Occurrence of Cotton leaf curl Multan virus and associated betasatellites with leaf curl disease of Bhut-Jolokia chillies (Capsicum chinense Jacq.) in India

Abstract

Geminiviridae comprises the largest family of plant viruses which causes severe crop losses in India. The highest pungency chilli Bhut-Jolokia or ghost pepper (Capsicum chinense Jaqc.) hails from North-East region of India and is used in many dishes to add flavors and also for its medicinal value. However, this chilli variety is also affected by viruses leading to crop and economic losses. The present study reports the identification of begomoviruses in the infected chilli Bhut-Jolokia leaf samples collected from eight different places of North-East region (Manipur) of India. The infected leaf samples were screened for the presence of viral genome by rolling circle amplification (RCA) followed by PCR using degenerate primer pairs. The subsequent analyses using restriction fragment length polymorphism and sequencing revealed the presence of Cotton leaf curl Multan virus (CLCuMuV), and Tomato leaf curl Patna betasatellite (ToLCPaB). The findings focus on the phylogenetic relatedness, probable recombinational hot-spots and evolutionary divergence of the viral DNA sequences with the current reported begomoviral genome. To the best of our knowledge, this is the first report showing the presence of CLCuMuV, and associated non-cognate ToLCPaB with leaf curl disease of Bhut-Jolokia chillies. The study reveals potential recombination sites on both viral genome and betsatellite which, during the course of evolution, may have aided the virus to progress and successfully establish infection in chilli plants. Taken together, our results suggest a possible spread of CLCuMuV to the hitherto non-host crop in the North-East region of India.

Molecular phylogenetics and evolutionary analysis of a highly recombinant begomovirus, Cotton leaf curl Multan virus, and associated satellites

“…Several factors including enhanced viral replication, mixed infections, increased host range, and vector are known to significantly regulate the recombination ( Qadir et al 2019 ). High frequencies of recombination detection in CP and Rep gene have been previously reported for cotton-infecting begomoviruses ( Saleem et al 2016 ), while for others, CP has been the hot spot of recombination ( Yogindran et al 2021 ). Recently, it has been demonstrated that several resistant-breaking variants of CLCuMuV and other cotton-infecting begomoviruses displayed significant recombination events not only in the viral genomes but also in the associated betasatellites ( Chakrabarty et al 2020 ).…”

Roles of two distinct alphasatellites modulating geminivirus pathogenesis

“…In recent years, the association of CLCuMuV with Malvaceae (cotton, okra, hollyhock, hibiscus species), Solanaceae (chilli, tomato), Cucurbitaceae (luffa species) family of crop plants have been extensively studied in India and Pakistan (Figs. 2 , 3 ) [ 39 – 41 ] . However, the role of satellites in disease-complex has not been elucidated in detail.…”

Journal of Plant Protection Research

“…The regions of DNA-A, in which recombination is occur were identified as intergenic region (160 and 386 nt recombinations occur), replication-associated protein and AC4 protein (1,733-2,369; 2,552-2,692; 2,571-2,683 nts) respectively. Therefore, the GC plot analysis suggests that PFLCuV associated with leaf curl disease of passion fruit may undergo recombination at below average GC content regions of its genome The literature surveyed also showed similar results in regions having low GC content as potential recombination sites in plant infecting begomovirus (Yogindran et al 2021) and human adenovirus, which may facilitate virus molecules to evolve and also allow a species to increase its host range in a new environmental niche (Robinson et al 2013).…”

“…The low GC region in DNA-A of the PFLCuV associated leaf curl disease of passion fruit might serve as potential recombination sites for facilitating the evolution of a virus as documented in many viruses infecting plants and animals (Yogindran et al 2021;Robinson et al 2013). The sequence with high GC content has more stability due to a triple hydrogen bond, stacking interactions between the bases and is also linked with topology and orientation of DNA strands (Ninh 2013;Yogindran et al 2021). A higher number of bonds between bases in a DNA strand, generally requires more energy to break the strand.…”