Table 1.
Evolutionary analyses of genes encoding choline-binding proteinsa
| Genes | Number of sequencesb | dN/dS | Coverage of comparable codons relative to whole protein in TIGR4 | Codons evolving under positive selection | Codons evolving under purifying selection | % of codons under purifying selection relative to total codons | |||
|---|---|---|---|---|---|---|---|---|---|
| cbpA | 19 | 0.864 | 22.334% | (155/694) | 3.226% | (5/155) | 7.742% | (12/155) | 1.729 |
| cbpC | 13 | − | 0% | (0/93) | − | − | 0.000 | ||
| cbpD | 19 | 0.359 | 75.278% | (338/449) | 0.296% | (1/338) | 3.550% | (12/338) | 2.672 |
| cbpE | 18 | 0.325 | 99.363% | (624/628) | 0.160% | (1/624) | 4.968% | (31/624) | 4.936 |
| cbpF | 19 | 0.395 | 60.411% | (206/341) | 0.485% | (1/206) | 3.398% | (7/206) | 2.053 |
| cbpG | 21 | − | 0% | (0/286) | − | − | 0.000 | ||
| cbpI | 2 | − | − | − | − | − | |||
| cbpJ | 15 | 0.346 | 84.084% | (280/333) | 1.429% | (4/280) | 18.571% | (52/280) | 15.616 |
| cbpK | 11 | 0.353 | 85.630% | (292/341) | 0.342% | (1/292) | 3.082% | (9/292) | 2.639 |
| cbpL | 20 | − | 0% | (0/333) | − | − | 0.000 | ||
| cbpM | 10 | 0.642 | 98.462% | (128/130)c | 0% | (0/128) | 0% | (0/128) | 0.000 |
| lytA | 14 | 0.141 | 80.564% | (257/319) | 0% | (0/257) | 17.121% | (44/257) | 13.793 |
| lytB | 22 | 0.185 | 92.868% | (612/659) | 0% | (0/612) | 4.739% | (29/612) | 4.401 |
| lytC | 23 | 0.400 | 19.348% | (95/491) | 0% | (0/95) | 5.263% | (5/95) | 1.018 |
| pcpA | 18 | 0.261 | 77.010% | (479/622) | 0% | (0/479) | 0.418% | (2/479) | 0.322 |
| pspA | 24 | 0.857 | 19.060% | (142/745) | 6.338% | (9/142) | 12.676% | (18/142) | 2.416 |
aEvolutionary analysis was performed by Bayesian inference of aligned cbp sequences from complete genomes of S. pneumoniae with the two-rate fixed-effects likelihood function in the HyPhy software package. dN/dS is the ratio of non-synonymous to synonymous changes in overall analysed genes. Individual codons with a statistically significant signature were also calculated and are expressed as a percentage of the total number of codons included in the analysis.
bSequences with 100% identity were treated as the same sequence; ccompared to D39