Network analyses structure genetic diversity in independent genetic worlds - PubMed (original) (raw)

Network analyses structure genetic diversity in independent genetic worlds

Sébastien Halary et al. Proc Natl Acad Sci U S A. 2010.

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.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.

Fig. 1.

Network of shared DNA families among cellular, plasmid, and phage genomes. (A) Global network in which each node represents a genome, either cellular (green for bacterial chromosome, yellow for eukaryotic chromosomes, and cyan for archaeal chromosome), plasmidic (purple), or phage (red). Two nodes are connected by an edge if they share homologous DNA (reciprocal best BLAST hit with a minimum of 1e-20 score, and 20% minimum identity). Edges are weighted by the number of shared DNA families. The layout was produced by Cytoscape, using an edge-weighted spring-embedded model, meaning that genomes sharing more DNA families are closer on the display. There are 3,207 nodes on that network. (B) Global network displaying connections between genomes (same color code) for a minimum of 95% identity. Imposing a minimum identity percentage on the definition of CHDs roughly filters for more recent sharing events. Bacterial clusters are indicated as follows: Burkholderia (1), Xanthomonas (2), Yersinia, (3) Streptococcus (4), Prochlorococcus/Synechocystis (5), Clostridium (6), Legionella (7), Rhodopseudomonas (8), and Helicobacter (9). There are 1,529 nodes on that network.

Fig. 2.

Fig. 2.

Betweenness of nodes as function of their degree for various identity threshold networks. Cellular chromosomes are displayed as green circles, plasmids as purple triangles, and phages as red squares. When the betweenness of a node is significantly higher than expected (P < 0.05), the corresponding symbol is filled, and it is empty otherwise. Although betweenness generally increases with degree, plasmids and cellular clearly show higher betweenness values, suggesting they play a central role in the sharing of DNA. Note that scale differs among plots. There are 171 nodes for a 100% identity threshold, 342 for a 95% identity threshold, 372 for a 90% identity threshold, 509 for a 80% identity threshold, 618 for a 70% identity threshold, and 1,029 for a 40% identity threshold.

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References

    1. Whitman WB. The modern concept of the procaryote. J Bacteriol. 2009;191:2000–2005. - PMC - PubMed
    1. Dagan T, Martin W. Getting a better picture of microbial evolution en route to a network of genomes. Philos Trans R Soc Lond B Biol Sci. 2009;364:2187–2196. - PMC - PubMed
    1. Ragan MA, McInerney JO, Lake JA. The network of life: genome beginnings and evolution. Introduction. Philos Trans R Soc Lond B Biol Sci. 2009;364:2169–2175. - PMC - PubMed
    1. Rohwer F, Thurber RV. Viruses manipulate the marine environment. Nature. 2009;459:207–212. - PubMed
    1. Norman A, Hansen LH, Sørensen SJ. Conjugative plasmids: vessels of the communal gene pool. Philos Trans R Soc Lond B Biol Sci. 2009;364:2275–2289. - PMC - PubMed

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