Genetic Structure and Population Variability of Tomato Yellow Leaf Curl China Virus

Abstract

Geminiviruses have circular single-stranded DNA genomes and are important pathogens in tropical and subtropical regions, but their population diversity and variability are poorly understood. Here, we have investigated variations accumulating in Tomato yellow leaf curl China virus (TYLCCNV), a geminivirus in the genus Begomovirus of the family Geminiviridae. The population variation was analyzed in a naturally infected tomato (Solanum lycopersicom) plant and in Nicotiana benthamiana and tomato plants experimentally infected with a swarm of TYLCCNV DNA clones to provide an identical sequence for initiation of infection. Our results demonstrate that the population of TYLCCNV in a naturally infected tomato plant was genetically heterogeneous and that rapid mutation occurred in the populations amplified from N. benthamiana and tomato plants that had been infected with cloned DNA. This feature of the population of TYLCCNV in these plants consisted of the consensus sequence and a pool of mutants that are not identical but are closely related to the consensus sequence, and it coincides with the quasispecies concept described for many RNA viruses. The mutation frequency was circa 10 ؊4 in N. benthamiana and tomato at 60 days postinoculation, a value comparable to that reported for plant RNA viruses. The quasispecies-like nature of the TYLCCNV populations suggested that TYLCCNV is capable of rapid evolution and adaptation in response to changing agricultural practices.Virus-resistant crops, characterized by their resistance to a particular strain of a virus, offer one of the most cost-effective strategies for the management of plant viral diseases. However, the dynamic nature of virus populations permits the evolution of new strains that can adapt to increasingly changing agricultural practices. In particular, such variability should enable viruses with quasispecies pools to overcome crop resistance and subsequently result in epidemics of viral diseases (22). Thus, the effective use of virus-resistant cultivars and management of viral diseases requires a better understanding of the genetic structures and evolutionary trajectories of virus populations.Previous research on plant viral population structures and evolution has mainly focused on plant RNA viruses (reviewed in references 9, 12, and 27-29). The populations of plant RNA viruses are intrinsically genetically heterogeneous, and such populations are designated as quasispecies. The quasispecies concept suggests that the population of a virus, even in a single replicating population, is essentially a collection of variants varying around the consensus sequence (6, 7).Members of the genus Begomovirus of the family Geminiviridae, which have circular single-stranded DNA genomes, are transmitted by the whitefly Bemisia tabaci Genn. in a semipersistent circulating manner (26). Due to the worldwide increases in the population and distribution of the insect vector and global movement of plant materials, begomovirus-induced diseases have become a major constraint on crop produ...

Molecular Evidence of Recombination on Korean Isolates of Tomato yellow leaf curl virus by Nucleotide Transversions and Transitions

“…However, non-homologous recombination facilitates the rearrangement of cellular or other viral genes via insertion (Padidam et al, 1999). A recent controlled study of the host variability of TYLCV in China demonstrated an average mutation frequency of approximately 3.5 × 10 −4 per base over 60 days of infection of a tobacco plant (Ge et al, 2007). This frequency is similar to that reported previously for plant RNA viruses, including Tobacco mosaic virus, Cucumber mosaic virus, and Cowpea chlorotic mottle virus (Schneider and Roossinck, 2001).…”

Genetic diversity, host range, and distribution of tomato yellow leaf curl virus in Iran

“…It could be considered as heterogeneity among Iranian TYLCV isolates as it had been mentioned before (Hajimorad et al, 1996). Naturally infected tomatoes were infected with heterogenic TYLCV populations (Ge et al, 2007). Genetic variation in TYLCV genome either through mutation or DNA recombination is responsible for most of variations (Hanley-Bowdin et al, 1999).…”

Time - the emerging dimension of plant virus studies

“…Wu et al (2008) noted that in the study of TYLCV from China (Ge et al, 2007) only 'four nucleotide positions accounted for close to half (18 of 41) of the observed substitutions'. Furthermore, the sites varying in one species may differ from those varying in another.…”