Genetic variability and population structure of the New World begomovirus Euphorbia yellow mosaic virus

Abstract

The emergence of begomoviruses (whitefly-transmitted viruses classified in the genus Begomovirus, family Geminiviridae) in Brazil probably occurred by horizontal transfer from non-cultivated plants after the introduction of Bemisia tabaci MEAM1. The centre of diversity of Euphorbia heterophylla (Euphorbiaceae) is located in Brazil and Paraguay, where it is an invasive species in soybean and other crops. Reports of possible begomovirus infection of E. heterophylla in Brazil date back to the 1950s. In 2011, Euphorbia yellow mosaic virus (EuYMV) was described in symptomatic plants collected in the Brazilian state of Goiás. Here we assess the genetic variability and population structure of begomoviruses infecting E. heterophylla in samples collected throughout nine Brazilian states from 2009 to 2014. A total of 158 and 57 haplotypes were compared in DNA-A and DNA-B datasets, respectively. Analysis comparing population structure in a large sampled area enabled us to differentiate two subpopulations. Further, the application of discriminant analysis of principal components allowed the differentiation of six subpopulations according to sampling locations and in agreement with phylogenetic analysis. In general, negative selection was predominant in all six subpopulations. Interestingly, we were able to reconstruct the phylogeny based on the information from the 23 sites that contributed most to the geographical structure proposed, demonstrating that these polymorphisms hold supporting information to discriminate between subpopulations. These sites were mapped in the genome and compared at the level of amino acid changes, providing insights into how genetic drift and selection contribute to maintain the patterns of begomovirus population variability from a geographical structuring point of view.

Evolutionary dynamics of bipartite begomoviruses revealed by complete genome analysis

“…Sampling of intermediate regions between AL and MG may 2 provide a better picture of the genetic make-up of the BlYSV population. 3 In agreement with Mar et al (44), a near perfect segregation based on geography 4 was observed in the EuYMV DNA-A and DNA-B trees ( Figure 2C). For the DNA-A, two 5 major clades were well supported, with isolates sampled in Rio Grande do Sul (RS) and 6 Paraná states (PR) clustered separately from those sampled in Góias (GO) and Mato Grosso 7 do Sul (MS).…”

“…Therefore, even with DNA-A and DNA-B working together 14 as a single functional unit, with both components necessary to systemically infect the plant, 15 only those regulatory elements required to maintain the integrity and functionality of 16 genome may show similar evolutionary rates driven by reciprocal selection, unlike the 17 remaining of the genome. 18 Previous studies, based only on the DNA-A analysis, have shown that 19 begomoviruses populations segregate based on geographical location on a global as well as 20 on a local scale (41,44,48,86). Our results showed this to occur for the DNA-B as well.…”

Caracterização dos padrões de recombinação das principais subpopulações globais de begomovírus

“…Vários estudos indicam que populações de begomovírus apresentam altos níveis de variabilidade genética (Ariyo et al, 2005;Ge et al, 2007;Silva et al, 2012;Mar et al, 2017).…”

“…São vírus de grande importância para a agricultura que causam perdas severas em várias culturas como, por exemplo, tomateiro, mandioca, algodão, dentre outras (Esterhuizen et al, 2013;Brown et al, 2015). Esses patógenos também causam doenças em espécies de plantas silvestres e invasoras (Moriones et al, 2011;Tavares et al, 2012;Barreto et al, 2013;Mar et al, 2017).…”

“…Vários estudos sobre processos evolutivos em escala populacional têm sido realizados recentemente (Rocha et al, 2013;Mahatma et al, 2016;Kumar et al, 2017a;Macedo et al, 2017;Mar et al, 2017). A estrutura genética (padrão de distribuição da variabilidade genética dentro e entre subpopulações) da metapopulação (conjunto de várias subpopulações) global de begomovírus foi analisada por Prasanna et al (2010).…”