Table 2.
Primers used for amplification and sequencing, PCR annealing temperatures, and the region used for phylogenetic analysis
| Gene | Primer | Nucleotide sequence (5′–3′) | Amplicon size (bp) | Annealing temp (°C) | Region used for MLSA (bp)a |
|---|---|---|---|---|---|
| atpD | atpD-35F | CCGTGGTGGATATTCAGT | 491 | 50 | 85–480 |
| atpD-522R | CTTGGCGATGTTGTTGAT | ||||
| icd | icd-685F | CTGGTSCACAAGGGCAACAT | 532 | 55 | 832–1167 |
| icd-1216R | ACACCTGVGTSGCVCCTTC | ||||
| recA | recA-64F | TCGCAGATCGAAAAGCAGTT | 549 | 50 | 133–591 |
| recA-615R | CATGCGGATCTGGTTGATGAAG | ||||
| rpoB | rpoB-903F | GCTGGCCAAGAACATCGT | 586 | 50 | 958–1470 |
| rpoB-1488R | GTGCGGCATYAGGTTTTC | ||||
| tyrB | tyrB-391F | CCSAGCTGGGAAAACCAYCG | 477 | 58 | 454–843 |
| tyrB-867R | CGGGTTGSAGTAGWTGGYG | ||||
| 16S rRNA | 16f27 | AGAGTTTGATCMTGGCTCAG | 1495 | 55 | 89–1397 |
| 16r1492 | TACGGYTACCTTGTTACGACTT | ||||
| 16f357 | ACTCCTACGGGAGGCAGCAG |
a
Position relative to A. xylosoxidans A8 genomic sequence.