TABLE 3.
Genetic diversity at seven loci based on 76 L. lactis isolates included in Fig. 2 and 3 for which sequences are available for all locia
| Locus | Gene length (bp) | Amplified fragment length (bp) | Analyzed fragment length (bp) | No. of polymorphic sites | % of variable nucleotide sites | No. of alleles | Avg G+C content (%) | dN/dS ratiob |
|---|---|---|---|---|---|---|---|---|
| atpA | 1,503 | 1,141 | 409 | 55 | 13.5 | 31 | 42 | 0.1408 |
| rpoA | 939 | 814 | 438 | 29 | 6.6 | 22 | 42 | ND |
| pheS | 2,533 | 618 | 397 | 46 | 11.6 | 30 | ND | ND |
| pepN | 1,023 | 482 | 411 | 65 | 15.8 | 38 | 37 | 0.0741 |
| bcaT | 1,047 | 493 | 315 | 87 | 27.6 | 39 | 39 | 0.0738 |
| pepX | 2,269 | 602 | 422 | 81 | 19.3 | 26 | 39 | 0.0806 |
| SSU rRNA | 4,050 | 650 | 420 | 14 | 3.3 | 15 | ND | ND |
a
This subset, apart from pheS, does not comprise any ambiguous nucleotides.
b
Pairwise ratios of nonsynonymous to synonymous substitutions (dN/dS) in sequences were calculated by using the method of Nei and Gojobori (25). ND, not determined.