Species diversity, phylogeny and genetic variability of begomovirus populations infecting leguminous weeds in northeastern Brazil

Abstract

A survey of begomoviruses infecting leguminous weeds (family Fabaceae) was carried out in four states of northeastern Brazil. A total of 26 full-length begomovirus components (19 DNA-A and seven DNA-B, with three pairs of cognate A and B components) were amplified using rolling-circle amplification, then cloned and sequenced. Sequence analysis indicated the presence of six species, four of them novel. In phylogenetic analysis five of the viruses clustered with other Brazilian begomoviruses, but one of them (Euphorbia yellow mosaic virus, EuYMV) clustered with viruses from other countries in Central and South America. Evidence of recombination was found among isolates of Macroptilium yellow spot virus (MaYSV). The MaYSV population had a high degree of genetic variability. Macroptilium lathyroides was revealed as a common host for several of these viruses, and could act as a mixing vessel from which recombinant viruses could emerge. The results indicate that leguminous weeds are reservoirs of several begomoviruses in Brazil, and could play a significant role in begomovirus epidemics, both as inoculum sources and as sources of emerging novel viruses.

Brazilian Begomovirus Populations Are Highly Recombinant, Rapidly Evolving, and Segregated Based on Geographical Location

“…One possible explanation is that intraspecies begomovirus variability reflects the genetic variability of the host. We have recently observed similar mutation frequencies in a population of Macroptilium yellow spot virus (MaYSV), a novel bipartite begomovirus species described as infecting the ubiquitous noncultivated host Macroptilium lathyroides in northeastern Brazil (79). Further studies analyzing mutation frequencies of begomovirus populations (ideally of the same virus) infecting cultivated and noncultivated hosts must be carried out to verify this hypothesis.…”

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

“…Although previous studies indicate that the main type of selection acting on the CP and Rep genes in begomovirus populations is purifying selection (García-Andrés et al, 2007a;Sanz et al, 1999;Silva et al, 2011Silva et al, , 2012, we also assessed the possible contribution of adaptive selection in shaping the standing genetic variability in the ToSRV and MaYSV populations, since a small fraction of codons could be under different selective constraints. Interestingly, the d N /d S ratio estimated for the ToSRV CP was markedly high (v50.446), even after the exclusion of the recombinant isolate Vic20 (v50.274).…”

“…Several species of non-cultivated plants, especially of the families Malvaceae, Euphorbiaceae, Fabaceae and Solanaceae, are known hosts of begomoviruses (Morales & Anderson, 2001). These weed/wild hosts can serve as reservoirs for infection of nearby crops (Alabi et al, 2008;Barbosa et al, 2009;Bedford et al, 1998;García-Andrés et al, 2006), as overwintering refugia (Alabi et al, 2007(Alabi et al, , 2008García-Andrés et al, 2006) and as 'mixing vessels' for interspecific coinfection and recombination (García-Andrés et al, 2006;Monde et al, 2010;Silva et al, 2012). Increased host use and diminished bottlenecks would both potentially increase the effective population size of begomovirus populations (Power, 2000;Seal et al, 2006).…”

Characterization of a New World Monopartite Begomovirus Causing Leaf Curl Disease of Tomato in Ecuador and Peru Reveals a New Direction in Geminivirus Evolution

“…The absence of indigenous monopartite begomoviruses in the NW can be explained by the predominance of a bipartite progenitor(s) on the landmasses that gave rise to the NW or a subsequent introduction event. Local evolution events then drove the emergence of new begomovirus species that reflected the genome structure of the virus(es) in a given geographical area, i.e., bipartite species in the NW (1,5,7,20,21,(59)(60)(61) and monopartite (1,48) and, to a lesser extent, bipartite species in the OW (1,11,62). In addition, a few evolutionary events in the OW have involved changes in the viral genome structure, e.g., the aforementioned TYLCTHV, which can exist as a bipartite or monopartite virus, and the monopartite Sri Lankan cassava mosaic virus, which acquired a DNA-B component and became bipartite (9).…”