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Table 3 Sequence analysis for the seven loci of the MLSA scheme

From: Multilocus genetics to reconstruct aeromonad evolution

Locus Genus or Clade No. of alleles (% per clade) No. (%) of polymorphic sites Genetic diversity (h)a No. of non-synonymous codons dN/dS ratio G+C%b
dnaK Genus (n=191) 160 273 (33.5) 0.9970 56 0.27 58.8
  A. caviae (n=34) 26 (76.5) 70 (8.6) 0.9697 3 0.006 60.1
  A. hydrophila (n=35) 29 (82.9) 87 (10.7) 0.9882 0 0 59.5
  A. veronii (n=71) 57 (81.4) 119 (14.6) 0.9901 0 0 57.8
  P value NS 6.10-8 - 0.036 - -
gltA Genus (n=191) 141 160 (30.5) 0.9900 21 0.048 61.5
  A. caviae (n=34) 18 (52.9) 28 (6.1) 0.8324 4 0.089 61.8
  A. hydrophila (n=35) 26 (74.3) 41 (8.9) 0.9714 1 0.006 62.5
  A. veronii (n=71) 50 (75.7) 70 (15.1) 0.9735 1 0.002 60.8
  P value NS 6.10-7 - NS - -
gyrB Genus (n=191) 154 278 (35.1) 0.9966 39 0.035 59.1
  A. caviae (n=34) 26 (76.5) 58 (7.3) 0.9786 2 0.004 60.7
  A. hydrophila (n=35) 28 (80.0) 92 (11.6) 0.9885 3 0.005 59.6
  A. veronii (n=71) 55 (82.9) 137 (17.3) 0.9884 7 0.012 58
  P value NS 10-10 - NS - -
radA Genus (n=191) 148 194 (46.6) 0.9955 30 0.061 62.6
  A. caviae (n=34) 23 (67.6) 28 (6.7) 0.9661 1 0.007 63.4
  A. hydrophila (n=35) 28 (80.0) 61 (14.5) 0.9832 5 0.029 64.6
  A. veronii (n=71) 50 (71.4) 66 (15.7) 0.9801 6 0.009 61.1
  P value NS 10-14 - NS - -
rpoB Genus (n=191) 111 98 (23.0) 0.9846 6 0.004 57
  A. caviae (n=34) 13 (38.2) 18 (4.2) 0.7683 1 0.013 58.7
  A. hydrophila (n=35) 24 (68.6) 24 (5.6) 0.9681 0 0 56.3
  A. veronii (n=71) 31 (44.3) 25 (5.9) 0.9528 0 0 56.4
  P value 0.02 0.31 - NS - -
tsf Genus (n=191) 118 177 (27.1) 0.9844 30 0.068 55.8
  A. caviae (n=34) 16 (47.1) 16 (2.3) 0.9073 1 0.015 56.5
  A. hydrophila (n=35) 21 (60.0) 24 (3.4) 0.9445 1 0.008 55.9
  A. veronii (n=71) 37 (52.9) 79 (11.8) 0.9288 9 0.032 55.3
  P value NS 3.10-5 - 0.004 - -
zipA Genus (n=191) 137 380 (70.8) 0.9929 130 0.333 52.4
  A. caviae (n=34) 20 (58.8) 98 (18.3) 0.9358 31 0.276 52.9
  A. hydrophila (n=35) 25 (71.4) 31 (5.8) 0.9697 6 0.071 53.6
  A. veronii (n=71) 46 (66.2) 50 (9.3) 0.9718 12 0.158 51.3
  P value NS 3.10-5 - 10-5 - -
  1. aMean genetic diversity (H) among strains for the whole genus: 0.9916 ± 0.0020 and for the main 3 A. hydrophila, A. caviae, A. veronii clades: 0.9724 ± 0.0055, 0.9083 ± 0.0301 and 0.9694± 0.0082, respectively.
  2. bMean G+C% values for the 7 loci: 58.15% for the 191 Aeromonas spp. strains of this study, 59.2% for A. caviae clade, 58.9% A. hydrophila clade and 57.2% A. veronii clade.
  3. NS: not significant, dN/dS: rate of non-synonymous versus synonymous substitutions.
  4. -: not determined.
  5. P value indicates result of statistical tests for data comparison between clades.