Table 1.
In silico specificity test of primers and probes targeting 16S rRNA genes of ANME-1 group and its subgroups
| Oligonucleotide name (orientation) | Sequence (5′→3′) | Reference |
In silico specificity test result (%)a |
||||
|---|---|---|---|---|---|---|---|
| ANME-1a | ANME-1b | ANME-1AT | ANME-1GBa | Negative controls | |||
| ANME1-305(F) | AGCCCGGAGATGGGTTCT | 25 | 96 | 75 | 80 | 0 | 0, 12, 26 |
| ANME1-350(R) | AGTTTTCGCGCCTGATGC | 98 | 98 | 80 | 0 | 0, 20, 90 | |
| ANME1-632(F) | TCAGGGAATACTGCTTGG | 50 | 75 | 0 | 0 | 0, 0, 0 | |
| ANME1-830(R) | TCGCAGTAATGCCAACAC | 84 | 88 | 0 | 0 | 0, 0 0 | |
| Mix of primers ANME1-395(F) | AACTCTGAGTGCCTCCTA | 26 | 80 | 92 | 80 | 0 | 0, 0, 0 |
| AACTCTGAGTGCCTCCAA | |||||||
| AACTCTGAGTGCCCCCTA | |||||||
| ANME1-1417(R) | CCTCACCTAAAYCCCACT | 63 | 94 | 0 | 0 | 0, 0, 6 | |
| ANME1GBHS-183(F) | ATACCTGGAATGGGCGGA | 0 | 0 | 0 | 100 | 0, 0, 0 | |
| ANME1GBHS-841(R) | AACACCGGCACCACTCGT | 0 | 0 | 0 | 100 | 0, 0, 0 | |
| ANME-1-337(F) | AGGTCCTACGGGACGCAT | 27 | 94 | 96 | 80 | 0 | 0, 0, 0 |
| ANME-1-724(R) | GGTCAGACGCCTTCGCT | 92 | 85 | 80 | 0 | 0, 0, 11 | |
| ANME-1-25(F) | GAGGCYACTGCYATCAGMGT | This study | 95 | 97 | 100 | 100 | 0, 0, 11 |
| ANME-1-1118(F) | CYCRCAGTTGCCAGCATCTC | 68 | 96 | 100 | 83 | 0, 0, 4 | |
| ANME-1-1406(R) | AYCYCACTCGGYTGGCTTGA | 100 | 100 | 100 | 100 | 0, 0, 13 | |
| ANME-1-GI812(R) | CTGGCCCACATCGTTTAC | 7 | 16 | 0 | 0 | 0 | 0, 0, 11 |
| cANME-1-GI812(R) | CTAGCCCGCATCGTTTAC | 56 | 15 | 80 | 0 | 10, 23, 50 | |
| ANME-1-GII186(R) | GGACATCCTGCATTCCAG | 0 | 0 | 60 | 0 | 0, 0, 0 | |
| ANME1-628(F) | GCTTTCAGGGAATACTGC | 28 | 38 | 74 | 0 | 0 | 0, 0, 2 |
| ARCH-915(R) | GTGCTCCCCCGCCAATTCCT | 29 | 80 | 96 | 100 | 100 | 91, 97, 98 |
a
The results of in silico specificity tests are presented as percentages of perfectly matching sequences and, for negative controls, as a series of three numbers, the first of which shows the percentage of perfectly matching sequences, and the second and third of which show the percentages of sequences exhibiting one and two mismatches, respectively. As negative controls, we used the 16S rRNA gene sequences of the type strains of archaeal species available from the RDP database (RDP release 10, update 28, 12 January 2012), representing 342 out of the 374 currently recognized archaeal species.