TABLE 3.
Distribution of non-TIGR4 and non-R6 DNA sequences and RNA transcripts from PCR and RT-PCR analyses
| Clone/contig name | Amplimer size | PCR/RT-PCR: results for individual S. pneumoniae strains
|
No. of strains with novel sequences (DNA/RNA) | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| BS 68 (Type 9) | BS 69 (Type 14) | BS 70 (Type 11) | BS71 (Type 3) | BS 72 (Type 23) | BS 73 (Type 6) | BS 74 (Type 18) | BS 75 (Type 19) | TIGR 4 | R6 | |||
| SP11_0001_B02 | 330 | −/− | −/− | +/+ | −/− | −/− | −/− | −/− | −/− | −/− | −/− | 1/1 |
| SP11_0001_N20 | 325 | −/− | −/− | +/+ | +/+ | +/+ | +/+ | −/− | −/− | −/− | −/− | 4/4 |
| SP11_0001_O05 | 424 | −/− | −/− | +/+ | +/+ | +/+ | +/+ | −/− | −/− | −/− | −/− | 4/4 |
| SP11_0002_A02 | 126 | −/− | −/− | +/+ | +/+ | +/+ | +/− | +/+ | +/+ | −/− | −/− | 6/5 |
| SP11_0002_B05 | 382 | +/+ | +/+ | +/+ | +/+ | +/+ | +/− | +/− | +/+ | −/− | −/− | 8/6 |
| SP14_0001_D21 | 156 | +/+ | +/+ | −/− | −/− | −/− | +/+ | −/− | −/− | −/− | −/− | 3/3 |
| SP14_0001_F07 | 162 | +/+ | +/− | −/− | +/+ | +/− | +/− | −/− | +/− | −/− | −/− | 6/2 |
| SP14_0001_G03 | 185 | +/+ | +/+ | −/− | +/+ | +/+ | +/+ | −/− | +/+ | −/− | −/− | 6/6 |
| SP14_0001_J05 | 147 | −/− | +/+ | −/− | −/− | −/− | −/− | −/− | −/− | −/− | −/− | 1/1 |
| SP14_0001_N13 | 107 | −/− | +/+ | −/− | −/− | −/− | −/− | −/− | −/− | −/− | −/− | 1/1 |
| SP14_0001_O12 | 156 | −/− | +/− | +/− | −/− | −/− | −/− | +/− | +/+ | −/− | −/− | 4/1 |
| SP14_0002_K23 | 156 | −/− | +/+ | −/− | −/− | −/− | −/− | +/+ | −/− | −/− | −/− | 2/2 |
| SP14_0002_O02 | 144 | +/+ | +/+ | +/+ | −/− | −/− | −/− | +/+ | −/− | −/− | −/− | 4/4 |
| SP18_0001_K21 | 271 | −/− | −/− | −/− | +/− | −/− | −/− | +/+ | −/− | −/− | −/− | 2/1 |
| SP18_0001_N06 | 108 | +/+ | +/+ | +/+ | +/+ | +/+ | −/− | +/− | −/− | −/− | −/− | 6/5 |
| SP18_0002_L08/0003_F11 | 246 | −/− | −/− | −/− | +/− | −/− | +/+ | +/+ | +/+ | −/− | −/− | 4/3 |
| SP18_0002_O09 | 112 | −/− | −/− | −/− | +/− | −/− | −/− | +/+ | −/− | −/− | −/− | 2/1 |
| SP18_0002_P11 | 107 | −/− | −/− | +/+ | +/+ | +/+ | +/+ | +/+ | +/+ | −/− | −/− | 6/6 |
| SP19_0001_C10 | 129 | +/− | +/− | +/+ | +/+ | +/− | +/− | +/− | +/+ | −/− | −/− | 8/3 |
| SP19_0001_E12 | 228 | −/− | +/+ | +/+ | +/+ | −/− | +/+ | −/− | +/− | −/− | −/− | 5/4 |
| SP23_0001_O05 | 110 | −/− | −/− | −/− | −/− | +/+ | −/− | −/− | −/− | −/− | −/− | 1/1 |
| SP23_0002_C12 | 366 | −/− | −/− | −/− | +/+ | +/+ | +/− | −/− | −/− | −/− | −/− | 3/2 |
| SP23_0002_F06 | 113 | −/− | −/− | −/− | +/+ | +/+ | +/− | −/− | −/− | −/− | −/− | 3/2 |
| SP23_0002_F23 | 120 | −/− | −/− | −/− | −/− | +/+ | −/− | −/− | −/− | −/− | −/− | 1/1 |
| SP23_0002_G12 | 130 | −/− | −/− | −/− | +/+ | +/+ | +/− | −/− | −/− | −/− | −/− | 3/2 |
| SP23_0002_I15 | 123 | −/− | −/− | −/− | −/− | +/+ | −/− | −/− | −/− | −/− | −/− | 1/1 |
| SP23_0002_K13 | 125 | +/+ | −/− | −/− | +/+ | +/+ | +/+ | −/− | +/+ | −/− | −/− | 5/5 |
| SP23_0002_K23 | 121 | +/+ | +/+ | −/− | −/− | +/− | −/− | −/− | −/− | −/− | −/− | 3/2 |
| SP23_0002_O09 | 98 | +/+ | −/− | +/+ | +/+ | +/+ | −/− | −/− | +/+ | −/− | −/− | 5/5 |
| SP23_0002_O13 | 294 | −/− | −/− | −/− | +/+ | +/+ | −/− | −/− | −/− | −/− | −/− | 2/2 |
| SP3_0001_D02 | 167 | −/− | −/− | −/− | +/+ | +/+ | −/− | +/+ | −/− | −/− | −/− | 3/3 |
| SP3_0001_E06 | 116 | −/− | −/− | −/− | +/− | −/− | −/− | +/+ | −/− | −/− | −/− | 2/1 |
| SP3_0001_O13 | 168 | −/− | −/− | −/− | +/+ | −/− | −/− | −/− | −/− | −/− | −/− | 1/1 |
| SP3_0002_B15/0001_103 | 132 | +/+ | +/+ | −/− | +/− | −/− | −/− | +/+ | +/+ | −/− | −/− | 5/4 |
| SP3_0002_H04 | 177 | −/− | −/− | +/− | +/+ | −/− | +/+ | −/− | −/− | −/− | −/− | 3/2 |
| SP6_0001_A22 | 113 | −/− | −/− | −/− | −/− | −/− | +/+ | −/− | −/− | −/− | −/− | 1/1 |
| SP6_0001_C18 | 109 | −/− | −/− | −/− | −/− | −/− | +/+ | −/− | −/− | −/− | −/− | 1/1 |
| SP6_0001_D01 | 150 | +/+ | +/+ | +/+ | +/+ | +/+ | +/+ | +/+ | +/+ | −/− | −/− | 8/8 |
| SP6_0001_D08 | 127 | +/+ | +/+ | +/+ | +/+ | +/+ | +/+ | +/+ | +/+ | −/− | −/− | 8/8 |
| SP6_0001_K19 | 113 | +/+ | +/− | −/− | +/+ | +/+ | +/+ | −/− | +/+ | −/− | −/− | 6/5 |
| SP6_0001_P13 | 112 | +/+ | +/+ | −/− | +/+ | +/+ | +/+ | −/− | +/+ | −/− | −/− | 6/6 |
| SP6_0002_F09 | 118 | +/+ | −/− | +/− | −/− | −/− | +/− | −/− | −/− | −/− | −/− | 3/1 |
| SP9_0001_D22 | 115 | +/+ | −/− | −/− | −/− | −/− | −/− | −/− | −/− | −/− | −/− | 1/1 |
| SP9_0001_G17 | 229 | +/+ | +/+ | +/+ | +/+ | −/− | −/− | −/− | +/− | −/− | −/− | 5/4 |
| SP9_0001_G20/0001_H19/ 0001_O09 | 103 | +/+ | −/− | −/− | −/− | −/− | −/− | −/− | −/− | −/− | −/− | 1/1 |
| SP9_0001_K08 | 143 | +/+ | −/− | −/− | −/− | −/− | −/− | −/− | −/− | −/− | −/− | 1/1 |
| SP9_0001_P13 | 95 | +/+ | −/− | −/− | −/− | +/+ | +/+ | −/− | +/+ | −/− | −/− | 4/4 |
| SP9_0002_C16 | 110 | +/+ | −/− | +/+ | +/+ | +/+ | −/− | −/− | +/+ | −/− | −/− | 5/5 |
| SP9_0002_D05 | 110 | +/+ | −/− | −/− | −/− | −/− | −/− | −/− | −/− | −/− | −/− | 1/1 |
| SP9_0002_I18 | 121 | +/+ | +/+ | −/− | +/+ | −/− | −/− | −/− | −/− | −/− | −/− | 3/3 |
| SP9_0002_I19 | 112 | +/− | +/− | −/− | +/− | +/− | +/+ | +/+ | +/+ | −/− | −/− | 7/3 |
| SP9_0002_N02/0001_B10 | 139 | +/+ | +/+ | +/+ | +/+ | +/+ | −/− | +/+ | −/− | −/− | −/− | 6/6 |
| SP9_0002_O20 | 118 | +/+ | −/− | +/+ | +/+ | +/+ | +/+ | +/+ | +/+ | −/− | −/− | 7/7 |
| SP9_0003_A11 | 108 | +/+ | +/+ | −/− | −/− | −/− | −/− | −/− | −/− | −/− | −/− | 2/2 |
| SP9_0003_F08 | 153 | +/+ | +/+ | −/− | −/− | −/− | −/− | −/− | −/− | −/− | −/− | 2/2 |
| SP9_0003_H13 | 137 | +/+ | +/+ | −/− | +/− | −/− | −/− | −/− | +/+ | −/− | −/− | 4/3 |
| SP9_0003_N08 | 80 | +/− | +/− | +/− | −/− | −/− | −/− | +/+ | −/− | −/− | −/− | 4/1 |
| SP9_0003_O13 | 107 | +/+ | −/− | +/− | −/− | −/− | −/− | −/− | −/− | −/− | −/− | 2/1 |
| No. of novel sequences | 32 | 26 | 22 | 35 | 29 | 26 | 20 | 22 | 0 | 0 | 212 | |
| No. of novel transcripts | 29 | 20 | 17 | 28 | 25 | 18 | 16 | 19 | 0 | 0 | 172 | |
| No. of non-TIGR4/R6 DNA sequences found exclusively in this strain | 4 | 2 | 1 | 1 | 3 | 2 | 0 | 0 | 0 | 0 | 13 | |
| No. of non-TIGR4/R6 RNA transcripts found exclusively in this strain | 6 | 2 | 1 | 1 | 3 | 2 | 4 | 1 | 0 | 0 | 20 | |