Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Comment
. 2017 Feb 23;10(2):e1296614.
doi: 10.1080/19420889.2017.1296614. eCollection 2017.

A network perspective on the virus world

Affiliations
Comment

A network perspective on the virus world

Jaime Iranzo et al. Commun Integr Biol. .

Abstract

Viral evolution is characterized by high rates of horizontal gene transfer and fast sequence divergence. Furthermore, there are no universal genes shared by all viruses. As a result, distant relationships among viruses are better represented by a network than by a tree. Here we discuss 3 network representations of the virus world with decreasing levels of complexity, from a multilayer network that integrates sequence conservation and patterns of gene sharing to a classic genome similarity network. As new tools for network analysis are developed, we expect that novel insights into virus evolution will result from the study of more complex representations of the virus world.

Keywords: bipartite network; gene sharing network; multilayer network; phylogenomics; viral evolution; viral taxonomy.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Three network representations of a toy virus world composed of 4 viral genomes (squares) and 12 genes (black circles) that belong to 5 gene families (white circles). (A) Two-layer network, with the gene layer on top and the genome layer at the bottom. Black edges of different thickness indicate the similarity between sequences in the gene layer. (B) Bipartite network, which results from clustering groups of homologous genes in the gene layer into gene family nodes. (C) Genome similarity network; the thickness of the links is proportional to the number of shared gene families.
Figure 2.
Figure 2.
Hierarchical structure of a portion of the bipartite network for tailed bacteriophages (order Caudovirales). On the small scale, sets of related viruses and their associated gene families form densely connected modules. Within a module, genome nodes are represented as colored circles, whereas gene family nodes are denoted by the points where the edges (gray and colored lines) join. Colored edges connect the genomes of a module with the module's signature genes. On the large scale, modules connect with each other through shared connector genes, represented here as small gray circles. The 4 hallmark genes that are shared by most members of the order Caudovirales occupy a central position in the network (small black circles). This portion of the network corresponds to modules 9a, 9d, 12, 13, and 18 from ref.  MCP, major capsid protein.

Comment on

References

    1. Puigbò P, Wolf YI, Koonin EV. Search for a ‘Tree of Life’ in the thicket of the phylogenetic forest. J Biol 2009; 8(6):59; PMID:19594957; http://dx.doi.org/10.1186/jbiol159 - DOI - PMC - PubMed
    1. Koonin EV, Dolja VV. Virus world as an evolutionary network of viruses and capsidless selfish elements. Microbiol Mol Biol Rev 2014; 78(2):278-303; PMID:24847023; http://dx.doi.org/10.1128/MMBR.00049-13 - DOI - PMC - PubMed
    1. Corel E, Lopez P, Méheust R, Bapteste E. Network-thinking: Graphs to analyze microbial complexity and evolution. Trends Microbiol 2016; 24(3):224-37; PMID:26774999; http://dx.doi.org/10.1016/j.tim.2015.12.003 - DOI - PMC - PubMed
    1. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000; 28(1):33-6; PMID:10592175; http://dx.doi.org/10.1093/nar/28.1.33 - DOI - PMC - PubMed
    1. Li L, Stoeckert CJ Jr., Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003; 13(9):2178-89; PMID:12952885; http://dx.doi.org/10.1101/gr.1224503 - DOI - PMC - PubMed

LinkOut - more resources