UBC Theses and Dissertations
Diversity and evolution of single-stranded DNA viruses in marine environments Labonté, Jessica
Viruses are the most abundant and genetically diverse life forms in the biosphere. By infecting specific subsets of microbial communities, they influence community composition, thereby affecting nutrient and energy cycling. Single-stranded (ss) DNA viruses are major pathogens of plants and animals that have been well studied for years due to their economic and human-health effects. Recent advances in metagenomics show that marine ssDNA viruses are widespread in marine and freshwater environments, but their diversity and evolutionary relationships remain relatively unexplored. This dissertation focuses on characterizing the diversity and evolutionary relationships among marine ssDNA viruses. First, metagenomic data were gathered and analyzed to assess the genetic diversity of ssDNA viruses, leading to the identification 129 genetically distinct groups of ssDNA viruses that had no recognizable similarity to each other or to other sequenced viruses. Each group was represented by at least one complete genome, with most falling into 11 well-defined groups. Comparison and phylogenetic analysis of sequences from marine and terrestrial viruses indicate that ssDNA viruses share a common origin and that terrestrial viruses likely co-evolved with their hosts when they transitioned from the ocean to the land. The second part focused on one particular subfamily of viruses, the Gokushovirinae (family Microviridae) to understand their relationship with the environment. Five complete genomes were assembled and primers were designed to amplify a fragment of the major capsid protein to look at the distribution of gokushoviruses in various marine environments. Phylogenetic analysis revealed that most sequences were distantly related to those from cultured representatives, falling into many new distinct evolutionary groups. Finally, a protocol for fluorescence in situ hybridization was developed to observe cells infected by gokushoviruses. The results presented in this dissertation greatly expand the known sequence space for ssDNA, nearly doubling the number of complete available genomes, and revealing much greater genetic richness than previously though. The vast diversity of ssDNA viruses in the sea and their similarity with viruses infecting eukaryotes is consistent with their role as significant pathogens of marine phytoplankton and microzooplankton.
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