pRleTA1a nodA 662 bp encoding fragment of acyltransferase nodulation protein nodA-1
5'-TGCRGTGGAARNTRNNCTGGGAAA-3'
nodA-2
5'-GGNCCGTCRTCRAAWGTCARGTA-3'
AY904443
  nifNE 649 bp fragment encoding nitrogenase MoFe cofactor biosynthesis proteins NifNFw
5'-CCGGTCGGCGCATCTGTTCC-3'
NifNRw
5'-GGTGCGCTGCCAATACTCCAT-3'
DQ471906
  thiC 478 bp encoding fragment of thiamine biosynthesis protein thi3
5'-GGCCGGGGTTTTCGCGGATGGCGA-3'
thi5
5'-TTCCGGCTGAGGACTGGGTCTCCAAT-3'
DQ535897
  acdS 890 bp encoding fragment 1-aminocyclopropane-1-carboxylate deaminase acdSFw
5'-GTTCGAACGCTACCCGCTCACCTT-3'
acdSRw
5'-TCCCCTGCATCGACTTTCCCTCAT-3'
EU700492
  repAa 774 bp fragment encoding replication/partition protein of pRleTA1a repAaFw
5'-TCCTYYGCTGCGAAGATTACACG-3'
repAaRw
5'-CGCGCCCAGGGTCAGATAGC-3'
HM032068
  repCa 773 bp fragment encoding putative replication protein of pRleTA1a repCaFw
5'-GGGATYGCCGCCTACCGTGACAGT-3'
repCaRw
5'-GCATAWCGGCCGACCCTCCCTACA-3'
HM032068
  1. a -ch-chromosome