Table 5. Genes for which there is sequencing-based evidence of phase variation in N. gonorrhoeae strain NCCP11945.
| Gene | FA1090 locus* | Repeat in FA1090* | NCCP11945 locus† | Repeat in NCCP11945† | Repeat in FA19‡ | Repeat in FA6140§ | Repeat in 35/02|| | Repeat in MS11¶ | N. gonorrhoeae candidacy# | Ion Torrent* * | Illumina†† |
|---|---|---|---|---|---|---|---|---|---|---|---|
| ispH | NGO0072 | (G)8 | NGK_0106 | (G)8 | (G)8 | (G)8 | (G)8 | (G)8 | (yes) | Repeat varies | Repeat does not vary |
| virG | NGO0985 | (AAGC)3 | NGK_0804 | (AAGC)3 | (AAGC)2 | (AAGC)3 | (AAGC)3 | (AAGC)3 | Yes | Repeat does not vary | Repeat does not vary |
| Hypothetical | NGO0964 | (AAGC)4 | NGK_0831a | (AAGC)8 | (AAGC)15 | (AAGC)7 | (AAGC)9 | (AAGC)7 | Yes | Repeat varies | Repeat varies |
| Membrane protein | NGO0691 | (G)6 | NGK_1211 | (G)7 | (G)7 | (G)6 | (G)7 | (G)7 | Yes | Repeat varies | Repeat does not vary |
| Hypothetical | NGO0527 | (C)6A(C)9GC | NGK_1405 | (C)6A(C)8GC | (C)7A(C)4T(C)3GC | (C)7A(C)4T(C)3GC | (C)11A(C)8GCGC | (C)6A(C)14GCC | Yes | Repeat varies | Repeat does not vary |
| Replication initiation factor | NGO_06695 | (C)8TTATCTAACA(G)7 | NGK1486 | (C)9TTATCTAACA(G)7 | (C)7TTATCTAACA(G)7 | (C)9TTATCTAACA(G)6 | (C)11TT ATCTAACA(G)8 | (C)9T T AT CT AACA(G)7 | Yes | Repeat varies | Repeat varies |
| mafB cassette | NGO1386 | (C)7 | NGK_1624 | (C)9 | {deletion} | (C)10 | (C)8 | (C)10 | Yes | Repeat varies | Repeat varies |
| Adhesion | NGO1445 | (CAAG)20CAAA | NGK_1705 | (CAAG)12CAAA | (CAAG)12CAAA | (CAAG)6CAAA | (CAAG)9CAAA | (CAAG)6CAA A | Yes | Repeat varies | Repeat varies |
| Replication initiation factor | NGO_06135 | (C)8TTATCTAACA(G)7 | NGK_1957 | (C)11TTATCTAACA(G)8 | (C)7TTATCTAACA(G)7 | (C)6TTATCTAACA(G)5 | (C)11TTATCTAACA(G)8 | (C)10T TAT C TAACA(G)7 | Yes | Repeat varies | Repeat varies |
| Pilin cassette | NGO_11140 | CCGC | NGK_2161 | (C)8 | (C)5GCC | CCGCC | (C)5 | CCT (C)5 | Yes | Repeat varies | Repeat varies |
| Pyrimidine 5′-nucleotidase | NGO2055 & NGO2054II | (C)6 | NGK_2176 | CAAACCCC | CAAACCCC | CAAACCCC | (C)9 | (C)10 | Yes | No repeat | No repeat |
| Lipoprotein | NGO2047 | (A)9 | NGK_2186§§ | (A)8 | (A)8 | (A)9 | (A)9 | (A)8 | Yes | Repeat varies | Repeat varies |
| Hypothetical | NGO1953 | (C)8 | NGK_2297 | (C)8 | (C)8 | (C)8 | (C)9 | (C)8 | Yes | Repeat varies | Repeat does not vary |
| Repetitive large surface lipoprotein | NGO_09875 & NGO_09870II | (G)8 | NGK_2422 & NGK_2423|| | (G)7 | (G)7 | (G)7 | (G)7 | (G)7 | Yes | Repeat varies | Repeat does not vary |
| fetA / frpB | NGO2093 | (C)13 | NGK_2557 | (C)14 | (C)10 | (C)11 | (C)11 | (C)11 | Known | Repeat varies | Repeat varies |
| pilC 1 | NGO1912 | (G)11 | NGK_2342 | (G)13 | (G)11 | GGGC(G)11 | (G)15 | (G)11 | Known | Repeat varies | Repeat varies |
| opa | NGO0950a | (CTTCT)16CTTCC | NGK_0847 | (CTTCT)19CTTCC | (CTTCT)13CTTCC | (CTTCT)16CTTCC | (CTTCT)8CTTCC | (CT T CT )4CT TCC | Known | No reads through repeat | Repeat varies |
*From the N. gonorrhoeae strain FA1090 genome sequence (NC_002946.2).
†From the N. gonorrhoeae strain NCCP11945 genome sequence (CP00150.1).
‡From the N. gonorrhoeae strain FA19 genome sequence (NZ_CP012026.1).
§From the N. gonorrhoeae strain FA6140 genome sequence (NZ_CP012027.1).
||From the N. gonorrhoeae strain 35/02 genome sequence (NZ_CP012028.1).
¶From the N. gonorrhoeae strain MS11 genome sequence (NC_022240.1).
#Gene phase variation candidacy in N. gonorrhoeae. Known, phase variation has been reported in the literature. Yes, there is evidence of repeat tract variation between strains supporting phase variation. (Yes), although there is no variation between strains investigated here, tracts of this length vary on other genes (Chen et al., 1998; Shafer et al., 2002; Adamczyk-Poplawska et al., 2011).
**Based on Ion Torrent sequencing data from cultures grown with passage for 8 weeks and from cultures grown with passage for 20 weeks (accession numbers SRR3547950, SRR3547951, SRR3547952, SRR3547953).
††Based on Illumina sequencing data from cultures grown with passage for 20 weeks (accession numbers SRR3547954, SRR3547955, SRR3547956, SRR3547957).
‡‡There is a 400 bp deletion in this strain encompassing the region that would contain this repeat.
§§NGK_2186 and NGO2047 annotations are on opposite strands.
||||This coding sequence appears to be frame-shifted and annotated as two coding sequences.