Molecular genetic analysis of virus isolates from wild and cultivated plants demonstrates that East Africa is a hotspot for the evolution and diversification of Sweet potato feathery mottle virus

Abstract

Sweet potato feathery mottle virus (SPFMV, genus Potyvirus) is globally the most common pathogen of cultivated sweet potatoes (Ipomoea batatas; Convolvulaceae). Although more than 150 SPFMV isolates have been sequence-characterized from cultivated sweet potatos across the world, little is known about SPFMV isolates from wild hosts and the evolutionary forces shaping SPFMV population structures. In this study, 46 SPFMV isolates from 14 wild species of genera Ipomoea, Hewittia and Lepistemon (barcoded for the matK gene in this study) and 13 isolates from cultivated sweet potatoes were partially sequenced. Wild plants were infected with the EA, C or O strain, or co-infected with the EA and C strains of SPFMV. In East Africa, SPFMV populations in wild species and sweet potato were genetically undifferentiated, suggesting inter-host transmission of SPFMV. Globally, spatial diversification of the 178 isolates analysed was observed, strain EA being largely geographically restricted to East Africa. Recombination was frequently detected in the 6K2-VPg-NIaPro region of the EA strain, demonstrating a recombination 'hotspot'. Recombination between strains EA and C was rare, despite their frequent co-infections in wild plants, suggesting purifying selection against strain EA/C recombinants. Positive selection was predicted on 17 amino acids distributed over the entire coat protein in the globally distributed strain C, as compared to only four amino acids in the coat protein N-terminus of the EA strain. This selection implies a more recent introduction of the C strain and a higher adaptation of the EA strain to the local ecosystem. Thus, East Africa appears as a hotspot for evolution and diversification of SPFMV.

Evolution of cassava brown streak disease-associated viruses

“…While similar results have been obtained on SPMMV (Tugume et al, 2010b) and Sweet potato virus C (previously known as the strain C of Sweet potato feathery mottle virus, genus Potyvirus) (Tugume et al, 2010a), the findings contrast the data on most of the potyviruses studied in which amino acid residues under positive selection are usually found at the CP N terminus (García-Arenal et al, 2001;Moury et al, 2002). The central part of the potyviral CP is involved in viral cell-to-cell and long distance movement in plants (Dolja et al, 1994(Dolja et al, , 1995Varrelmann & Maiss, 2000) and positive selection in this region can be implemented in host adaptation to ensure efficient systemic infection and subsequent transmission by vectors (e.g., Lalić et al, 2010).…”

The P1N-PISPO trans -Frame Gene of Sweet Potato Feathery Mottle Potyvirus Is Produced during Virus Infection and Functions as an RNA Silencing Suppressor

“…2A) and selected CP sequences of individual viruses. In the case of the SPFMV isolate, a comparison of trees constructed with whole-genome and CP sequences suggested that it can be placed in the group of recombinant isolates, a frequent occurrence among SPFMV isolates (40,41). Comparison of our sequence with those of two selected isolates (Piu3 and RC-ARg, accession numbers FJ155666.1 and KF386014.1, respectively) is illustrated in Fig.…”

Mixed Infections of Four Viruses, the Incidence and Phylogenetic Relationships of Sweet Potato Chlorotic Fleck Virus (Betaflexiviridae) Isolates in Wild Species and Sweetpotatoes in Uganda and Evidence of Distinct Isolates in East Africa

“…Although some metagenomic surveys have explored virus diversity in wild plant communities [14–19], only a few studies have described the genetic variability of individual virus species in wild plants in relation to isolates found in cultivated plants [20–27]. Moreover, few studies have compared isolates of plant viruses from wild and cultivated hosts across broad geographical areas [22–24, 28–30]. Thus, studies comparing virus populations in weeds or wild species and crop species that share an agro-ecological interface are needed to gain insights into the evolutionary and ecological dynamics of plant virus populations, which in turn are needed to facilitate plant virus disease management [8, 31, 32].…”