Abstract
The genome sequence of a bipartite begomovirus was identified in an ornamental plant, Golden duranta (GD) (Duranta erecta) exhibiting crinkled leaves and apical leaf curling, collected from three districts Lucknow (Lko), Basti (Bas) and Deoria (Deo) of Eastern Uttar Pradesh, India. Three complete genome sequences of each DNA-A and DNA-B, were amplified by rolling circular amplification (RCA), cloned and sequenced. The analysis for both DNA-A and DNA-B revealed 91–99% nucleotide sequence identity to tomato leaf curl New Delhi virus (ToLCNDV). Phylogenetic studies revealed that all three ToLCNDV-A isolates form a separate clade, whereas, isolates of ToLCNDV-B clustered together with ToLCNDV-Chi- RKG2 (MT264782). Furthermore, when compared to other DNA-A and DNA-B, ToLCNDV-[GD-Deo-In] DNA-A showed the most recombination events. The nucleotide substitution rates of ToLCNDV-A and ToLCNDV-B were established to be 8.152 10− 4 substitutions site− 1 year− 1 and 6.684 10− 4 substitutions site− 1 year− 1 respectively. However, the transitional and transversal substitution rates were shown to be higher in DNA-B with a total number of mutations (η) 691 in comparison with DNA-A. The combined negative values of the neutrality tests, Tajima’s D and Fu and Li’s D*, indicate purified selection with low-frequency polymorphism. The dN/dS ratio for ToLCNDV-A and ToLCNDV-B revealed the selective control of evolutionary relationships. Our study supports the theory that begomoviruses have expanded their host range and that the fast evolutionary rates are mostly due to recurrent recombination and mutation. This is the first record of bipartite ToLCNDV infecting D. erecta in India.
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Data availability
All sequencing data of virus isolates are available in the NCBI database. Further data analysis will be available from the corresponding authors upon request.
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Acknowledgements
The authors are thankful to the Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur Uttar Pradesh, India. A.A. is also grateful to the Office of Research and Sponsored Program, The University of Tulsa, Oklahoma. AKS and NSM thank International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi for providing the laboratory space.
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AKS, VP and AS contributed equally to the experiments and computational work. RKV helped with computational analysis. NSM, AA and RKG. are the mentor and supervised the experiments, edited, proofread, and finalized the manuscript. All authors have read and agreed to the published version of the manuscript.
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Sahu, A., Pandey, V., Srivastava, A. et al. Molecular characterization of a bipartite begomovirus associated with leaf crinkle and curling symptoms of Duranta erecta in India. Indian Phytopathology 77, 191–201 (2024). https://doi.org/10.1007/s42360-024-00718-0
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DOI: https://doi.org/10.1007/s42360-024-00718-0