Browsing by Author "Monjane, A L"

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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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    Panicum streak virus diversity is similar to that observed for maize streak virus
    (Springer Verlag, 2008) Varsani, A; Oluwafemi, S; Windram, P; Shepherd, D N; Monjane, A L; Owor, B E; Rybicki, E P; Lefeuvre, P; Martin, D P
    Panicum streak virus (PanSV; genus Mastrevirus, family Geminiviridae) is, together with maize streak virus (MSV), sugarcane streak virus (SSV), sugarcane streak Reunion virus (SSRV) and sugarcane streak Egypt virus (SSEV), one of the currently described “African streak virus” (AfSV) species [6]. As with all the other AfSV species other than MSV, very little is known about PanSV genomic sequence diversity across Africa. Only two PanSV full genome sequences have ever been reported: one from Kenya [2], and the other from South Africa [17]. Both these genomes were isolated from Panicum maximum plants, but share only approximately 90% sequence identity. The reason this is noteworthy is that throughout mainland Africa all MSV genomes ever sampled from maize have been found to share >97% sequence identity. Although other MSV strains sharing between 78 and 90% identity with the maize-adapted strain (MSV-A) have been described, these have all been isolated from different host species, indicating that host adaptation is probably the main force driving MSV diversification. MSV and PanSV share common vector species (leafhoppers in the genus Cicadulina) and probably also share some host species. Although the host range of PanSV is currently unknown, the MSV host range is extensive and includes P. maximum [3]. One might therefore expect that similar evolutionary forces acting on both species might result in their sharing similar patterns of both geographical and host-associated diversity. Here we describe the full genome sequences of five new PanSV isolates (including two new strains) sampled from southern and western Africa, and report that PanSV and MSV do indeed have similar patterns of diversity. We find, however, that unlike with MSV, geographical separation rather than host adaptation is possibly the dominant force driving PanSV diversification.