Distribution of variable genes with nonsynonymous allelic variation by functiona

  • a A list of variable genes with nonsynonymous changes (i.e., with an altered amino acid sequence) was derived by analysis of alignments of derived amino acid sequence for each variable gene detected in the 25 pairs of persistent meningococcal isolates (Table 1). These genes were classified into one of five functional groups based on known functions or a homology-based analysis. Variable genes were also separated by occurrence in a carrier with or without high levels of HGT, with these classifications predicted to separate genes whose variation occurred by recombination from mutation.

  • b The denominator for calculating the percentage of variable genes was determined by multiplying the total number of genes in the class by the number of carriers.

  • c Numbers of carriers in each group: all carriers, n = 25; without HGT, n = 21; HGT only, n = 4 (V54, V82, V128, and V222).

  • d Nucleotide diversity was calculated by using the average diversity for all genes to estimate the number of variants in a gene of 1,000 bp and then dividing this number by the total length of genes in a class (calculated by multiplying the number of genes by 1,000).

  • e P, <0.001; chi-square test of observed versus expected.

  • f Not significant by a chi-square test of observed versus expected for the number of variable genes or in one-way analysis of variance (ANOVA) for nucleotide diversity.

  • g P, <0.01, chi-square test of observed versus expected.