Table 1 PCR primers used in this study
A. Primers used for detection of multiple RD2 genes, Q-PCR and tiling. | ||
|---|---|---|
Primer name | Primer sequence | Source |
emm sequencing | Â | |
CDC emm1 | TATT(C/G)GCTTAGAAAATTAA | [19] |
CDC emm2 | GCAAGTTCTTCAGCTTGTTT | [19] |
Detection of circular form | Â | |
#1 | GAAAACAAAAGTTTCTTCATGCGTTTGGCG | this work |
#2 | CAATTAATAGAAACATATGGTCATTTG | this work |
#3 | GGAATTAGCCCACTAGAATATAAGC | this work |
#4 | TAGCAAGTAAACCCTAGATTGTCTATGTTC | this work |
Detection of genes encoding extracellular RD2 proteins | Â | |
M28_Spy1306F | ACTAAGCCAAGCGAGGACAA | [1] |
M28_Spy1306R | CCAAAACCGTGTAGCCTGTA | [1] |
M28_Spy 1307F | TCATCGTCAAAAGCCATCTC | [1] |
M28_Spy 1307R | TTGCTCTGATAAACCTCAAG | [1] |
M28_Spy1308F | TACGACAGAAGCAGGTGGAG | [1] |
M28_Spy1308R | ACCGAGTTTCGCAGGATTG | [1] |
M28_Spy1325F | TGAATGATGCGGGGACTTAT | [1] |
M28_Spy1325R | TGTAAAAGGCTGCTGGGTCT | [1] |
M28_Spy1326F | ACACCGACTGAGATTGCTGA | [1] |
M28_Spy1326R | TTGGCTTGTGAGGTTTGAGA | [1] |
M28_Spy1332F | ATGCCAAAAACCAAAGGAAG | [1] |
M28_Spy1332R | TCATACTTTTCAGGTACACAAGCA | [1] |
M28_Spy1336F | GATACTTCACAGACGAAACAACG | [1] |
M28_Spy1336R | ATCACGACTCCCATCACTCC | [1] |
Quantitative PCR (Taqman) | Â | |
proS_F | TGAGTTTATTATGAAAGAGGCTATAGTTTC | [15] |
proS_R | AATAGCTTCGTAAGCTTGACGATAAT | [15] |
proS_P | TCGTAGGTCACATCTAATCTTCATAGTTG | [15] |
M28_Spy1306 F | CGTTGTTCCTGCTACTGGATCTGCTAC | this work |
M28_Spy1306 P | ACGATTGCAAGTATTGCTTTG | this work |
M28_Spy1306 R | CAATCGGTGTCGTTGGTTG | this work |
M28_Spy1325 F | ACCGTCGCAAGGACCTTGTCTTTCTG | [8] |
M28_Spy1325 P | CAGCATACGCATGACCTC | [8] |
M28_Spy1325 R | AGTGATAACACTACCATCTGATAAAG | [8] |
M28_Spy1336 F | ACAGAAGCTGCACCAAACTTGAACTTCTTAATTGA | this work |
M28_Spy1336 P | GTAGATGCAGCAACTATTGAC | this work |
M28_Spy1336 R | ATGATACTTCACAGACGAAACAAC | this work |
M28_Spy0784_RD0 F | AGCAGAGTATGAAGGCGGTTTT | this work |
M28_Spy0784_RD0 P | ATATTCTATCTGAAACGGCTCG | this work |
M28_Spy0784_RD0 R | AACATCTCTGCGAGTCGTTCTATACTT | this work |
M28_Spy0980_6180.1 F | TCGTTAGGACTGGCGGTAGAG | this work |
M28_Spy0980_6180.1 P | TGCAACTGCTGTCTTAA | this work |
M28_Spy0980_6180.1 R | AACAGTCTTTGCCACCACCAT | this work |
M28_Spy1087_RD1 F | TGTTTTTTGAATCTCTGACTTCTTTCC | this work |
M28_Spy1087_RD1 P | AGAATTGCAGCTACTTGTATT | this work |
M28_Spy1087_RD1 R | TGCAGACGAAAATAGCTGTAACTACTC | this work |
M28_Spy1231_6180.2 F | GCAGTTGCTTGTTGCGTTGA | this work |
M28_Spy1231_6180.2 P | TGCAACCCACTGATTT | this work |
M28_Spy1231_6180.2 R | GCGCGTAGAGCTGGAGTCA | this work |
M28_Spy1805_6180.3 F | AAAGGGCTATGGACGAACGA | this work |
M28_Spy1805_6180.3 P | CAGACCAGCCTTTG | this work |
M28_Spy1805_6180.3 R | GGTAAACCGATATTTTTCATCAATGA | this work |
B. Primer combinations used for tiling across RD2 element, after [1]. | ||
Tiling fragment | Amplified region | Primer sequence |
1 | M28_Spy1299-1304 | GGTTTCGACAAGGTCAGAGC |
| Â | Â | TGTGAGTGTTCCTGTACCAGATG |
2 | M28_Spy1304-1306 | ACGGCTACCTTTCCCCCTA |
| Â | Â | ACTAAGCCAAGCGAGGACAA |
3 | M28_Spy1306-1307 | CCAAAACCGTGTAGCCTGTA |
| Â | Â | TCATCGTCAAAAGCCATCTC |
4 | M28_Spy1307-1308 | TTGCTCTGATAAACCTCAAG |
| Â | Â | TACGACAGAAGCAGGTGGAG |
5 | M28_Spy1308-1310 | ACCGAGTTTCGCAGGATTG |
| Â | Â | GCTTGGAGGTGTTTCCTTTC |
6 | M28_Spy1310-1314 | CCTTGTTCTGCTTGATGTCC |
| Â | Â | ATCAAGCAAGCAACAAAACG |
7 | M28_Spy1314-1322 | TTTCCACCCATCAGTTCAGG |
| Â | Â | GACTGGTGGCGGTAAGACTG |
8 | M28_Spy1322-1325 | TTTCATCCCCAAAAAGCATC |
| Â | Â | TGAATGATGCGGGGACTTAT |
9 | M28_Spy1325-1326 | TGTAAAAGGCTGCTGGGTCT |
| Â | Â | ACACCGACTGAGATTGCTGA |
10 | M28_Spy1326-1331 | TTGGCTTGTGAGGTTTGAGA |
| Â | Â | TCATACTTTTCAGGTACACAAGCA |
11 | M28_Spy1331-1336 | ATGCCAAAAACCAAAGGAAG |
| Â | Â | GATACTTCACAGACGAAACAACG |
12 | M28_Spy1336-1338 | ATCACGACTCCCATCACTCC |
| Â | Â | CAAAGTTCCTGCCCCAAC |