Approaches to detect and classify Megavirales

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Date(s) - 23/10/2015
14 h 00 min - 16 h 00 min


Soutenance de thèse

Nucleocytoplasmic large DNA viruses (NCLDVs), or representatives from the proposed order Megavirales, belong to families of giant viruses that infect a large number of eukaryotic hosts. This order includes families Mimiviridae, Marseilleviridae, Ascoviridae, Iridoviridae, Phycodnaviridae, Poxviridae, Asfarviridae, and pandoraviruses, Pithovirus sibericum, faustoviruses and Mollivirus sibericum that likely represents new viral families. These viruses have genomes whose size ranges from 100 kilobase to 2.5 megabase pairs and which have surprising gene contents and features, which raised various questions about their origin and evolution. Environmental metagenomic studies showed that there is a “dark matter”, composed of sequences not linked to any known organism. However, sequence identification was mainly determined using ribosomal DNA (rDNA) sequences, which led therefore to ignore viruses, including megaviruses, because they are devoid of such genes. Core informational genes, including DNA-dependant RNA polymerase (RNAP), are other markers that appear as more appropriate for a comprehensive classification as they are conserved in cellular organisms (Bacteria, Archaea and Eukarya) and in Megavirales. For our phylogenetic analyses, we have selected a representative set of cellular organisms using TimeTree. We used a small set of universally conserved genes that included RNAP and reconstructed ancestral sequences to search for megavirus relatives in sequence databases and to perform phylogeny reconstructions. This allowed identified three megaviral sequences that were misannotated as Hydra magnipapillata, Marine group II Euryarcheota and Phytophthora parasitica, and new viral clades in environmental databases. In addition, we delineated Megavirales as a fourth monophylogenetic branch aside Bacteria, Archaea and Eukarya, which was named TRUC (for Things Resisting Uncompleted Classification). Moreover, we classified by phylogenetic and phyletic analyses based on informational genes new giant viruses including pandoraviruses and Pithovirus sibericum as new bona fide members of the fourth TRUC. Our analyses shows that RNAP as well as a few other genes used in our studies allow a more comprehensive overview and classification of the biological diversity than rDNA, that RNAP can be an universal probe to uncover new viral sequences, and that using putative ancestral sequences recreated for conserved genes can identify distant, undescribed viral clades. Thus, we detected hidden microbes and classified new Megavirales representatives.

{{Keywords :}} Giant virus; Megavirales; NCLDV; Informational genes; TRUC; Domains of life; Phylogeny; Hierarchical clustering.

*Directeurs de thèse :

Didier RAOULT, URMITE, UMR7278, Marseille
Pierre PONTAROTTI, I2M, Marseille

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