Análises da rede de diversidade da estrutura genética em mundos genéticos independentes

Network analyses structure genetic diversity in independent genetic worlds

Sébastien Halary1, Jessica W. Leigh1, Bachar Cheaib, Philippe Lopez and Eric Bapteste2

- Author Affiliations

Unité Mixte de Recherche, Centre National de la Recherche Scientifique 7138, Systématique, Adaptation, Evolution, Université Pierre et Marie Curie, 75005 Paris, France

Edited by W. Ford Doolittle, Dalhousie University, Halifax, NS, Canada, and approved November 6, 2009 (received for review August 7, 2009)

↵1 S.H. and J.W.L. contributed equally to this work.

Abstract

DNA flows between chromosomes and mobile elements, following rules that are poorly understood. This limited knowledge is partly explained by the limits of current approaches to study the structure and evolution of genetic diversity. Network analyses of 119,381 homologous DNA families, sampled from 111 cellular genomes and from 165,529 phage, plasmid, and environmental virome sequences, offer challenging insights. Our results support a disconnected yet highly structured network of genetic diversity, revealing the existence of multiple “genetic worlds.” These divides define multiple isolated groups of DNA vehicles drawing on distinct gene pools. Mathematical studies of the centralities of these worlds’ subnetworks demonstrate that plasmids, not viruses, were key vectors of genetic exchange between bacterial chromosomes, both recently and in the past. Furthermore, network methodology introduces new ways of quantifying current sampling of genetic diversity.

evolution lateral gene transfer mobile genetic elements phages plasmids

Footnotes

2To whom correspondence should be addressed. E-mail: eric.bapteste@snv.jussieu.fr

Author contributions: P.L. and E.B. designed research; S.H., J.W.L., B.C., and P.L. performed research; S.H. and J.W.L. contributed new reagents/analytic tools; S.H., J.W.L., P.L., and E.B. analyzed data; and P.L. and E.B. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

This article contains supporting information online at www.pnas.org/cgi/content/full/0908978107/DCSupplemental.

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