Browsing by Author "Muhire, B M"

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    Evidence of pervasive biologically functional secondary-structures within the genomes of eukaryotic single-stranded DNA viruses
    (American Society for Microbiology, 2013) Muhire, B M; Golden, M; Murrell, B; Lefeuvre, P; Lett, J-M; Gray, A; Poon, Art Y F; Ngandu, N K; Semegni, Y; Tanov, E P; Monjane, A L; Harkins, G W; Varsani, A; Shepherd, D N; Martin, D P
    Single-stranded DNA (ssDNA) viruses have genomes that are potentially capable of forming complex secondary-structures through Watson-Crick base-pairing between their constituent nucleotides. A few of the structural elements formed by such base-pairings are, in fact, known to have important functions during the replication of many ssDNA viruses. What is unknown, however, is (i) whether numerous additional ssDNA virus genomic structural elements predicted to exist by computational DNA folding methods actually exist, and (ii) whether those structures that do exist have any biological relevance. We therefore computationally inferred lists of the most evolutionarily conserved structures within a diverse selection of animal- and plant-infecting ssDNA viruses drawn from the families Circoviridae, Anelloviridae, Parvoviridae, Nanoviridae andGeminiviridae, and analysed these for evidence of natural selection favouring the maintenance of these structures. While we find evidence that is consistent with purifying selection being stronger at nucleotide sites that are predicted to be base-paired than it is at sites predicted to be unpaired, we also find strong associations between sites that are predicted to pair with one another and site pairs that are apparently coevolving in a complementary fashion. Collectively, these results indicate that natural selection actively preserves much of the pervasive secondary-structure that is evident within eukaryote-infecting ssDNA virus genomes and, therefore, that much of this structure is biologically functional. Lastly, we provide examples of various highly conserved but completely uncharacterised structural elements that likely have important functions within some of the ssDNA virus genomes analysed here.
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    Molecular diversity of Chickpea chlorotic dwarf virus in Sudan: High rates of intra-species recombination – a driving force in the emergence of new strains
    (Elsevier, 2015) Kraberger, S; Kumari, S G; Hamed, A A; Gronenborn, B; Thomas, J E; Sharman, M; Harkins, G W; Muhire, B M; Martin, D P; Varsan, A
    Sudan Chickpea chlorotic dwarf virus (CpCDV, genus Mastrevirus, family Geminiviridae) is an important pathogen of pulses that are grown both for local consumption, and for export. Although a few studies have characterised CpCDV genomes from countries in the Middle East, Africa and the Indian subcontinent, little is known about CpCDV diversity in any of the major chickpea production areas in these regions. Here we analyse the diversity of 146 CpCDV isolates characterised from pulses collected across the chickpea growing regions of Sudan. Although we find that seven of the twelve known CpCDV strains are present within the country, strain CpCDV-H alone accounted for 73% of the infections analysed. Additionally we identified four new strains (CpCDV-M, -N, -O and -P) and show that recombination has played a significant role in the diversification of CpCDV, at least in this region. Accounting for observed recombination events, we use the large amounts of data generated here to compare patterns of natural selection within protein coding regions of CpCDV and other dicot-infecting mastrevirus species.