TABLE 2.
Primers used in this study
| IGR | Primer sequence (5′-3′)
|
Amplicon size (nt)a | Reference | NCBI accession no. | |
|---|---|---|---|---|---|
| Forward | Reverse | ||||
| spo0J-abcT1 | AAAGATTTGGAAGAATTAGACTTGAT | TTTGCTTAAACCAACCATTTC A | 320 | 21 | EF216182-EF216218 |
| RR0155-rpmB | TTTCTAGCAGCGGTTGTTTTATCC | TTAGCCCATGTTGACAGGTTTACT | 290 | This study | EF216032-EF216068 |
| RR0345-tolC | AGAAGCTTCCGGATGTAATA | AGCAAATAAAAACCCTAATAAC | 238 | This study | EF216069-EF216105 |
| cspA-ksgA | CATCACTGCTTCGCTTATTTT | ATTTCTTTTCTTCCTCTTCATCAA | 405 | This study | EF215859-EF215895 |
| RR1372-RR1373 | TCCCGCGCCAGTATCCA | CGGCGGCCAAAATGCTA | 349 | This study | EF216114-EF216150 |
| RR1240-tlc5b | CGGGATAACGCCGAGTAATA | ATGCCGCTCTGAATTTGTTT | 357 | 21 | EF215969-EF216005 |
| tRNAPhe-nifR3 | TTGAACCAACGACACAAGGA | CCGTAACACCTGACATTGGA | NP | 21 | |
| RC0098-dcd | CCGATGCAAGGCAAATAATA | CGCAAAGGGCCTTATCATAC | 402 | 21 | EF216025-EF216031 |
| RC0102-RC0103 | GCGATAAGCGATTTATTAGGC | GAAAGCCTAAAGCCTCCACA | NP | 21 | |
| RC0280-23S rRNA | CAAAAAGCCGACAAAGCCTA | CCTTCATCGCCTTCTAGTGC | NP | 21 | |
| acrD-hupA | GGGCGTTTAATACAAATTTTAGACA | CAATTCTCCTTTGATAGGTTAATATGT | NP | 21 | |
| pal-RC1201 | TGCAAGCACACATAATGCAA | TCAAAATCGATTCCTCTTTTCC | 292 | 21 | EF216014-EF216016 |
| secB-czcR | ATGCAGGATTCCAGCCTTTA | GGCTCGCCTTCAATTAACAA | 336 | 21 | EF216167-EF216174 |
| groES-RC0970 | CTTGCATCGGCTTTTCTTTT | AGCTTTGAGCTGATGGGCTA | 353 | 21 | EF215926-EF215933 |
| secA-prsA | GCAGGTTCAAGCGAGTTAATTT | AAAAGCAATACCGGAAAGCA | 370 | 21 | EF216151-EF216158 |
| RC0604-RC0605 | AAAGGCAATAACGGCAAAAA | AGCTCGCCAGTTCATTCATC | NP | 21 | |
| RC0409-trmU | AACCTTGACGTGCATATTCTAAA | GCCTGACATTGCGACAACTA | 400 | 21 | EF216106-EF216113 |
| yqiX-gatB | CTGCGGCAGTACCGACTATT | ATCCGACGCTTGTGAATCAG | 398 | 21 | EF216175-EF216181 |
| rne-coxW | CGGAAAAGAATGCAGAGTCTTG | CCATTTTGTAATTAAACTTTTCTG C | NP | 21 | |
| dnaN-RC0584 | TCGTCATGCCTGTTAAGGTG | TTGGATAATCACCCGCTAAGA | 457 | 21 | EF215904-EF215910 |
| lig-tgt | TTTTTGTGCTTCCTCTTCAGAT | CCAAAATCTCATGAGCCGTA | 395 | 21 | EF215950-EF215957 |
| rho-RC0760c | CGGTATTGTTAAGTTCTGCTGTG | TGCATGCCATTACTTATTACAAATG | 433 | 21 | EF216017-EF216024 |
| folC-bioY | AGGTCGGCACCGGAAAAT | TACGGCGGCGTATTACCTT | 340 | 21 | EF215911-EF215917 |
| ntrY-rpsU | AGCTGCTGTTGCTAAAGTAAAAA | CAAGAAGCAGCAAGAAGACAGA | 493 | 21 | EF215942-EF215949 |
| dksA-xerC | TCCCATAGGTAATTTAGGTGTTTC | TACTACCGCATATCCAATTAAAAA | 225 | 21 | EF215896-EF215903 |
| murG-RC0563 | GAAGAAAAGAAGGGCATAAGCTA | CAAGCTGAAAGTAAAAACATTCC | 500 | 21 | EF215934-EF215941 |
| fabZ-lpxD | TGTTAGGATCGATTTTAAGTACTCTATCT | TGGATTGGCATAGACAATCTATTA | 357 | 21 | EF215918-EF215925 |
| rrf-pyrH | GAGCTTTCTCCATCTTTTCTTG | AAAGGGGAATATACGACAATTGAG | 369 | 21 | EF216006-EF216013 |
| tRNAGly-tRNATyr | AGCTTGGAAGGCTGGAACTC | ATCCTTCTCCCTCCACCACT | 193 | 21 | EF216159-EF216166 |
| nusG-rplK | CAGTTGCAATATTGGTAAAGCA | CAGCAGCTGGAATTATCAAGTT | 390 | 21 | EF215958-EF215965 |
| pcnB-sca1-1d | GCTCCCGCGGCACTTAGA | TGCAAATCATATGGCGGTAGG | 250 | This study | EF421161-EF421163 |
| pcnB-sca1-2d | TCATGGTAAAAGGCAGAGATAA | AAGGCATTTTTGGAGCAGT | 202 | This study | EF421164-EF421166 |
| pcnB-sca1-3d | AATTTCGGCTTTCTCACA | CTTGGCGTTTGCTTGGTCT | 292 | This study | EF421161-EF421162 |
| RC1027-xthA2 | GGTATGTAAATGAGCCTTATCAATACT | TCAGTAGTATAAGTAGCTCCTGCTGTC | 192 | 21 | EF215966-EF215968 |
a
Size is based on the R. rickettsii Sheila Smith genome sequence from NCBI. NP, no product (a PCR product was not obtained from some or all isolates tested).
b
The name of this primer was changed to more accurately define the IGR in R. rickettsii. In the cited text, it is named RC1137-tlc5.
c
This primer has been modified from the published R. conorii sequence to match the R. rickettsii Sheila Smith genome sequence. The underlined base is the modified base.
d
Identification of these loci as IGRs was based on a preliminary annotation of the R. rickettsii Sheila Smith genome. The most current version of the annotation indicates that this region may in fact contain as many as three hypothetical coding regions.