TABLE 5.
Compositional characteristics of genes in MLST scheme for S. uberis
| Gene | Fragment size (bp) | No. of allelesa | % G+Ca | No. of polymorphic sites
|
No. of parsimony-informative sites
|
Pairwise nt difference
|
No. of substitutions
|
dN/dS
|
|||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Synonymous
|
Non- Synonymous
|
||||||||||||||
| Alla | Coreb | Alla | Coreb | Alla | Coreb | Alla | Coreb | Alla | Coreb | Alla | Coreb | ||||
| cpn60 | 537 | 12 | 0.39 | 93 | 19 | 13 | 11 | 7.3 | 4.1 | 94 | 20 | 5 | 0 | 0.01 | 0.00 |
| gapC | 843 | 10 | 0.40 | 67 | 11 | 7 | 7 | 4.1 | 1.7 | 55c | 8 | 9c | 3 | 0.07 | 0.12 |
| oppF | 723 | 14 | 0.40 | NA | 14 | NA | 9 | NA | 2.3 | NA | 12 | NA | 2 | NA | 0.05 |
| pauA | 861 | 11 | 0.34 | NA | 16 | NA | 9 | NA | 3.4 | NA | 4c | NA | 9c | NA | 1.20 |
| sod | 429 | 9 | 0.38 | 99 | 10 | 8 | 6 | 5.3 | 1.7 | 76 | 6 | 24 | 4 | 0.06 | 0.05 |
| tuf | 657 | 11 | 0.40 | 45 | 14 | 9 | 8 | 3.9 | 2.9 | 35 | 11 | 10 | 3 | 0.11 | 0.12 |
a
Based on all 50 S. uberis isolates, with the exception of oppF (no amplicon from FSL Z1-015) and pauA (no amplicon from FSL S3-314 and FSL Z1-015). NA, not applicable.
b
Based on core set of 48 (pauA) or 49 (other genes) S. uberis isolates. Isolate FSL Z1-015 with strongly divergent sequence was excluded from analysis to avoid skewing of results.
c
One complex codon (triplet of sites segregating for multiple codons; DnaSP version 4.0) was excluded from the analysis.