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This article is part of the Research Topic Microbial genomics challenge Darwin

Review ARTICLE

Front. Cell. Infect. Microbiol., 04 May 2012 | http://dx.doi.org/10.3389/fcimb.2012.00060

How microbiology helps define the rhizome of life

  • Faculté de Médecine La Timone, Unité de Recherche en Maladies Infectieuses Tropical Emergentes (URMITE), CNRS-IRD UMR 6236-198, Université de la Méditerranée, Marseille, France

In contrast to the tree of life (TOF) theory, species are mosaics of gene sequences with different origins. Observations of the extensive lateral sequence transfers in all organisms have demonstrated that the genomes of all life forms are collections of genes with different evolutionary histories that cannot be represented by a single TOF. Moreover, genes themselves commonly have several origins due to recombination. The human genome is not free from recombination events, so it is a mosaic like other organisms' genomes. Recent studies have demonstrated evidence for the integration of parasitic DNA into the human genome. Lateral transfer events have been accepted as major contributors of genome evolution in free-living bacteria. Furthermore, the accumulation of genomic sequence data provides evidence for extended genetic exchanges in intracellular bacteria and suggests that such events constitute an agent that promotes and maintains all bacterial species. Archaea and viruses also form chimeras containing primarily bacterial but also eukaryotic sequences. In addition to lateral transfers, orphan genes are indicative of the fact that gene creation is a permanent and unsettled phenomenon. Currently, a rhizome may more adequately represent the multiplicity and de novo creation of a genome. We wanted to confirm that the term “rhizome” in evolutionary biology applies to the entire cellular life history. This view of evolution should resemble a clump of roots representing the multiple origins of the repertoires of the genes of each species.

Keywords: rhizome, genealogic tree, horizontal sequence transfer, recombination, orphan genes

Citation: Georgiades K and Raoult D (2012) How microbiology helps define the rhizome of life. Front. Cell. Inf. Microbio. 2:60. doi: 10.3389/fcimb.2012.00060

Received: 18 January 2012; Accepted: 16 April 2012;
Published online: 04 May 2012.

Edited by:

Eugene V. Koonin, National Institutes of Health, USA

Reviewed by:

Richard Hayward, University College London (UCL) and Birkbeck, University of London, UK
Eric Bapteste, Centre national de la recherche scientifique, France

Copyright: © 2012 Georgiades and Raoult. This is an open-access article distributed under the terms of the Creative Commons Attribution Non Commercial License, which permits non-commercial use, distribution, and reproduction in other forums, provided the original authors and source are credited.

*Correspondence: Didier Raoult, Faculté de Médecine La Timone, Unité de Recherche en Maladies Infectieuses Tropical Emergentes (URMITE), CNRS-IRD UMR 6236-198, Université de la Méditerranée, 27, Bd Jean Moulin, 13385, Marseille cedex 5, France. e-mail: didier.raoult@gmail.com