Synonymous site variation due to recombination explains higher genetic variability in begomovirus populations infecting non-cultivated hosts

Abstract

Begomoviruses are ssDNA plant viruses that cause serious epidemics in economically important crops worldwide. Non-cultivated plants also harbour many begomoviruses, and it is believed that these hosts may act as reservoirs and as mixing vessels where recombination may occur. Begomoviruses are notoriously recombination-prone, and also display nucleotide substitution rates equivalent to those of RNA viruses. In Brazil, several indigenous begomoviruses have been described infecting tomatoes following the introduction of a novel biotype of the whitefly vector in the mid-1990s. More recently, a number of viruses from non-cultivated hosts have also been described. Previous work has suggested that viruses infecting non-cultivated hosts have a higher degree of genetic variability compared with crop-infecting viruses. We intensively sampled cultivated and non-cultivated plants in similarly sized geographical areas known to harbour either the weed-infecting Macroptilium yellow spot virus (MaYSV) or the crop-infecting Tomato severe rugose virus (ToSRV), and compared the molecular evolution and population genetics of these two distantly related begomoviruses. The results reinforce the assertion that infection of non-cultivated plant species leads to higher levels of standing genetic variability, and indicate that recombination, not adaptive selection, explains the higher begomovirus variability in non-cultivated hosts.

Complexity of begomovirus and betasatellite populations associated with chilli leaf curl disease in India

“…ChiLCD-associated begomoviruses possess higher genetic variability than observed in other begomoviruses (Melgarejo et al, 2013;Rocha et al, 2013;Silva et al, 2012). As described by Lima et al (2013), the nucleotide diversity in these begomoviruses was noticed to be non-uniformly distributed throughout the genome. Our results emphasize that purifying selection is the major evolutionary determinant leading to the emergence of these begomoviruses and betasatellites, in agreement with other studies Rocha et al, 2013;Silva et al, 2012).…”

Recombination and pseudorecombination driving the evolution of the begomoviruses Tomato severe rugose virus (ToSRV) and Tomato rugose mosaic virus (ToRMV): two recombinant DNA-A components sharing the same DNA-B

“…The role of recombination in the emergence, establishment and evolution of novel, better adapted begomoviruses is well established [19-27]. In Spain, a recombinant between Tomato yellow leaf curl virus (TYLCV) and Tomato yellow leaf curl Sardinia virus (TYLCSV) displayed a wider host range compared to both parental viruses, and became established in the field [22].…”

Begomovirus associated with alternative host weeds: a critical appraisal

“…This new group of viruses was designated as begomovirus (Goodman 1977b) and these viruses are transmitted by the insect vectors. Begomovirus species have the propensity to infect phloem cells of host plant (Arguello-Astorga et al 1994;Lima et al 2013).…”