Table 2. Primers designed and used to amplify MLST genes for Rathayibacter toxicus.
| Primer Name | Primer Sequence (5’-3’) | Amplicon Size (bp) | Edited Sequence Size (bp) | PCR Conditions | Target Gene |
|---|---|---|---|---|---|
| Chr-F1 | AAATGCACGTCATCGTCGGT | 1014 | 912 | Ta = 59°C (60 s);Te = 72°C (80 s) | Chromosome partition protein SMC |
| Chr-R1 | GTTCCCGGGCGTGCAACT | ||||
| tRNA-F1 | GATGACGACGGACTGAAGGAT | 1155 | 998 | Ta = 59°C (60 s);Te = 72°C (80 s) | tRNA dihydrouridine synthase |
| tRNA-R1 | AACCTCGCGGGAGTCGAG | ||||
| Cys-F1 | CGTGATCCGCTAATTGTCGA | 1137 | 766 | Ta = 55°C (60 s); Te = 72°C (120 s) | Cystein desulfurase |
| Cys-R1 | GCGACCAGAAACCCGTAG | ||||
| Crispr-F | ATGTATGTCGATATTGATATATTGCAGACCG | 1110 | 941 | Ta = 56°C (60 s); Te = 72°C (120 s) | CRISPR-associated protein, cse4 family |
| Crispr-R | TCATGAGACGCCACCGAGG | ||||
| VanA-F | ATGAACACACTGACCGTAG | 1041 | 831 | Ta = 52°C (60 s); Te = 72°C (120 s) | Vancomycin resistant protein vanA |
| VanA-R | TCATGCCACTGTCTCCG | ||||
| SecA-F | GTGGCCTCAGTTCTCGAAAAGGTCC | 1262 | 734* | Ta = 61°C (60 s); Te = 72°C (120 s) | secA ATPase |
| SecA-R | ACGACCTGCTCGAACTTGACCTG | ||||
| SecA-R1 | AGCGGAGTGTTGACCGACTC |
*For sequencing, secA-R1 was used instead of secA-R; Ta-Annealing temperature; Te-Extension temperature