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Molecular evolution and phylogenetics of circular single-stranded DNA viruses
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Seah, Yee Mey. Molecular evolution and phylogenetics of circular single-stranded DNA viruses. Retrieved from https://doi.org/doi:10.7282/T31C1ZVC

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TitleMolecular evolution and phylogenetics of circular single-stranded DNA viruses
NameSeah, Yee Mey (author); Duffy, Siobain (chair); Rutgers University; Graduate School - New Brunswick
Date Created2015
Other Date2015-10 (degree)
SubjectMicrobiology and Molecular Genetics, Molecular evolution, DNA
Extent1 online resource (ix, 130 p. : ill.)
DescriptionViruses infect a wide variety of hosts across all domains of life. Despite their ubiquity, and a long history of virus research, fundamental questions such as what constitutes a virus species, and how viruses evolve and are modeled, have yet to be adequately answered. We compared viral sequences across five genomic architectures (single- and double-stranded DNA and RNA) and demonstrate the presence of substitution bias, especially in single-stranded viruses. Most striking is a consistent pattern of over-represented cytosine-to- thymine substitutions in single-stranded DNA (ssDNA) viruses. This led us to question the validity of using time-reversible nucleotide substitution models in viral phylogenetic inference, as these models assume equal rates of forward and reverse substitutions. We found that an unrestricted substitution model fit the data better for most single- and double-stranded viral datasets, as measured by corrected Akaike Information Criterion, and hierarchical likelihood ratio test scores. We also approached the question of virus species identification by examining members of the most species-rich viral genus Begomovirus (Family Geminiviridae), which are circular single-stranded DNA (ssDNA) viral crop pathogens transmitted by whitefly vectors. We used novel sweet potato-infecting begomoviruses (sweepoviruses) collected during a recent vector-enabled metagenomic survey to evaluate the concept of pairwise percent nucleotide identity threshold as a criterion for species demarcation. We demonstrate that species demarcation based on pairwise percent nucleotide identities group divergent sweepovirus clusters together, and is highly influenced by when, and how much sampling occurs.
NotePh.D.
NoteIncludes bibliographical references
Noteby Yee Mey Seah
Genretheses, ETD doctoral
Persistent URLhttps://doi.org/doi:10.7282/T31C1ZVC
Languageeng
CollectionGraduate School - New Brunswick Electronic Theses and Dissertations
Organization NameRutgers, The State University of New Jersey
RightsThe author owns the copyright to this work.
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