Recombination and selection pressure in the ipomovirus sweet potato mild mottle virus (Potyviridae) in wild species and cultivated sweetpotato in the centre of evolution in East Africa

Abstract

Sweet potato mild mottle virus (SPMMV) is the type member of the genus Ipomovirus (family Potyviridae). SPMMV occurs in cultivated sweetpotatoes (Ipomoea batatas Lam.; Convolvulaceae) in East Africa, but its natural wild hosts are unknown. In this study, SPMMV was detected in 283 (9.8 %) of the 2864 wild plants (family Convolvulaceae) sampled from different agro-ecological zones of Uganda. The infected plants belonged to 21 species that were previously not known to be natural hosts of SPMMV. The size of the SPMMV coat protein (CP) was determined by Western blot analysis, N-terminal protein sequencing and peptide mass fingerprinting. Data implicated a proteolytic cleavage site, VYVEPH/A, at the NIb/CP junction, resulting in a CP of approximately 35 kDa. Nearly complete sequences of 13 SPMMV isolates were characterized. Phylogenetic analysis of non-recombinant CP-encoding sequences placed five isolates from wild species sampled in the central zone of Uganda into a separate cluster. Recombination events were detected in the 59-and 39-proximal parts of the genome, providing novel evidence of recombination in the genus Ipomovirus. Thirteen amino acids in the N terminus of the P1 protein were under positive selection, whereas purifying selection was implicated for the HC-Pro-, P3-, 6K1-and CP-encoding regions. These data, supported by previous studies on ipomoviruses, provide indications of an evolutionary process in which the P1 proteinase responds to the needs of adaptation.

Sequence diversity and potential recombination events in the coat protein gene of Apple stem pitting virus

“…Similar results were described for coat protein genes of Grapevine rupestris stem pittingassociated virus (Alabi et al, 2010) and Sweet potato mild mottle virus (SPMMV) (Tugume et al, 2010). In contrast, animal viruses experience strong diversifying selection (Drummond et al, 2003;Yang and Bielawski, 2000) which is caused predominantly by pressure from the immune system of the host.…”

“…This signal may be significant especially in the case of codon number 20, as positive selection was detected using three (SLAC, REL, FEL) out of four methods. Such phenomenon was also observed for SPMMV where 13 amino acids in the P1 proteinase were under positive selection, whereas purifying selection was implicated for the rest of the sites (Tugume et al, 2010). It is not surprising that various codons are under different Table 2 The …”

Evolution of cassava brown streak disease-associated viruses

“…No evidence of heterologous recombination between the two viruses was found, which is consistent with previous studies, indicating that heterologous recombinants between divergent genomes (,90 % nt identity) of RNA viruses are rare due to their associated fitness deficits As compared with other genera in the family Potyviridae, the structural variability observed in the 59-end of the genomes of ipomoviruses is unusually extensive and implies that recombination may be particularly important for the evolution of ipomoviruses (Valli et al, 2007;Mbanzibwa et al, 2009a). Recombination events have been demonstrated in the 59-and 39-proximal parts of the genome in SPMMV, the type member of the genus Ipomovirus (Tugume et al, 2010b). Analysis of the whole genomes of CBSV and UCBSV in this study showed that the majority of recombination junctions in these viruses were located at the 39-proximal part within the HAM1h-and CP-encoding sequences and 39-UTR.…”

“…Alternatively, HAM1h may have been acquired at different times or evolves more rapidly than CP, the only other viral region that could be analysed from a large number of virus isolates in this study. Previous studies on ipomoviruses have found low genetic diversity in Cucumber vein yellowing virus (Janssen et al, 2007) and high diversity in SPMMV (Tugume et al, 2010b). In general, viruses in the family Potyviridae exhibit rather low genetic diversity (reviewed by García-Arenal et al, 2001).…”

“…1) and functions as a suppressor of RNA silencing (Mbanzibwa et al, 2009a). These four ipomoviruses do not encode a helper component proteinase (HC-Pro) located downstream from P1 in the polyprotein of Sweet potato mild mottle virus (SPMMV), the type species of the genus Ipomovirus (Tugume et al, 2010b). The most Fig.…”