Founder effect, plant host, and recombination shape the emergent population of begomoviruses that cause the tomato yellow leaf curl disease in the Mediterranean basin

Abstract

Tomato yellow leaf curl disease (TYLCD)-associated viruses present a highly structured population in the western Mediterranean basin, depending on host, geographical region and time. About 1,900 tomato and common bean samples were analyzed from which 111 isolates were characterized genetically based on a genome sequence that comprises coding and non-coding regions. Isolates of three distinct begomoviruses previously described were found (Tomato yellow leaf curl virus, TYLCV, Tomato yellow leaf curl Sardinia virus, TYLCSV, and Tomato yellow leaf curl Málaga virus, TYLCMalV), together with a novel recombinant virus. Mixed infections were detected in single plants, rationalizing the occurrence of recombinants. Except for TYLCV-type strain, single, undifferentiated subpopulations were present for each virus type, probably the result of founder effects. Limited genetic variation was observed in genomic regions, with selection against amino acid change in coding regions.

Rapid evolution of the population of begomoviruses associated with the tomato yellow leaf curl disease after invasion of a new ecological niche: a review

“…Thus, in addition to be readily transmissible by B. tabaci, they exhibited a host range wider than either parental virus (Table 3), which is consistent with selection for a better natural fit. Notably, as shown in Figure 4, it was found for TYLCMalV that soon after its first detection in the epidemics, it displaced almost completely TYLCV in common bean, suggesting its better adaptation to this host (García-Andrés et al, 2007a). TYLCAxV was found at high frequencies in the population of the wild host plant Solanum nigrum L. (García-Andrés et al, 2006) and its spread into cultivated host plants was confirmed (García-Andrés et al, 2007a).…”

“…This strain was found to be well adapted to the ecological circumstances present in the invaded area showing that soon after its introduction it was the predominant virus type in TYLCD epidemics. Moreover, evolution of TYLCV-IL frequencies in several geographical region sampled suggested that a progressive colonization of the different regions occurred, first Almería, then Murcia, and finally Málaga (García-Andrés et al, 2007a). It should be noted that striking molecular differences existed between TYLCV-Mld and TYLCV-IL genomes in the region covering the 5'-part of the IR and the 5' two thirds of the Rep ORF (Fig.…”

“…Thus, as shown in Figure 4, based on samplings performed in that area (García-Andrés et al, 2007a), phylogenetic analyses revealed presence of isolates that grouped with four distinct TYLCD-associated begomovirus species, and strains of the same virus species: the Sar, Sic and ES a Samples were tested by tissue blot hybridization on positively charged nylon membranes using digoxigenin-labeled DNA probes specific to TYLCSV or TYLCV. Percentages were calculated over the total number of collected samples.…”

Diversity of Plant Virus Populations: A Valuable Tool for Epidemiological Studies

“…Analysis of their sequences indicates that both mechanisms contribute significantly to the generation of variability in the evolution and diversification of certain taxonomic groups [11][12][13][14][15][16]. Recombination and reassortment events may involve members of the same plant virus species [17][18][19], members of different species [20][21][22][23][24] or even genus [25]. Genetic exchange by recombination or reassortment may have important epidemiological implications of practical relevance, even more than mutation, as it has been associated to host jumps, host range expansion, changes in virulence, breaking of host resistance and finally, the emergence of new viral plant diseases.…”

Emerging threats of begomoviruses to the cultivation of medicinal and aromatic crops and their management strategies

“…recombination-dependent replication is responsible for generating diversity in the viral genome [118]. Recombination is an evolutionary process that effects greatly on genomic evolution of geminiviruses [21,47,49,105,109,134]. Apart from recombination, pseudo-recombination is also responsible for the genetic diversity in the genus begomovirus.…”