Genomic Variation and Diversification in Begomovirus Genome in Implication to Host and Vector Adaptation

Abstract

Begomoviruses (family Geminiviridae, genus Begomovirus) are DNA viruses transmitted in a circulative, persistent manner by the whitefly Bemisia tabaci (Gennadius). As revealed by their wide host range (more than 420 plant species), worldwide distribution, and effective vector transmission, begomoviruses are highly adaptive. Still, the genetic factors that facilitate their adaptation to a diverse array of hosts and vectors remain poorly understood. Mutations in the virus genome may confer a selective advantage for essential functions, such as transmission, replication, evading host responses, and movement within the host. Therefore, genetic variation is vital to virus evolution and, in response to selection pressure, is demonstrated as the emergence of new strains and species adapted to diverse hosts or with unique pathogenicity. The combination of variation and selection forms a genetic imprint on the genome. This review focuses on factors that contribute to the evolution of Begomovirus and their global spread, for which an unforeseen diversity and dispersal has been recognized and continues to expand.

Keywords: SNP; adaption; begomovirus; diversity; host range; satellite.

Figure 1

Model for Begomoviral genomic diversity and adaptation. (A) A Begomoviral master genome. Begomovirus (BGVs) encodes 6–7 proteins (V2 and V1) from the sense strand and C3, C2, C1, and C4 in the antisense strand. (B) BGVs may be transmitted by their vector (B. tabaci) in genetically diverse hosts (species, cultivars, or landraces). Due to various environmental climates and geographical niches, the genotype of the plant and vector may differ. Virus replication and selection within-host is a continuous process. During this process, the interaction of begomoviral proteins with pro-viral and antiviral proteins (host and vector) regulates the balance between variation and selection, leading to the selection of the fittest, most adapted strains. Vectors contribute to selection by transmitting the virus in new plant species or different genotypes/cultivars of the same species. Some BGVs retain a satellite called DNA β (betasatellite), and this interaction is called begomovirus–betasatellite complexes (red dotted arrows). Betastaellites depend on the helper virus for their replication and spread within and between hosts. Selection pressure enforced on a virus genome by a given environment will alter the virus population, excluding less fit entities. Mutations that offer a beneficial advantage are probable to be fixed in the genome. Some mutations generated in alternates hosts (from different niches) might break resistance and expand the host range. (C) During the evolutionary process, beneficial mutations (non-synonymous), including sites under positive selection, differentially accumulate in different viral proteins. They might contribute to fitness by enhancing stability, transmission, replication competence, escape from immunity, suppression of immune responses, or a combination.