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Referee Comments: Referee 2 (Ulrike G. Munderloh)

Posted by PLOS_ONE_Group on 17 Apr 2008 at 18:25 GMT

Referee 2's Review (Ulrike G. Munderloh):

N.B. These are the comments made by the referee when reviewing an earlier version of this paper. Prior to publication the manuscript has been revised in light of these comments and to address other editorial requirements.

Gillespie and colleagues present an extraordinarily interesting analysis of rickettsial phylogenomics based on complete rickettsial genome sequences available at the time of study. Maybe not unexpected, but nevertheless surprising, is the conclusion that what essentially characterizes rickettsial species and their assignment to the groups previously proposed by Gillespie et al., is the loss of genes and gene function. This comprehensive scrutiny is lucidly explained and clearly presented, using novel tools for identification of shared and unique cogs. I am impressed with the elegant way in which a vast amount of sequence data analysis is logically derived, without any bias induced by previously held assumptions, yet taking into account, and carefully re-evaluating the existing body of knowledge of the subject. This exemplary study goes well beyond the more commonly published hunter-gatherer style sequence collection and analysis, to suggest interesting evolutionary and biological phenomena without ever appearing artificial or contrived. Although, or perhaps because, the authors make it clear that much remains to be done, especially with respect to laboratory-based research, this analysis has the potential to revolutionize how genomics are sourced, presented, and made useful. It will have significant impact on rickettsial phylogenomics and provide logical starting points for research on biology and pathogenesis of rickettsiae.