Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands

Jon Bohlin, Mark W. J. van Passel, Lars Snipen, Anja B. Kristoffersen, David Ussery, Simon P. Hardy

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    Abstract

    Background: We sought to assess whether the concept of relative entropy (information capacity), could aid our understanding of the process of horizontal gene transfer in microbes. We analyzed the differences in information capacity between prokaryotic chromosomes, genomic islands (GI), phages, and plasmids. Relative entropy was estimated using the Kullback-Leibler measure.
    Results: Relative entropy was highest in bacterial chromosomes and had the sequence chromosomes > GI > phage > plasmid. There was an association between relative entropy and AT content in chromosomes, phages, plasmids and GIs with the strongest association being in phages. Relative entropy was also found to be lower in the obligate intracellular Mycobacterium leprae than in the related M. tuberculosis when measured on a shared set of highly conserved genes.
    Conclusions: We argue that relative entropy differences reflect how plasmids, phages and GIs interact with microbial host chromosomes and that all these biological entities are, or have been, subjected to different selective pressures. The rate at which amelioration of horizontally acquired DNA occurs within the chromosome is likely to account for the small differences between chromosomes and stably incorporated GIs compared to the transient or independent replicons such as phages and plasmids.

    Original languageEnglish
    JournalB M C Genomics
    Volume13
    Issue number66
    Number of pages12
    ISSN1471-2164
    DOIs
    Publication statusPublished - 2012

    Bibliographical note

    © 2012 Bohlin et al; licensee BioMed Central Ltd.
    This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

    Keywords

    • BIOTECHNOLOGY
    • GENETICS
    • USAGE PATTERNS
    • SEQUENCES
    • PROKARYOTES
    • COMMUNICATION
    • REDUCTION
    • DIVERSITY
    • ANCESTOR

    Cite this

    Bohlin, J., van Passel, M. W. J., Snipen, L., Kristoffersen, A. B., Ussery, D., & Hardy, S. P. (2012). Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands. B M C Genomics, 13(66). https://doi.org/10.1186/1471-2164-13-66