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Measuring genome divergence in bacteria: A case study using Chlamydian data
Department of Molecular Evolution, University of Uppsala, Uppsala .
Department of Mathematics, Royal High School of Technology, Stockholm.ORCID iD: 0000-0002-6444-7878
Department of Mathematics and Physics, Mälardalens högskola, Västerås.
Department of Molecular Evolution, University of Uppsala, Uppsala .
2002 (English)In: Journal of Molecular Evolution, ISSN 0022-2844, E-ISSN 1432-1432, Vol. 55, p. 24-36Article in journal (Refereed) Published
Abstract [en]

We have studied the relative contribution of inversions, transpositions, deletions, and nucleotide substitutions to the evolution of Chlamydia trachomatis and Chlamydia pneumoniae. The minimal number of rearrangement events required for converting the gene order structure of one genome into that of the other was estimated to 59 6 events, including 13% inversions, 38% short inversions, and 49% transpositions. In contrast to previous findings, no examples of horizontal gene transfer subsequent to species divergence were identified, nor any evidence for an excessive number of tandem gene duplications. A statistical model was used to compare nucleotide frequencies for a set of genes uniquely present in one species to a set of orthologous genes present in both species. The two data sets were not significantly different, which is indicative of a low frequency of horizontal gene transfer events. This is based on the assumption that a foreign gene of different nucleotide content will not have become completely ameliorated, as verified by simulations of the amelioration rate at twofold and fourfold degenerate codon sites. The frequencies of nucleotide substitutions at twofold and fourfold degenerate sites, deletions, inversions, and translocations were estimated to 1.42, 0.62, 0,18, 0.01, and 0.01 per site, respectively.

Place, publisher, year, edition, pages
New York, USA: Springer-Verlag New York, 2002. Vol. 55, p. 24-36
Keywords [en]
Amelioration, Chlamydia, Deletions, Inversions, Rearrangements, Substitutions, Transpositions
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:oru:diva-41755DOI: 10.1007/s00239-001-0087-9ISI: 000176243200003PubMedID: 12165840Scopus ID: 2-s2.0-0036017379OAI: oai:DiVA.org:oru-41755DiVA, id: diva2:781043
Available from: 2015-01-15 Created: 2015-01-15 Last updated: 2017-12-05Bibliographically approved

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Eriksen, Niklas

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