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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