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Speciation in Chlamydia: Genomewide Phylogenetic Analyses Identified a Reliable Set of Acquired Genes

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Abstract

Horizontal gene transfer (HGT), a process through which genomes acquire sequences from distantly related organisms, is believed to be a major source of genetic diversity in bacteria. A central question concerning the impact of HGT on bacterial genome evolution is the proportion of horizontally transferred sequences within genomes. This issue, however, remains unresolved because the various methods developed to detect potential HGT events identify different sets of genes. The present-day consensus is that phylogenetic analysis of individual genes is still the most objective and accurate approach for determining the occurrence and directionality of HGT. Here we present a genome-scale phylogenetic analysis of protein-encoding genes from five closely related Chlamydia, identifying a reliable set of sequences that have arisen via HGT since the divergence of the Chlamydia lineage. According to our knowledge, this is the first systematic phylogenetic inference-based attempt to establish a reliable set of acquired genes in a bacterial genome. Although Chlamydia are obligate intracellular parasites of higher eukaryotes, and thus suspected to be isolated from HGT more than the free-living species, our results show that their diversification has involved the introduction of foreign sequences into their genome. Furthermore, we also identified a complete set of genes that have undergone deletion, duplication, or rearrangement during this evolutionary period leading to the radiation of Chlamydia species. Our analysis may provide a deeper insight into how these medically important pathogens emerged and evolved from a common ancestor.

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Acknowledgements

We are grateful to the NIIF (National Information and Infrastructure Development Institute) Supercomputing Centre, Budapest, Hungary, for the computational support. We thank two anonymous reviewers for their helpful and valuable comments. This work was supported by Grants OTKA F034933 and FKFP 0041/2001 to T. Vellai.

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Authors and Affiliations

  1. Department of Genetics, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, H-1117, Hungary

    Csaba Ortutay, Edit Jáger, Gábor Vida, László Orosz & Tibor Vellai

  2. Department of Organic Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary

    Zoltán Gáspári

  3. Agricultural Biotechnology Center, Szent-Györgyi A. u. 4, Gödöllö, H-2100, Hungary

    Gábor Tóth & László Orosz

  4. Research Group of the Hungarian Academy of Sciences, Department of Genetics, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, H-1117y, Hungary

    Edit Jáger, Gábor Vida & László Orosz

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  1. Csaba Ortutay
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  2. Zoltán Gáspári
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Correspondence to Tibor Vellai.

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Ortutay, C., Gáspári, Z., Tóth, G. et al. Speciation in Chlamydia: Genomewide Phylogenetic Analyses Identified a Reliable Set of Acquired Genes . J Mol Evol 57, 672–680 (2003). https://doi.org/10.1007/s00239-003-2517-3

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  • DOI: https://doi.org/10.1007/s00239-003-2517-3

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