TABLE 5.

Compositional characteristics of genes in MLST scheme for S. uberis

GeneFragment size (bp)No. of allelesa% G+CaNo. of polymorphic sitesNo. of parsimony-informative sitesPairwise nt differenceNo. of substitutionsdN/dS
SynonymousNon- Synonymous
AllaCorebAllaCorebAllaCorebAllaCorebAllaCorebAllaCoreb
cpn60 537120.39931913117.34.19420500.010.00
gapC 843100.406711774.11.755c89c30.070.12
oppF 723140.40NA14NA9NA2.3NA12NA2NA0.05
pauA 861110.34NA16NA9NA3.4NA4cNA9cNA1.20
sod 42990.389910865.31.77662440.060.05
tuf 657110.404514983.92.935111030.110.12
  • 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.