Table 2.
Parallel or Convergent Evolution in Niche-Passaged Pneumococcal Lineages.
| Gene (Amino Acid Change Caused by SNP)a | D39V Annotationb | In Passage 20 Nasopharynx Lineages? (n/10) | In Passage 20 Lung Lineages? (n/10) | In Control Passage Lineages or Ancestor? | COG Category |
|---|---|---|---|---|---|
|
mutX1 (P29S) |
SPV_0644 MutT/Nudix Family Protein | 2 | N | Nucleotide Transport and Metabolism | |
|
D39N_00979 (Y331C) |
SPV_0961 lafA | 3 | N | Cell wall/membrane biogenesis | |
|
sdhB (G14R) |
SPV_0103 sdhB | 2 | N | Amino acid transport and metabolism | |
|
arnB (S192F, A197G, A96V, P11S) |
SPV_1619 aatB | 3 | 2 | Y (A96V) | Amino acid transport and metabolism |
|
D39N_01974 (A608S, L170M) |
SPV_1969 Glycosyl hydrolase-related protein | 3 | 3 | Y | Carbohydrate transport and metabolism |
|
yknX (S331N) (L333V) |
SPV_0686 Periplasmic component of efflux system | 2 | 1 | N | Cell wall/membrane biogenesis |
|
D39N_01029 (T62I, Y19H) |
SPV_0912 pvaA | 2 | N | Cell wall/membrane biogenesis | |
|
gpsA (G208R) |
SPV_1918 gpsA | 2 | N | Lipid transport and metabolism |
a
All genes in which nonsynonymous single nucleotide polymorphisms were identified in more than one independently evolved lineage are shown.
b
The corresponding gene in the D39 genome was recently published by Slager et al. (2018).