A Giant Virus in Amoebae

Scola, Bernard La; Audic, Stéphane; Robert, Caroline; Liang, Jungang; Lamballerie, Xavier de; Drancourt, Michel; Birtles, Richard J.; Claverie, Jean‐Michel; Raoult, Didier

doi:10.1126/science.1081867

Cited by 733 publications

(700 citation statements)

References 5 publications

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“…More practically, the small genomes of viruses did not contain enough information to reliably position them on the tree of life [4]. The latter argument was weakened by the discovery of Mimivirus, a nucleocytoplasmic large DNA virus (NCLDV) with a genome of unprecedented size (1.2Mb) and coding capacity ( 1,000 ORFs), exceeding that of many cellular organisms [5], [6]. In an initial phylogenetic analysis, Mimivirus emerged from the branch joining Archaea and Eukaryotes, suggesting that it might represent a distinct fourth domain of life [6].…”

Section: Introductionmentioning

confidence: 99%

Informational Gene Phylogenies Do Not Support a Fourth Domain of Life for Nucleocytoplasmic Large DNA Viruses

2011

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Mimivirus is a nucleocytoplasmic large DNA virus (NCLDV) with a genome size (1.2 Mb) and coding capacity ( 1000 genes) comparable to that of some cellular organisms. Unlike other viruses, Mimivirus and its NCLDV relatives encode homologs of broadly conserved informational genes found in Bacteria, Archaea, and Eukaryotes, raising the possibility that they could be placed on the tree of life. A recent phylogenetic analysis of these genes showed the NCLDVs emerging as a monophyletic group branching between Eukaryotes and Archaea. These trees were interpreted as evidence for an independent “fourth domain” of life that may have contributed DNA processing genes to the ancestral eukaryote. However, the analysis of ancient evolutionary events is challenging, and tree reconstruction is susceptible to bias resulting from non-phylogenetic signals in the data. These include compositional heterogeneity and homoplasy, which can lead to the spurious grouping of compositionally-similar or fast-evolving sequences. Here, we show that these informational gene alignments contain both significant compositional heterogeneity and homoplasy, which were not adequately modelled in the original analysis. When we use more realistic evolutionary models that better fit the data, the resulting trees are unable to reject a simple null hypothesis in which these informational genes, like many other NCLDV genes, were acquired by horizontal transfer from eukaryotic hosts. Our results suggest that a fourth domain is not required to explain the available sequence data.

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Section: Introductionmentioning

confidence: 99%

Informational Gene Phylogenies Do Not Support a Fourth Domain of Life for Nucleocytoplasmic Large DNA Viruses

2011

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“…Three of the proteins were unique to SfAV-1a. Recently, a very large icosahedral dsDNA virus has been reported from amoebae (La Scola et al, 2003), but the limited number of genes cloned and sequenced from this virus did not allow us to include it in our analyses.…”

Section: Identification Of Sfav-1a Homologues In Other Dsdna Virusesmentioning

confidence: 99%

Evidence for the evolution of ascoviruses from iridoviruses

Stasiak

Renault

Demattei

et al. 2003

Journal of General Virology

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Ascoviruses (family Ascoviridae) are large, enveloped, double-stranded (ds)DNA viruses that attack lepidopteran larvae and pupae, and are unusual in that they are transmitted by parasitic wasps during oviposition. Previous comparisons of DNA polymerase sequences from vertebrate and invertebrate viruses suggested that ascoviruses are closely related to iridoviruses. This relationship was unexpected because these viruses differ markedly in virion symmetry, genome configuration and cellular pathology. Here we present evidence based on sequence comparisons and phylogenetic analyses of a greater range of ascovirus proteins and their homologues in other large dsDNA viruses that ascoviruses evolved from iridoviruses. Consensus trees for the major capsid protein, DNA polymerase, thymidine kinase and ATPase III from representative ascoviruses, algal viruses (family Phycodnaviridae), vertebrate and invertebrate iridoviruses (family Iridoviridae) and African swine fever virus (ASFV; family Asfarviridae) showed that ascovirus proteins clustered most closely with those of the lepidopteran iridovirus Chilo iridescent virus (CIV) (Invertebrate iridescent virus 6). Moreover, analysis of the presence or absence of homologues of an additional 50 proteins encoded in the genome of Spodoptera frugiperda ascovirus showed that about 40 % occurred in CIV, with lower percentages encoded by the genomes of, respectively, vertebrate iridoviruses, phycodnaviruses and ASFV. The occurrence of three of these genes in SfAV-1a but not CIV was indicative of the evolutionary differentiation of ascoviruses from invertebrate iridoviruses.

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“…This hypothesis rose with the discovery of a new type of viruses characterized by their large size (comparable to that of small prokaryotic cells) and genomes much bigger than those of the classical viruses previously known. The first to be described was the mimivirus [20], and the analysis of its huge genome (1.2 Mbp, the largest characterized in a virus until then) unveiled an unprecedented number of genes involved in transcription and translation homologous to those of cellular organisms [21]. Even more surprising, the phylogenetic analysis of a concatenation of the sequences of seven of those genes appeared to support that the mimivirus might represent a fourth domain of life, sister to the eukaryotes [21].…”

Section: The Elusive Fourth Domain Of Lifementioning

confidence: 99%

Evolution of viruses and cells: do we need a fourth domain of life to explain the origin of eukaryotes?

Moreira¹,

López‐García²

2015

Phil. Trans. R. Soc. B

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The recent discovery of diverse very large viruses, such as the mimivirus, has fostered a profusion of hypotheses positing that these viruses define a new domain of life together with the three cellular ones (Archaea, Bacteria and Eucarya). It has also been speculated that they have played a key role in the origin of eukaryotes as donors of important genes or even as the structures at the origin of the nucleus. Thanks to the increasing availability of genome sequences for these giant viruses, those hypotheses are amenable to testing via comparative genomic and phylogenetic analyses. This task is made very difficult by the high evolutionary rate of viruses, which induces phylogenetic artefacts, such as long branch attraction, when inadequate methods are applied. It can be demonstrated that phylogenetic trees supporting viruses as a fourth domain of life are artefactual. In most cases, the presence of homologues of cellular genes in viruses is best explained by recurrent horizontal gene transfer from cellular hosts to their infecting viruses and not the opposite. Today, there is no solid evidence for the existence of a viral domain of life or for a significant implication of viruses in the origin of the cellular domains.

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A Giant Virus in Amoebae

Cited by 733 publications

References 5 publications

Informational Gene Phylogenies Do Not Support a Fourth Domain of Life for Nucleocytoplasmic Large DNA Viruses

Informational Gene Phylogenies Do Not Support a Fourth Domain of Life for Nucleocytoplasmic Large DNA Viruses

Evidence for the evolution of ascoviruses from iridoviruses

Evolution of viruses and cells: do we need a fourth domain of life to explain the origin of eukaryotes?

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