Tomato yellow leaf curl virus (TYLCV) in Kuwait and global analysis of the population structure and evolutionary pattern of TYLCV

Tomato yellow leaf curl virus (Family Geminiviridae, Genus Begomovirus) is a serious menace in the cultivation of tomato causing Tomato leaf curl disease (ToLCD). Recently, we presented the TYLCV isolates having additional genomic features (nucleotides insertions) characterized from the tomato fields of Kuwait adding up to the genetic diversity repertoire of these viruses. The widespread prevalence of disease in tropics across the continents, emergence of genetic variants and ever increasing complete genome sequences of virus isolates in public database warrant a global analysis to infer the genetic diversity, evolutionary pattern so as to devise suitable disease control stratagems. Molecular phylogeny suggested the monophyletic origin of the TYLCV Kuwait isolates and TYLCV reported from Asian countries revealing their genetic relatedness. Though genetic diversity of TYLCV reported from elsewhere (TYLCV others) is two folds higher (0.11765) than TYLCV Kuwait, a relatively high number of polymorphic sites in the latter imply their inherent genetic diversity. Neutrality tests of TYLCV as a whole suggest the operation of phenomenon of purifying selection indicating deleterious mutations are being weeded out from the population. Recombination analysis discloses that TYLCV Kuwait isolates are potential genetic recombinants or involved in the generation of potential recombinants as parents. The results of the neutrality tests were further strengthened by the outcome of codon substitution analysis indicating the operation of purifying selection in the codons of C1 ORF of TYLCV population as a whole and in the sub-group TYLCV Kuwait. The implications of these results are discussed.