Citrus tristeza virus (CTV), a member of the aphid-transmitted closterovirus group, is the causal agent of the notorious tristeza disease in several citrus species worldwide. The codon usage patterns of viruses reflect the evolutionary changes for optimization of their survival and adaptation in their fitness to the external environment and the hosts. The codon usage adaptation of CTV to specific citrus hosts remains to be studied; thus, its role in CTV evolution is not clearly comprehended. Therefore, to better explain the host–virus interaction and evolutionary history of CTV, the codon usage patterns of the coat protein (CP) genes of 122 CTV isolates originating from three economically important citrus hosts (55 isolate from Citrus sinensis, 38 from C. reticulata, and 29 from C. aurantifolia) were studied using several codon usage indices and multivariate statistical methods. The present study shows that CTV displays low codon usage bias (CUB) and higher genomic stability. Neutrality plot and relative synonymous codon usage analyses revealed that the overall influence of natural selection was more profound than that of mutation pressure in shaping the CUB of CTV. The contribution of high-frequency codon analysis and codon adaptation index value show that CTV has host-specific codon usage patterns, resulting in higheradaptability of CTV isolates originating from C. reticulata (Cr-CTV), and low adaptability in the isolates originating from C. aurantifolia (Ca-CTV) and C. sinensis (Cs-CTV). The combination of codon analysis of CTV with citrus genealogy suggests that CTV evolved in C. reticulata or other Citrus progenitors. The outcome of the study enhances the understanding of the factors involved in viral adaptation, evolution, and fitness toward their hosts. This information will definitely help devise better management strategies of CTV.

Cotton leaf curl disease (CLCuD), caused by whitefly (Bemisiatabaci) transmitted single-stranded DNA viruses belonging to the Genus, Begomovirus (family, Geminiviridae) in association with satellite molecules; is responsible for major economic losses in cotton in three northwest (NW) Indian states Haryana, Punjab, and Rajasthan. Annual CLCuD incidences during 2012 to 2014 were estimated to be 37.5%, 63.6%, and 38.8% respectively. Cotton leaves were collected from symptomatic plants annually for three years and subjected to DNA isolation, followed by rolling circle amplification (RCA), cloning, and DNA sequencing of apparently full-length begomoviral genomes and associated betasatellites and alphasatellites. Among the thirteen CLCuD-begomoviral genomes recovered, eight were identified as Cotton leaf curl Multan virus-Rajasthan (CLCuMuV-Ra), one as -Pakistan (PK) and another as -Faisalabad (Fai), whereas, three were as Cotton leaf curl Kokhran virus-Burewala (CLCuKoV-Bu), indicating that CLCuMuV-Ra was the most prevalent begomovirus species. Five of the eight CLCuMuV-Ra sequences were found to be recombinants. The CLCuMuV-Ra- associated satellites consisted of Cotton leaf curl Multan betasatellite (CLCuMB), and Gossypium darwinii symptomless alphasatellite (GDarSLA), and Croton yellow vein mosaic alphasatellite (CrYVMoA). The second most abundant helper virus species, CLCuKoV-Bu, was associated with CLCuMB and GDarSLA.

Cotton leaf curl disease (CLCuD) is a major constraint for production of cotton (Gossypium sp.) in Northwest India. CLCuD is caused by a monopartite, circular ssDNA virus belonging to the genus Begomovirus in association with betasatellites and alphasatellites, and ttransmitted by a whitefly vector (Bemisia tabaci). To explore the genetic variability in betasatellites and alphasatellite associated with the CLCuD-begomovirus complex in Northwest India. A survey was conducted for successive three years of 2014 to 2016 and twig samples from symptomatic and healthy cotton plants randomly were collected. Total plant DNAs were isolated, subjected to rolling circle amplification (RCA), cloning and sequencing. Full-length genome of 12 betasatellites and 13 alphasatellites, those were obtained in the present study, were analyzed. Sequence analysis showed that all the present betasatellites shared 85–99 percent nucleotide identity (PNI) among themselves and 84–95 PNI with other members of Cotton leaf curl Multan betasatellite (CLCuMB) and fell into one genogroup along with CLCuMB. But in close observation the present betasatellites clustered into two phylogenetic subgroups under single CLCuMB. The present alphasatellites showed 72–100 PNI among themselves and fell under three alphasatellite species, Gossypium Darwinii symptomless alphasatellite (GDarSLA), Cotton leaf curl Multan alphasatellite (CLCuMA) and Cotton leaf curl Burewala alphasatellite (CLCuBuA). In the recombination analysis, all the present betasatellites and alphasatellites were found to be recombinants involving intra species recombination in betasatellite, and interspecies recombination in alphasatellite species. The present study indicated that the betasatellite and alphasatellite molecules associated with CLCuD-begomovirus complex in Northwest India are genetically diverse.

Tomato (Solanum lycopersicum L.), the second most important vegetable crop globally, faces a significant threat from various viral diseases. A newly emerging disease, characterised by distinctive shoestring symptoms on leaves and the development of unripe, small, and hard fruit, poses a serious challenge to tomato cultivation in India. An initial survey in an experimental field revealed more than 50% of the plants displayed symptoms of the shoestring disease, resulting in substantial reductions in fruit yield and quality. Transmission electron microscopy (TEM) and molecular analyses identified an isolate of the tomato mottle mosaic virus (ToMMV) in the affected plants. When the partially purified virus was mechanically inoculated into tomato cv. Pusa Ruby plants, it reproduced the characteristic shoestring symptoms, confirming its causal relationship with the disease. Notably, the present shoestring isolate of ToMMV (ToMMV-Tss) was found to induce similar shoestring symptoms in most of the major commercial tomato varieties when inoculated under controlled experimental conditions in the glasshouse, indicating its aggressive nature. Host range studies demonstrated that the ToMMV-Tss can infect several solanaceous species, while cucurbitaceous hosts remained unaffected. Moreover, the virus was found to be seed-transmissible, with a small percentage of seedlings from infected plants displaying symptoms. These findings underscore the significant impact of ToMMV on tomato production in India and emphasise the need for reliable diagnostic tools and effective management strategies to curb the spread and mitigate the impact of this virus on commercial tomato cultivation.