Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements

Koonin, Eugene V.; Dolja, Valerian V.

doi:10.1128/mmbr.00049-13

Cited by 215 publications

(221 citation statements)

References 200 publications

(240 reference statements)

Supporting

Mentioning

211

Contrasting

Order By: Relevance

“…The particles also are morphologically similar to the much larger (165 to 190 nm) Chlorella viruses except for the spike structure at the vertex, which is not observed in prasinoviruses (45,48). Globally, they show icosahedral symmetry, like the great majority of the other dsDNA aquatic eukaryote viruses currently described (49), without any tail, in contrast to many archaeal and bacterial bacteriophages (50,51). The size of their genomes (around 200 kb) and the number of potential ORFs also are similar to those of the other sequenced prasinoviruses (17)(18)(19)(20).…”

Section: Discussionmentioning

confidence: 60%

Diversity of Viruses Infecting the Green Microalga Ostreococcus lucimarinus

Derelle

Monier

Cooke

et al. 2015

J Virol

View full text Add to dashboard Cite

The functional diversity of eukaryotic viruses infecting a single host strain from seawater samples originating from distant marine locations is unknown. To estimate this diversity, we used lysis plaque assays to detect viruses that infect the widespread species Ostreococcus lucimarinus, which is found in coastal and mesotrophic systems, and O. tauri, which was isolated from coastal and lagoon sites from the northwest Mediterranean Sea. Detection of viral lytic activities against O. tauri was not observed using seawater from most sites, except those close to the area where the host strain was isolated. In contrast, the more cosmopolitan O. lucimarinus species recovered viruses from locations in the Atlantic and Pacific Oceans and the Mediterranean Sea. Six new O. lucimarinus viruses (OlVs) then were characterized and their genomes sequenced. Two subgroups of OlVs were distinguished based on their genetic distances and on the inversion of a central 32-kb-long DNA fragment, but overall their genomes displayed a high level of synteny. The two groups did not correspond to proximity of isolation sites, and the phylogenetic distance between these subgroups was higher than the distances observed among viruses infecting O. tauri. Our study demonstrates that viruses originating from very distant sites are able to infect the same algal host strain and can be more diverse than those infecting different species of the same genus. Finally, distinctive features and evolutionary distances between these different viral subgroups does not appear to be linked to biogeography of the viral isolates. IMPORTANCEMarine eukaryotic phytoplankton virus diversity has yet to be addressed, and more specifically, it is unclear whether diversity is connected to geographical distance and whether differential infection and lysis patterns exist among such viruses that infect the same host strain. Here, we assessed the genetic distance of geographically segregated viruses that infect the ubiquitous green microalga Ostreococcus. This study provides the first glimpse into the diversity of predicted gene functions in Ostreococcus viruses originating from distant sites and provides new insights into potential host distributions and restrictions in the world oceans.

show abstract

Section: Discussionmentioning

confidence: 60%

Diversity of Viruses Infecting the Green Microalga Ostreococcus lucimarinus

Derelle

Monier

Cooke

et al. 2015

J Virol

View full text Add to dashboard Cite

show abstract

“…Some authors prefer a war-like metaphor to describe the virus-host relationship (Forterre andPrangishvili 2009, Brüssow 2009). Similar reports are arguing for a destructive/constructive dynamic between killer virus and surviving host (Koonin 2011, Koonin andDolja 2014). Thus, this is the accepted neodarwinian perspective of individual fittest type selection as essentially put forward by Dawkins (Dawkins 2006) and his selfish gene narrative.…”

Section: Before Group Selection Might Be Considered Group Identity Mmentioning

confidence: 71%

When Competing Viruses Unify: Evolution, Conservation, and Plasticity of Genetic Identities

Villarreal

Witzany

2015

J Mol Evol

View full text Add to dashboard Cite

In the early 1970s, Manfred Eigen and colleagues developed the quasispecies model (qs) for the population-based origin of RNAs representing the early genetic code. The Eigen idea is basically that a halo of mutants is generated by error-prone replication around the master fittest type which will behave similarly as a biological population. But almost from the start, very interesting and unexpected observations were made regarding competition versus co-operation which suggested more complex interactions. It thus became increasingly clear that although viruses functioned similar to biological species, their behavior was much more complex than the original theory could explain, especially adaptation without changing the consensus involving minority populations. With respect to the origin of natural codes, meaning, and code-use in interactions (communication), it also became clear that individual fittest type-based mechanisms were likewise unable to explain the origin of natural codes such as the genetic code with their context-and consortia-dependence (pragmatic nature). This, instead, required the participation of groups of agents competent in the code and able to edit code because natural codes do not code themselves. Three lines of inquiry, experimental virology, quasispecies theory, and the study of natural codes converged to indicate that consortia of cooperative RNA agents such as viruses must be involved in the fitness of RNA and its involvement in communication, i.e., code-competent interactions. We called this co-operative form quasispecies consortia (qs-c). They are the essential agents that constitute the possibility of evolution of biological group identity. Finally, the basic interactional motifs for the emergence of group identity, communication, and cooperation-together with its opposing functions-are explained by the ''Gangen'' hypothesis.

show abstract

“…Different from their cellular hosts, viruses and related mobile elements lack universal genes (74,75). As a result, it is often challenging to accurately demonstrate evolutionary connections between distantly related groups of viruses.…”

Section: Discussionmentioning

confidence: 99%

Bipartite Network Analysis of the Archaeal Virosphere: Evolutionary Connections between Viruses and Capsidless Mobile Elements

Iranzo

Koonin

Prangishvili

et al. 2016

J Virol

Self Cite

View full text Add to dashboard Cite

Archaea and particularly hyperthermophilic crenarchaea are hosts to many unusual viruses with diverse virion shapes and distinct gene compositions. As is typical of viruses in general, there are no universal genes in the archaeal virosphere. Therefore, to obtain a comprehensive picture of the evolutionary relationships between viruses, network analysis methods are more productive than traditional phylogenetic approaches. Here we present a comprehensive comparative analysis of genomes and proteomes from all currently known taxonomically classified and unclassified, cultivated and uncultivated archaeal viruses. We constructed a bipartite network of archaeal viruses that includes two classes of nodes, the genomes and gene families that connect them. Dissection of this network using formal community detection methods reveals strong modularity, with 10 distinct modules and 3 putative supermodules. However, compared to similar previously analyzed networks of eukaryotic and bacterial viruses, the archaeal virus network is sparsely connected. With the exception of the tailed viruses related to bacteriophages of the order Caudovirales and the families Turriviridae and Sphaerolipoviridae that are linked to a distinct supermodule of eukaryotic and bacterial viruses, there are few connector genes shared by different archaeal virus modules. In contrast, most of these modules include, in addition to viruses, capsidless mobile elements, emphasizing tight evolutionary connections between the two types of entities in archaea. The relative contributions of distinct evolutionary origins, in particular from nonviral elements, and insufficient sampling to the sparsity of the archaeal virus network remain to be determined by further exploration of the archaeal virosphere. V iruses infecting archaea are among the most mysterious denizens of the virosphere. Archaeal viruses display a rich diversity of virion morphotypes and can be broadly divided into two categories: those that are structurally and genetically related to bacterial or eukaryotic viruses and those that are archaeon specific (1-4). The cosmopolitan fraction of archaeal viruses includes (i) head-tailed viruses of the order Caudovirales, with the 3 included families, Siphoviridae, Myoviridae, and Podoviridae; (ii) tailless icosahedral viruses of the families Sphaerolipoviridae and Turriviridae; and (iii) enveloped pleomorphic viruses of the family Pleolipoviridae. All of these viruses, except for those of the family Turriviridae, propagate in members of the archaeal phylum Euryarchaeota, whereas most of the archaeon-specific virus groups infect hyperthermophilic organisms of the phylum Crenarchaeota.The order Caudovirales contains three families, the Siphoviridae, Myoviridae, and Podoviridae, and includes both bacterial and archaeal viruses. Members of the Caudovirales feature icosahedral capsids and helical tails attached to one of the vertices of the capsid. These viruses have been largely isolated from hyperhalophilic archaea (order Halobacteriales), although one...

show abstract

Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements

Cited by 215 publications

References 200 publications

Diversity of Viruses Infecting the Green Microalga Ostreococcus lucimarinus

Diversity of Viruses Infecting the Green Microalga Ostreococcus lucimarinus

When Competing Viruses Unify: Evolution, Conservation, and Plasticity of Genetic Identities

Bipartite Network Analysis of the Archaeal Virosphere: Evolutionary Connections between Viruses and Capsidless Mobile Elements

Contact Info

Product

Resources

About