Table 2.
Primers and DNA amplification conditions used in this study
| Primer | Sequence (5`- 3`)a | Target gene (position) † | PCR cycling | Reference |
|---|---|---|---|---|
| TSrecAf | CAACTGCMYTGCGTATCGTCGAAGG | recA (8-32) | 2 min 95°C, 35 X (45s 95°C, 30s 58°C, 1,5 min 72°C and 7 min 72°C. | Stepkowski et al. (2005) |
| TSrecAr | CGGATCTGGTTGATGAAGATCACCATG | recA (620-594) | ||
| TSatpDf | TCTGGTCCGYGGCCAGGAAG | atpD (189-208) | 2 min 95°C, 35 X (45s 95°C, 30s 58°C, 1,5 min 72°C and 7 min 72°C. | Stepkowski et al. (2005) |
| TSatpDr | CGACACTTCCGARCCSGCCTG | atpD (804-784) | ||
| TSglnIIf | AAGCTCGAGTACATCTGGCTCGACGG | glnII (13-38 | 2 min 95°C, 35 X (45s 95°C, 30s 58°C, 1,5 min 72°C and 7 min 72°C. | Stepkowski et al. (2005) |
| TSglnIIr | SGAGCCGTTCCAGTCGGTGTCG | glnII (681-660) | ||
| gyrB343F | TTCGACCAGAAYTCCTAYAAGG | gyrB (343-364) | 5 min 95°C, 5X (2 min 94°C, 2 min 58°C, 1 min 72°C) 28 X (30s 94°C, 1 min 58°C, 1 min 72°C and 5 min 72°C. | Martens et al. (2008) |
| gyrB1043R | AGCTTGTCCTTSGTCTGCG | gyrB (1061-1043) | ||
| rpoB83F | CCTSATCGAGGTTCACAGAAGGC | rpoB (1081-1061) | 5 min 95°C, 3X (2 min 94°C, 2 min 58°C, 1 min 72°C) 30 X (30s 94°C, 1 min 58°C, 1 min 72°C and 5 min 72°C. | Martens et al. (2008) |
| rpoB1061R | AGCGTGTTGCGGATATAGGCG | rpoB (83-103) | ||
| fD1 | AGAGTTTGATCCTGGCTCAG | 16S rRNA (9-29) | 2 min 95°C, 30 X (15s 94°C, 45s 93°C, 45s 55°C, 2 min 72°C and 5 min 72°C. | Weisburg et al. (1991) |
| rD1 | CTTAAGGAGGTGATCCAGCC | 16S rRNA (1474-1494) | ||
a
Mixtures of bases used at certain positions are given as: K, T or G; S, G or C; Y, C or T; R, A or G; M, A or C
†
Position of the primer in the corresponding sequence of Bradyrhizobium japonicum USDA 110