Genetic structure of populations of the begomoviruses Tomato mottle leaf curl virus and Sida mottle Alagoas virus infecting tomato (Solanum lycopersicum) and Sida spp., respectively

Abstract

Begomoviruses are among the most damaging pathogens infecting cultivated hosts worldwide, and are considered an important limiting factor in tomato fields. In the present study, foliar samples of tomato and Sida spp. were collected in Boqueirão, state of Paraíba, Brazil, in May 2014. Viral genomes were amplified, cloned and sequenced. A total of 30 DNA-A components were obtained. Pairwise comparisons indicated the presence of only two begomovirus species: Tomato mottle leaf curl virus (ToMoLCV) from tomato samples and Sida mottle Alagoas virus (SiMoAV) in Sida spp. ToMoLCV and SiMoAV subpopulations showed high genetic variability, with the ToMoLCV Rep gene being the most variable. Recombination events were detected only among ToMoLCV isolates, with recombination breakpoints occurring in the common region and in the Rep gene. Negative or purifying selection seems to be among the most important evolutionary mechanisms acting on the CP and Rep genes in both ToMoLCV and SiMoAV. Our results indicate that ToMoLCV remains as the main tomato-infecting begomovirus in northeastern Brazil, and that Sida spp. do not contribute to ToMoLCV epidemics in tomato. Keywords Geminiviridae. ssDNA virus. Evolutionary mechanisms The family Geminiviridae comprises circular ssDNA plant viruses encapsidated into quasi-icosahedral geminate particles, and is divided into seven genera (Becurtovirus, Begomovirus, Curtovirus, Eragrovirus, Mastrevirus, Topocuvirus and Turncurtovirus) according to the type of insect vector, host range, genome organization and phylogeny (Varsani et al. 2014). Viruses belonging to the genus Begomovirus have one (monopartite) or two (bipartite) genomic components known as DNA-A and DNA-B, and are transmitted by the whiteflies of the Bemisia tabaci sibling species group (Homoptera: Aleyrodidae) to dicotyledonous plants (Brown et al. 2012). Begomoviruses are economically important pathogens infecting cultivated plants worldwide (Legg and Fauquet 2004; Morales and Anderson 2001; Navas-Castillo et al. 2011; Varma and Malathi 2003), and are considered limiting factors to production of tomatoes, peppers and legumes in the New World (Morales 2006; Navas-Castillo et al. 2011). The emergence of begomoviruses as important pathogens in tomato-growing areas in Brazil coincided with the introduction and spread of B. tabaci Middle East-Asia Minor 1 (MEAM1, previously known as biotype B) in the early 1990's (

Geminiviridae and Alphasatellitidae Diversity Revealed by Metagenomic Analysis of Susceptible and Tolerant Tomato Cultivars across Distinct Brazilian Biomes

“…Thus far, ToMoLCV is the prevalent tomato-infecting begomovirus in the warm and semi-arid Northeast region of Brazil [39,44,46,60], corroborating the results of the present study. However, before our results, there were no reports in the literature of infections in tomato plants by SimMV in the Brazilian Northeast region.…”

How To Be a Successful Monopartite Begomovirus in a Bipartite-Dominated World: Emergence and Spread of Tomato Mottle Leaf Curl Virus in Brazil

“…The subsequent detection of DNA-A and DNA-B sequences in tomato mottle leaf curl disease (ToMoLCD) samples collected from the Federal District in 2004 was used to suggest that ToMoLCV has a bipartite genome (43). However, infectivity studies with infectious clones were not conducted, and analyses of ToMoLCD samples from other locations in Brazil failed to reveal evidence of a DNA-B component (39,40,44).…”