Table 1.
Candidate adaptive genes involved in ST-61 complex emergence from ST-21 clonal complex
| Name | Alias | Transcriptional unit no.* | Genome position on C. jejuni NCTC11168 reference genome | Predicted function† | COG family † | COG family description† | Prevalence in ST-21 complex, n = 113 (%) | Prevalence in ST-61 complex, n = 49 (%) | Prevalence in ST-42 complex, n = 22 (%) |
| Accessory genes highly prevalent in ST-61 and ST-42 complexes but missing in ST-21 complex | |||||||||
| CJM1_RS06530 | — | — | — | Hypothetical protein | — | — | 2 (1.77) | 44 (89.80) | 18 (81.82) |
| CJM1_RS06535 | — | — | — | Plasmid stabilization system protein | R | General function prediction only | 2 (1.77) | 44 (89.80) | 18 (81.82) |
| id1956_0137 | cj1340-like | — | — | Motility accessory factor (homolog) | S | Function unknown | 0 (0) | 45 (91.84) | 21 (95.45) |
| id3193_0984 | cj1341-like | — | — | Motility accessory factor (homolog) | S | Function unknown | 0 (0) | 44 (89.80) | 20 (90.91) |
| id380_0014 | — | — | — | Hypothetical protein | — | — | 4 (3.54) | 48 (97.96) | 22 (100) |
| id5316_0084 | — | — | — | Putative McrB subunit of the McrBC restriction endonuclease system | — | — | 0 (0) | 48 (97.96) | 15 (68.18) |
| Accessory genes highly prevalent in ST-21 complex but missing in ST-61 and ST-42 complexes | |||||||||
| Cj1319 | — | 495 | 1248624..1249595 | Putative nucleotide sugar dehydratase | M | Cell wall/membrane biogenesis | 113 (100) | 1 (2.04) | 0 (0) |
| Cj1320 | — | 495 | 1249588..1250742 | Putative DegT family aminotransferase | M | Cell wall/membrane biogenesis | 113 (100) | 2 (4.08) | 0 (0) |
| Cj1324 | — | 498 | 1252278..1253399 | Hypothetical protein | D | Cell cycle control, mitosis and meiosis | 112 (99.1) | 1 (2.04) | 0 (0) |
| Cj1325 | — | 498 | 1253417..1254092 | Putative methyltransferase | J | Translation | 112 (99.1) | 1 (2.04) | 0 (0) |
| Cj1327 | neuB2 | 498 | 1254132..1255136 | N-acetylneuraminic acid synthetase | M | Cell wall/membrane biogenesis | 113 (100) | 2 (4.08) | 0 (0) |
| cj1328 | neuC2 | 498 | 1255129..1256283 | Putative UDP-N-acetylglucosamine 2-epimerase | M | Cell wall/membrane biogenesis | 113 (100) | 1 (2.04) | 0 (0) |
| cj1329 | — | 498 | 1256292..1257317 | Putative sugar-phosphate nucleotide transferase | J | Translation | 113 (100) | 1 (2.04) | 0 (0) |
| cj1330 | — | 498 | 1257314..1258219 | Hypothetical protein | R | General function prediction only | 113 (100) | 1 (2.04) | 0 (0) |
| cj1331 | ptmB | 498 | 1258212..1258919 | Acylneuraminate cytidylyltransferase | M | Cell wall/membrane biogenesis | 113 (100) | 2 (4.08) | 0 (0) |
| cj1332 | ptmA | 498 | 1258919..1259689 | Flagellin modification protein A | I | Lipid transport and metabolism | 113 (100) | 2 (4.08) | 0 (0) |
| Alleles of core genes harboring recombination events highly prevalent in ST-61 and ST-42 complexes but missing in ST-21 complex | |||||||||
| cj0641 | pnk | 243 | 602326..603186 | Inorganic polyphosphate/ATP-NAD kinase | G | Carbohydrate transport and metabolism | 4 (3.54) | 39 (79.59) | 20 (90.91) |
| cj0665c | argG | 248 | 621392..622612 | Argininosuccinate synthase | E | Amino acid transport and metabolism | 4 (3.54) | 48 (97.96) | 21 (95.45) |
| cj0709 | ffh | 269 | 665788..667125 | Signal recognition particle protein | U | Intracellular trafficking and secretion | 4 (3.54) | 49 (100) | 20 (90.91) |
| cj1044c | thiH | 395 | 977626..978771 | Thiamine biosynthesis protein ThiH | H | Coenzyme transport and metabolism | 0 (0) | 49 (100) | 22 (100) |
| cj1082c | thiD | 405 | 1013374..1014186 | Phosphomethylpyrimidine kinase | H | Coenzyme transport and metabolism | 6 (5.31) | 39 (79.59) | 22 (100) |
| cj1349c | — | 500 | 1280992..1282299 | Putative fibronectin/fibrinogen-binding protein | K | Transcription | 0 (0) | 47 (95.92) | 17 (77.27) |
| cj1350 | mobA | 501 | 1282361..1282936 | Putative molybdopterin-guanine dinucleotide biosynthesis protein | H | Coenzyme transport and metabolism | 3 (2.65) | 42 (85.71) | 19 (86.36) |
| cj1352 | ceuB | 502 | 1284008..1284976 | Enterochelin uptake permease | P | Inorganic ion transport and metabolism | 3 (2.65) | 48 (97.96) | 22 (100) |
| cj1633 | — | 601 | 1558654..1559637 | Putative ATP-binding protein | J | Translation | 0 (0) | 44 (89.80) | 21 (95.45) |
ST-38 and ST-5161 intermediate isolates were not included in the prevalence calculations. One-letter abbreviations are linked to the functional categories in column 7 as defined by the Clusters of Orthologous Groups (COG) classification (37).
*
As predicted by the Prokaryotic Operon DataBase (ProOpDB) (38). Consecutive numbers reflect consecutive transcriptional units on the C. jejuni NCTC11168 reference genome.
†
As predicted by the WebMGA server (39).