First complete genome sequence of Tomato leaf curl virus (ToLCV) from Salvia splendens in India

Abstract

AbstractThe complete genome sequences of a Begomovirus and associated betasatellite were obtained by the rolling circle amplification method from a symptomatic Salvia (Salvia splendens) plant showing severe leaf curling, leaf deforming and yellowing, from Gorakhpur, Uttar Pradesh, India. The viral genome (DNA‐A) sequence showed the highest nucleotide identity (99.75%) with an isolate of Tomato Leaf Curl Virus (ToLCV), whereas the associated satellite sequence exhibited the highest nucleotide similarity of 98.47% with the isolate of Chilli leaf curl betasatellite (ChiLCB). The virus present in the infected salvia plant was successfully transmitted by whitefly to healthy salvia and tomato. The phylogenetic analysis reveals that although the ToLCV is segregated by the host but closely related to the isolate originating from India, whereas the same is found with the associated betasatellite. The study finds that evolutionary analysis along with recombination value solely cannot explain its relative frequency. Somehow, mutation, and nucleotide substitution, contributed to the evolution and diversification of this ToLCV together with the co‐adaptation of its betasatellite. However, ToLCV was found to have more diverse recombination events as compared with betasatellite. Consequently, the low frequency of polymorphism suggests a background selection or recent expansion occurring in populations of Begomoviruses. In addition, haplotype diversity (Hd) was detected as equal to 1 for ToLCV and very close to 1 for ChiLCB, signifying the uniqueness of the isolate. Our result indicates that S. splendens plants infected with ToLCV coupled with betasatellite act as an alternative host and that could lead to an increased incidence and emergence of new variants of tomato leaf curl diseases. To our knowledge, this is the first report of ToLCV and its associated betasatellite infecting Salvia in India. This study based on different evolutionary indices may provide insight into the future evolutionary study of different species of Begomoviruses.