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Single base change mutational and multi bases change recombinational events could be distinguished, and this showed that there has been extensive recombination, with 8 of the 26 genes having undergone recombination in either 6th or 7th pandemic lineage since divergence.
Our analysis also identified pmpG (NSS, MaxChi) and pmpI (MaxChi) as having undergone recombination.
None of the functional categories showed significantly higher percentages for having undergone recombination than the average of all functional categories (Additional File 2: Figure S3).
Genome regions having undergone recombination in strain NGBS472 included genes encoding major virulence factors, such as the 2-component system csrRS (32 ) and pili (33 ).
However, if we see that a substantial number of genes within a species show a signal of having undergone recombination, we can be more confident that the species in question is not evolving clonally.
The 8 genes identified as having undergone recombination by all 4 methods were three polymorphic outer membrane protein genes (pmpE (CT869), pmpF (CT870) & pmpH (CT872)), two hypothetical protein genes (CT049, CT144), Type III secretion structural protein gene (yscC (CT674), the major outer membrane protein gene (ompA (CT681)) and the gene encoding elongation factor Ts (tsf (CT679)) (Table 2).
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We executed a dose response study to determine the number of neurons that had undergone recombination in response to tamoxifen administered at doses ranging from 50 to 500 mg/kg.
Other groups have undergone recombination, e.g., AMC26, AMC24 and AER39.
The aligned regions were then analyzed to identify regions that had undergone recombination.
A single regulatory CDS (SSUBM407_0840) is found in the loci that appear to have undergone recombination.
For the segments that have undergone recombination, we have no knowledge of the donor strain, so cannot use such information to identify the incoming sequence.
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