The 1.2-Megabase Genome Sequence of Mimivirus

Raoult, Didier; Audic, Stéphane; Robert, Caroline; Abergel, Chantal; Renesto, Patricia; Ogata, Hiroyuki; Scola, Bernard La; Suzan, M; Claverie, Jean‐Michel

doi:10.1126/science.1101485

Cited by 934 publications

(1,137 citation statements)

References 32 publications

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“…Yet, currently available methods have potential limitations. For example, ssDNA and RNA viruses [11,42] and giant viruses [38] are under-counted when estimates are made via epiflourescence microscopy with standard DNA based stains. Likewise, virus-like particles may not always necessarily represent viruses, and total abundance estimates could include contributions from gene-transfer agents .…”

Section: G Outlier Identificationmentioning

confidence: 99%

Re-examination of the relationship between marine virus and microbial cell abundances

et al. 2016

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Marine viruses are critical drivers of ocean biogeochemistry and their abundances vary spatiotemporally in the global oceans, with upper estimates exceeding 10 8 per ml. Over many years, a consensus has emerged that virus abundances are typically 10-fold higher than prokaryote abundances. The use of a fixed-ratio suggests that the relationship between virus and prokaryote abundances is both predictable and linear. However, the true explanatory power of a linear relationship and its robustness across diverse ocean environments is unclear. Here, we compile 5671 prokaryote and virus abundance estimates from 25 distinct marine surveys to characterize the relationship between virus and prokaryote abundances. We find that the median virus-to-prokaryote ratio (VPR) is 10:1 and 16:1 in the near-and sub-surface oceans, respectively. Nonetheless, we observe substantial variation in the VPR and find either no or limited explanatory power using fixed-ratio models. Instead, virus abundances are better described as nonlinear, power-law functions of prokaryote abundances -particularly when considering relationships within distinct marine surveys. Estimated power-laws have scaling exponents that are typically less than 1, signifying that the VPR decreases with prokaryote density, rather than remaining fixed. The emergence of power-law scaling presents a challenge for mechanistic models seeking to understand the ecological causes and consequences of marine virusmicrobe interactions. Such power-law scaling also implies that efforts to average viral effects on microbial mortality and biogeochemical cycles using "representative" abundances or abundanceratios need to be refined if they are to be utilized to make quantitative predictions at regional or global ocean scales.

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Section: G Outlier Identificationmentioning

confidence: 99%

Re-examination of the relationship between marine virus and microbial cell abundances

et al. 2016

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“…Phylogenetic analysis has placed this virus at the end of an independent branch, deeply rooted close to the origin of eukaryotes and most likely representing a distinct domain of life [15]. Our analysis suggested affinity of the mimivirus NATs to those of protists (Figs.…”

Section: Nats In Protists and Associated Large Dna Virusesmentioning

confidence: 65%

Comparative genomic and phylogenetic investigation of the xenobiotic metabolizing arylamine N‐acetyltransferase enzyme family

et al. 2010

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a b s t r a c tArylamine N-acetyltransferases (NATs) are xenobiotic metabolizing enzymes characterized in several bacteria and eukaryotic organisms. We report a comprehensive phylogenetic analysis employing an exhaustive dataset of NAT-homologous sequences recovered through inspection of 2445 genomes. We describe the first NAT homologues in viruses, archaea, protists, many fungi and invertebrates, providing complete annotations in line with the consensus nomenclature. Contrary to the NAT genes of vertebrates, introns are commonly found within the homologous coding regions of lower eukaryotes. The NATs of fungi and higher animals are distinctly monophyletic, but evidence supports a mixed phylogeny of NATs among bacteria, protists and possibly some invertebrates.

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“…In particular, this result motivated the proposal that the lineage formed by Mimivirus and its NCLDV relatives might have contributed DNA processing genes to the ancestral eukaryote [7]. However, a subsequent re-analysis of the dataset used in [6] indicated that the position of Mimivirus was an artifact: the genes that were concatenated to build the phylogeny had been acquired by horizontal transfer (HGT) from different sources, resulting in an inconsistent phylogenetic signal that placed them as the outgroup to Eukaryotes [8]. Further analyses demonstrated that NCLDVs have obtained many genes by horizontal transfer from across the three cellular domains [9], [10].…”

Section: Introductionmentioning

confidence: 88%

“…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%

“…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]. The division of the tree of life into domains is difficult, because the existing classification is based on patterns of similarity in ribosomal RNAs that are not found in viruses [1].…”

Section: Introductionmentioning

confidence: 99%

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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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The 1.2-Megabase Genome Sequence of Mimivirus

Cited by 934 publications

References 32 publications

Re-examination of the relationship between marine virus and microbial cell abundances

Re-examination of the relationship between marine virus and microbial cell abundances

Comparative genomic and phylogenetic investigation of the xenobiotic metabolizing arylamine N‐acetyltransferase enzyme family

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

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