Comparative analysis of Panicum streak virus and Maize streak virus diversity, recombination patterns and phylogeography

Abstract

Background: Panicum streak virus (PanSV; Family Geminiviridae; Genus Mastrevirus) is a close relative of Maize streak virus (MSV), the most serious viral threat to maize production in Africa. PanSV and MSV have the same leafhopper vector species, largely overlapping natural host ranges and similar geographical distributions across Africa and its associated Indian Ocean Islands. Unlike MSV, however, PanSV has no known economic relevance.

Results: Here we report on 16 new PanSV full genome sequences sampled throughout Africa and use these together with others in public databases to reveal that PanSV and MSV populations in general share very similar patterns of genetic exchange and geographically structured diversity. A potentially important difference between the species, however, is that the movement of MSV strains throughout Africa is apparently less constrained than that of PanSV strains. Interestingly the MSV-A strain which causes maize streak disease is apparently the most mobile of all the PanSV and MSV strains investigated.

Conclusion: We therefore hypothesize that the generally increased mobility of MSV relative to other closely related species such as PanSV, may have been an important evolutionary step in the eventual emergence of MSV-A as a serious agricultural pathogen.The GenBank accession numbers for the sequences reported in this paper are GQ415386-GQ415401.

Figure 1

Maximum likelihood phylogenetic trees (both constructed with the GTR+G₄ nucleotide substitution model) indicating possible evolutionary relationships between 23 PanSV isolates. (a) Tree constructed using complete genome sequences. Virus names take the form "Strain [country-region-year of isolation]" (b) A tree constructed using recombination-free portions of the genome indicated beneath the genome map and recombination mosaic cartoons in c. (c) Linearised genome cartoons depicting unique recombinant mosaics detected amongst the PanSV sequences. Colours represent as best as possible the origins of different genome regions. Letters below the depicted recombination events correspond to detailed descriptions of each of the events given in Additional file 7. For labels on the genome map: mp = movement protein gene, cp = coat protein gene, rep = replication associated protein gene, repA = RepA gene. Whereas branches marked with filled and open circles were supported in >90% and 70-89% of bootstrap replicates, respectively, branches with <50% bootstrap support have been collapsed. The tree was rooted on the Sugarcane streak Reunion virus isolate SSRV-Bas (not shown).

Figure 2

Maximum likelihood phylogenetic trees (best fit nucleotide substitution models = GTR+G₄ for PanSV tree and GTR+I+G₄ for the MSV tree) depicting the sampling locations of 23 PanSV (tree a) and 181 MSV isolates (trees b and c). Branches are colored according to sampling locations (blue = southern African lineages, orange = East African lineages, green = West African lineages, purple = Indian Ocean island lineages). Wherever under a maximum parsimony criterion, it is <60% certain that ancestral sequences represented by tree nodes are from one of the four regions, the branches basal to that node have been left uncoloured. Whereas branches marked with filled and open circles were supported in >90% and 70-89% of bootstrap replicates, respectively, branches with <50% bootstrap support have been collapsed. The arrow on tree c indicates a clade of MSV-A sequences from West Africa nested within a clade of MSV-A sequences from East Africa indicating an instance of recent east to west movement of MSV-A isolates. All the trees were rooted on the Sugarcane streak Reunion virus isolate SSRV-Bas (not shown).