One such area of progress is the use and understanding of chlamydial recombination. There is considerable evidence for in vitro and in vivo recombination by chlamydiae, and the methods for generating chlamydial recombinants are becoming routine [4, 5, 24]. However, there remains a general lack of understanding regarding the cellular and molecular mechanisms associated with the process. The present study was initiated to address these challenges. We hypothesized
that an investigation of both the process of genetic recombination in chlamydiae and the correlation of specific chlamydial genotypes with phenotypes can be addressed using a combination of contemporary genome sequencing technologies with our ability to create genetic recombinants among chlamydiae. This approach has also been used by Nguyen and colleagues
 as part PD-0332991 purchase of a forward genetic strategy in these organisms, and the results of such experiments can be integrated with the recently developed chlamydial transformation system  to develop and validate correlations between gene structure and protein function. Evidence for recombination in chlamydiae was first provided by nucleotide sequencing of genes or genomes taken from a variety ALK inhibitor drugs of chlamydial strains. There are data in the literature suggesting that recombination hotspots might be present within or around ompA[7, 11, 12], and also at other locations in the genome . Our genome sequencing has added some support for this premise, as the D(s)/2923 genome discussed by Jeffrey et al.  has a hybrid D/E OmpA sequence, and apparent recombination sites within this strain are at or very
near sites seen in other, independently isolated, clinical strains [9, 11]. Other investigators have proposed and debated the concept of chlamydial recombination hotspots using analysis of chlamydial genome sequences from laboratory-generated or clinical strains [8, 24, 35]. In the present study, we used two strategies to investigate Amrubicin the possible clustering of recombination events in vitro. First, we analyzed apparent crossover sites by genome sequencing of 12 recombinant genomes, which led to the identification of a total of 190 primary recombination sites. The largest integrated fragment identified in these experiments was over 400,000 base pairs, which constitutes approximately 40% of the chlamydial genome. The long recombined region observed in these progeny strains are consistent with the original observations of Demars and Weinfurter , who discuss very large exchanges in their recombinants. Sequence data from clinical isolates do not provide evidence for such large exchanged fragments, but there is clear evidence of recombined regions of greater than 50,000 base pairs [6, 10, 35].