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

Abstract

eThe incidence of begomovirus infections in crop plants sharply increased in Brazil during the 1990s following the introduction of the invasive B biotype of the whitefly vector, Bemisia tabaci. It is believed that this biotype transmitted begomoviruses from noncultivated plants to crop species with greater efficiency than indigenous B. tabaci biotypes. Either through rapid host adaptation or selection pressure in genetically diverse populations of noncultivated hosts, over the past 20 years various previously unknown begomovirus species have became progressively more prevalent in cultivated species such as tomato. Here we assess the genetic structure of begomovirus populations infecting tomatoes and noncultivated hosts in southeastern Brazil. Between 2005 and 2010, we sampled and sequenced 126 DNA-A and 58 DNA-B full-length begomovirus components. We detected nine begomovirus species in tomatoes and eight in the noncultivated host samples, with four species common to both tomatoes and noncultivated hosts. Like many begomoviruses, most species are obvious interspecies recombinants. Furthermore, species identified in tomato have probable parental viruses from noncultivated hosts. While the population structures of five well-sampled viral species all displayed geographical subdivision, a noncultivated host-infecting virus was more genetically variable than the four predominantly tomato-infecting viruses.

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

“…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).…”

“…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.…”

Phylodynamic evidence of the migration of turnip mosaic potyvirus from Europe to Australia and New Zealand

“…This is especially true of those viruses that evolve at measurable rates and adapt rapidly to new or resistant hosts . These not only include plant viruses with RNA genomes but also those with single-and double-stranded DNA genomes, such as begomoviruses and mastreviruses in the family Geminiviridae Rocha et al, 2013) and cauliflower mosaic virus in the family Caulimoviridae (Yasaka et al, 2014). All of these reports have shown that the evolution of virus populations is shaped by founder effects, selection and recombination.…”

Tomato chlorotic mottle Guyane virus: a novel tomato-infecting bipartite begomovirus from French Guiana

“…[13]). In the last two decades, a diverse group of indigenous begomoviruses, commonly known as New World (NW) begomoviruses, has emerged as a major threat to tomato production in Latin America [1,5,6,11,12]. Except for the recently described indigenous monopartite virus tomato leaf deformation virus (ToLDeV) in Ecuador and Peru [9], all indigenous NW begomoviruses have a bipartite genome (two DNA components, each approximately 2.6 kb, referred to as DNA-A and DNA-B).…”