Fig 4.

Sequence diversity is generated by intragenic recombination. Evidence of intragenic recombination was apparent in the majority of analyzed alleles from small-, medium, and large-sized erp sequences (A, B, and C, respectively). The locations of recombination events are visualized by the changes in colors along the line representing the erp sequence; the identity of the donor erp allele is denoted above the colored line. For example, erp sequences 118a_AB39, 72a_N39, N40_erp26, and DN127_R39 (C, top) all contain a segment homologous to the erp sequence 94a_M41 near the 3′ end of the protein. Despite the diversity generated by recombination, identical alleles are present in multiple strains in all three size classes of erp sequences. All described recombination events were supported by at least three independent algorithms (see Table S1 in the supplemental material). Recombination events between alleles of different size classes could not be detected by the methods used here. The sequences of erp alleles carried by strains BL206 and Sh-2-82 are identical to sequences maintained by strains B31 and 297, respectively, and were omitted from these analyses since they did not provide unique information on genetic diversity (this work and reference 46). Asterisks at tree branches indicate bootstrap support values from 1,000 trials (***, >950; **, >850; *, >750; unmarked, ≤750).