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Génomique des virus géants, des virophages, et échanges génétiques avec leurs hôtes eucaryotes

Abstract : Nucleo Cytoplasmic Large DNA Viruses (NCLDV) form a very diverse group of double-stranded DNA viruses exclusively infecting eukaryotes. The NCLDVs contain the so-called "giant" viruses visible under light microscope, the first specimen of which, discovered in 2003, opened an unexplored field of viral biodiversity. Some families of NCLDVs could be as old as the emergence of contemporary cellular domains. These viruses inhabit a wide variety of environments (soils, oceans, etc.) where they contribute to the control of eukaryotic microbial populations (e.g., protists, phytoplankton). Moreover, some of these viruses are parasitized by smaller viruses, the virophages, that use the giant virus machinery for their own replication in a common cellular host. Understanding NCLDVs’ evolution, biodiversity and host / virus/virophage interactions is now one of the major areas of virology. Using genomics and bioinformatics approaches, I pursued two objectives in this thesis: (1) Characterize the biodiversity and evolution within the taxonomic family of Mimiviridae (NCLDV) through the description and comparative analysis of the genome of the virus "CeV" which infects the unicellular alga haptophyte Haptolina (ex Chrysochromulina) ericina; (2) Characterize the co-evolution of NCLDVs and virophages with their eukaryotic hosts. This second part was addressed by studying horizontal transfers of viral DNA in the available sequences of eukaryotic genomes. The icosahedral particle of the CeV virus has a diameter of 160 nm and contains a 474-kb genome. The analysis of the latter confirmed that CeV is related to the viruses of the Mimiviridae family, originally defined around the giant viruses prototypes Mimivirus and Megavirus which infect the amoebae. Other members of the Mimiviridae, closer to CeV, also infect unicellular algae. Together with CeV, the latter form a subgroup that we proposed to cluster into the subfamily Mesomimivirinae. Mesomimivirinae possess exclusive genomic characters: a second copy of the RNA polymerase gene, the presence of a gene coding for a second capsid protein, and 7 other groups of orthologous genes absent in other Mimiviridae. Despite their relatedness, each of these viruses possesses a majority of unique genes, the origin of which is unknown. On the other hand, several cases of parallel acquisitions by horizontal transfer of the same gene by CeV and other unrelated viruses were analyzed. This manuscript also documents genetic events that have occurred only in CeV, such as unique gene fusions. Bioinformatic screening of the sequence databases revealed DNA fragments of varying sizes (up to ~ 500Kb) integrated into the genomes of many eukaryotes, originally belonging to NCLDVs or virophages. Their analysis allowed to widen the spectrum of known NCLDVs’ hosts and suggest the existence of new viral families that remain to be discovered. Also, these inserts contain genes that are not found in the sequenced NCLDVs genomes, and could encode novel functionalities of the donor virus. Copies of virophage genomes integrated into the Bigelowiella natans algae genome suggest a new strategy for co-infection and dissemination of virophage, which may also constitute a defense mechanism against NCLDVs for the eukaryotic host.
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https://tel.archives-ouvertes.fr/tel-01668916
Contributor : Lucie Gallot-Lavallée <>
Submitted on : Wednesday, December 20, 2017 - 1:30:44 PM
Last modification on : Tuesday, January 14, 2020 - 1:48:28 PM

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Lucie Gallot-Lavallée. Génomique des virus géants, des virophages, et échanges génétiques avec leurs hôtes eucaryotes. Sciences du Vivant [q-bio]. Aix-Marseille Université (AMU), 2017. Français. ⟨NNT : 2017AIXM0458⟩. ⟨tel-01668916⟩

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