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In addition, the random insertion of the reporter gene may create position effects that prevent the reporters from serving as a faithful proxy for Pmp22 regulation.
Worse, given that LGT is frequent among cyanobacteria (Raymond et al. 2002; Mulkidjanian et al. 2006; Shi and Falkowski 2008; Dufresne et al. 2008), there is no reason to suspect that any "core" gene phylogeny will be a faithful proxy for the rest of the genome (Doolittle and Bapteste 2007).
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