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Abstract

RNA viruses are the largest group of viruses. Among them are some of the most notorious human, animal and plant pathogens. Many insects and nematodes are vectors of plant and animal RNA viruses. The latest studies of RNA viral diversity in invertebrates have demonstrated that the Protostomia lineage represents the center of RNA viral diversity. RNA viruses in numerous invertebrate groups have not yet been thorougly analysed, such as in platyhelminths, hymenopterans, lepidopterans, amphipods, copepods, the oldest hexapod lineages and the oldest animal lieages. The aim of my thesis was to analyse the RNA viromes of the above-mentioned invertebrate lineages; to demonstrate that the »explosion« of the RNA viral diversity was present in the oldest metazoan lineages; to demonstrate that the diversity of the RNA viromes is conserved in all invertebrate lineages; and to infer the genome and evolutionary dynamics of RNA viral clades. An extensive phylogenomic analysis of RNA viruses in numerous transcriptomic and genomic libraries of the above-mentioned invertebrate groups has been used to explore the distribution, evolution, genomic organization and endogenization of RNA viruses. The complete genomes of diverse representatives of the ssRNA (-), ssRNA (+), and dsRNA viruses have been found in rich transcriptome databases. The analysis of endogenized RNA viruses in the genomes of the above-mentioned invertebrate groups has shown the past infections of these organisms with various RNA viruses. By extensive phylogenetic analysis, I classified new RNA viruses and analyzed the evolution of RNA viruses in the above-mentioned invertebrate groups.
815 novel RNA viruses have been found and belong to the 22 out of 25 RNA viral clades. The following RNA viral clades were found in all analysed invertebrate groups: Hepe-Virga, Narna-Levi, Mono-Chu, Orthomyxo, Partiti-Picobirna, Picorna-Calici, Tombus-Noda and Toti-Chryso. The most abundant groups among ss(-)RNA, dsRNA, and ss(+)RNA viruses are: Mono-Chu, Partiti-Picobirna and Picorna-Calici. In the Picorna-Calici clade dicistroviruses, iflaviruses and aquatic picornaviruses are the most abundant. Dicistroviruses and iflaviruses were found in terrestrial and aquatic invertebrates, while aquatic picornaviruses are restricted to aquatic invertebrates. Phylogenetic analysis has shown that a number of novel RNA viruses formed new groups inside the defined viral clades. A rich repertoire of diverse RNA viral genomes has been found, many of them originated in the oldest metazoan lineages and remained conserved in all invertebrate groups. This can be most clearly seen in picornaviruses. The majority of the viral genome structures are similar to the known viruses of the same group. Complete genomes of the numerous oldest representatives of diverse RNA viral clades have been found in basal metazoans, they show also diverse characteristics of their genome structure. Representatives of the 12 RNA viral clades have been found endogenized in invertebrate genomes. Mono-Chu is the only clade that is endogenized in all analysed invertebrate phyla. In my thesis, I demonstrated that the first representatives of RNA viral clades originated in metazoan ancestors; the explosion of diverse RNA viral genomes occurred in the metazoan ancestor; the center of RNA viral diversity has been shifted from Protostomia to the oldest metazoan lineages; and RNA viral diversity is conserved in all invertebrate lineages.