Abstract
Whole-genome sequencing has become a powerful and informative approach for determining the genetic basis of known bacterial properties, predicting new properties, and enabling post-genomic tools. However, genome sequencing and annotation are most useful in the context of comparative genomic and evolutionary analysis, which allows the determination of phylogenetic relationships between extant organisms, provides insights into the evolution of different biological systems, and sheds light on processes accounting for organismal diversity. Genome sequence information is currently available for 20 species of Planctomycetes, Verrucomicrobia, and Lentisphaerae as well as for a number of chlamydial species. In this chapter, we show how this information can be employed to infer molecular mechanisms underlying important ecological, physiological, and evolutionary characteristics of these bacteria and address general questions regarding mechanisms of genome evolution in the PVC superphylum.
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Abbreviations
- PVC:
-
Planctomycetes–Verrucomicrobia–Chlamydiae
- HGT:
-
Horizontal gene transfer
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Acknowledgements
This work was supported by the National Institutes of Health (P20 RR016474 to O.K.K.) and National Science Foundation (NSF) (MCB-0920667 to N.L.W.). N.L.W. and O.K.K. were also partially supported by NSF EPS-0447681. The genomes analyzed in this study are already deposited in GenBank. However, the authors thank several researchers who provided access to unpublished genome data, particularly Jorge Rodrigues, Hauke Smidt, Stephen Giovannoni, and Nikos Kyripides. We also thank the many staff of the various sequencing centers whose work resulted in genome sequence data and analysis. Original and modified gene family alignments are available on request.
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Kamneva, O.K., Haft, D.H., Knight, S.J., Liberles, D.A., Ward, N.L. (2013). Genomics and Bioinformatics of the PVC Superphylum. In: Fuerst, J. (eds) Planctomycetes: Cell Structure, Origins and Biology. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-502-6_7
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