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 |