Table 2.
Primers specifically designed for this study or used in previous studiesa
| Primer name | Primer direction | Primer sequence (5′–3′) | Tm (°C) | Annealing site (5′–3′) | Reference or source |
|---|---|---|---|---|---|
| SL | F | DCCGTAGCCATTTTGGCTCAAG | 57.0 | Variable | 19 |
| AUAP | R | GGCCACGCGTCGACTAGTAC | 57.9 | Variable | Invitrogen |
| Nsf83 | F | GAAACTGCGAATGGCTCATT | 49.7 | 82–101 | 27 |
| 1528r | R | TGATCCTTCTGCAGGTTCACCTAC | 57.4 | 1777–1800 | 28 |
| 18SF8 | F | TTGATCCTGCCAGTAGTCATATGCTTG | 58.2 | 8–34 | 5 |
| ITSR01 | R | CCTTGTTACGACTTCTCCTTCCTC | 57.4 | 1748–1771 | 5 |
| 5.8S-b5′ed | F | GATGAAGAATGCAGCAAMATG | 50.5 | 2025–2045 | 39 |
| 5.8S-b3 | R | CAAGCAHACCTTCAAGMATATCC | 55.3 | 2112–2134 | 39 |
| M13F | F | GTAAAACGACGGCCAG | 45.9 | Invitrogen | |
| M13R | R | CAGGAAACAGCTATGA | 40.8 | Invitrogen | |
| sxt001 | F | TGCAGCGMTGCTACTCCTACTAC | 57.1 | 904–926 | 18 |
| sxt002 | R | GGTCGTGGTCYAGGAAGGAG | 55.9 | 1429–1449 | 18 |
| sxt007 | F | ATGCTCAACATGGGAGTCATCC | 54.8 | 3174–3195 | 18 |
| sxt008 | R | GGGTCCAGTAGATGTTGACGATG | 57.1 | 3865–3888 | 18 |
| sxtG71F | F | AGGACATGGACGAKAATAGCTG | 54.8 | 71–92 | This study |
| sxtG127F | F | TCCGGCGACTACGAGTTC | 52.6 | 127–144 | This study |
| sxtG206F | F | GGGCCGTGAAGGATTACCTGA | 56.3 | 206–226 | This study |
| sxtG206R | R | TCAGGTAATCCTTCACGGCCC | 56.3 | 206–226 | This study |
| sxtG221R | R | GTTTATGCCGTCGCGCTTCAGGT | 58.8 | 221–243 | This study |
| sxtG663F | F | CATGGAGTCGATGGTGAGCAAC | 56.7 | 663–684 | This study |
| sxtG663R | R | GTTGCTCACCATCGACTCCATG | 56.7 | 663–684 | This study |
| sxtG802F | F | CTGGACTCGMACACGATAATGA | 54.8 | 802–823 | This study |
| sxtG1008F | F | CGAGTCCTACGGCTACAAGC | 55.9 | 1008–1027 | This study |
| sxtG1009R | R | ATCGGCTTGTAGCCGTAGGACTC | 58.8 | 1009–1031 | This study |
| sxtG1042R | R | CGCAGAAGTTCATGTYGCATAT | 53.0 | 1042–1063 | This study |
| sxtGq559F | F | GACGGGAACGGCTACAA | 49.5 | 559–575 | This study |
| sxtGq605R | R | GCTCGAAGATCGGGTCCT | 52.6 | 605–622 | This study |
a
Melting temperature (Tm) calculated using OligoCalc (30). F, forward; R, reverse. Annealing sites are based on the mRNA sequence of A. fundyense and can vary slightly between species. sxtG intron presence is not considered. The primer pairs and PCR annealing temperature used were as follows: 60°C for sxtG127F/sxtG1009R, sxtG206F/sxtG1009R, sxtG127F/sxtG663R, sxtG206F/sxtG663R, and sxtG663F/sxtG1009R, and 56°C for sxtG71F/sxtG663R and sxtG663F/sxtG1042R.