Emergence of Asian endemic begomoviruses as a pandemic threat

Molecular characterization, genetic divergence, expression of encapsidiation and synergism by a bipartite begomovirus; Tomato leaf curl Palampur virus (ToLCPMV) infecting bitter gourd (Momordica charantia)

The Tomato leaf curl Palampur virus (ToLCPMV) is a bipartite begomovirus that poses a substantial risk to agriculture by infecting a variety of crops, including cucurbitaceous group. This study examines the manifestation of encapsidation and synergism by ToLCPMV in bitter gourd (Momordica charantia) and focuses on its epidemiological approaches and implications of managing this virus in tomatoes growing areas. Through the utilization of molecular and biological techniques, we have successfully ascertained the epidemiology of this highly destructive virus, highlighting the vital roles played by its two genetic components. An analysis was conducted to identify the mechanism by which the virus clusters its DNA into virions, known as the encapsidation process. Additionally, the impact of synergism with other viral or environmental factors over the degree of infection was examined. The evolutionary rate differences among sites were modeled deploying a discrete Gamma distribution with 5 categories and a [+G] parameter. The results of this study provide important and unique information about synergism, encapsidiation and host-virus interactions. Sequencing study revealed that the bipartite ToLCPMV is linked to the occurrence of leaf curl disease in bitter gourd. The DNA-A and DNA-B of the ToLCPMV isolates infecting bitter gourd (SP1-4) showed 89 %, 93 %, 95 %, and 98 % similarity respectively. Mean evolutionary rates in these categories were 0.19, 0.47, 0.79, 1.24, 2.31 substitutions per site. Unexpectedly, the DNA-A sequences of ToLCPMV that infect this particular host seemed to be an amalgamation of sequences that are closely associated with tomato leaf curl New Delhi virus (ToLCNDV). Additionally, reiterate cropping of tomatoes with vegetables expanded the virus's host geographic region. This understanding will create some specific ways to regulate the dissemination of ToLCPMV and minimize its adverse impacts in tomato growing regions. Through the implementation of these strategies, the ability of crops to withstand and recover from adverse conditions can be enhanced, so encouraging the adoption of sustainable farming practices in affected regions.

A virus induces alterations in root morphology while exerting minimal effects on the rhizosphere and endosphere microorganisms in rice

The highly destructive southern rice black-streaked dwarf virus (SRBSDV) causes significant losses in rice production. To understand its impact on rice root, we studied fibrous root development and root microbiota variation (rhizosphere and endosphere) after SRBSDV infection. SRBSDV infection reduced the number and length of fibrous roots in rice. Interestingly, the rhizosphere had higher bacterial diversity and abundance at the initial (0 days) and 30-day postinfection stages, while 30-day-old roots showed increased diversity and abundance. However, there were no significant differences in microbiota diversity between infected and noninfected rice plants. The major rhizosphere microbiota included Proteobacteria, Bacteroidota, Acidobacteriota, and Planctomycetota, comprising about 80% of the community. The endosphere was dominated by Proteobacteria and Cyanobacteria, constituting over 90%, with Bacteroidota as the next most prominent group. Further, we identified differentially expressed genes related to plant-pathogen interactions, plant hormone signal, and ABC transporters, potentially affecting root morphology. Notably, specific bacteria (e.g. Inquilinus and Actinoplanes) showed correlations with these pathways. In conclusion, SRBSDV primarily influences root growth through host metabolism, rather than exerting direct effects on the root microbiota. These insights into the interactions among the pathogen, rice plant, and associated microbiota could have implications for managing SRBSDV's detrimental effects on rice production.

The rising threat of geminiviruses: molecular insights into the disease mechanism and mitigation strategies

BACKGROUND

Geminiviruses are among the most threatening emerging plant viruses, accountable for a huge loss to agricultural production worldwide. These viruses have been responsible for some serious outbreaks during the last few decades across different parts of the world. Sincere efforts have been made to regulate the disease incidence by incorporating a multi-dimensional approach, and this process has been facilitated greatly by the advent of molecular techniques. But, the mixed infection due to the polyphagous nature of vectors results in viral recombination followed by the emergence of novel viral strains which thus renders the existing mitigation strategies ineffective. Hence, a multifaceted insight into the molecular mechanism of the disease is really needed to understand the regulatory points; much has been done in this direction during the last few years. The present review aims to explore all the latest developments made so far and to organize the information in a comprehensive manner so that some novel hypotheses for controlling the disease may be generated.

METHODS AND RESULTS

Starting with the background information, diverse genera of geminiviruses are listed along with their pathological and economic impacts. A comprehensive and detailed mechanism of infection is elaborated to study the interactions between vector, host, and virus at different stages in the life cycle of geminiviruses. Finally, an effort isalso made to analyze the progress made at the molecular level for the development of various mitigation strategies and suggest more effective and better approaches for controlling the disease.

CONCLUSION

The study has provided a thorough understanding of molecular mechanism of geminivirus infection.

Characterization of a recombinant tomato leaf curl New Delhi Virus (ToLCNDV) in a perennial medicinal climber host (Ipomoea cairica (L.) Sweet)

During the year 2020-2021, a disease syndrome very commonly observed in railway creepers (Ipomoea cairica (L.) Sweet) was taken into consideration from Gorakhpur Province (UP East region). Whitefly, a common vector for plant-related viral diseases was observed for wide transmission of disease. DNA from 17 infected leaf samples was isolated and analyzed through PCR using specific primers designed for the detection of Begomoviruses. Further amplification of isolated DNA fragments supporting a begomovirus infection with an estimated size of (2.7 kb). RCA of the isolated DNA sample was carried out using ϕ29 DNA polymerase by digesting it through a set of restriction endonucleases (such as BamHI, Kpn1, HindIII, EcoRI) obtaining the best result through KpnI. The amplified segment was cloned into pUC 18vectors. The obtained sequences were matched using the NCBI BLAST database showing the highest sequence similarity of 98.7% with ToLCNDV of snake gourd (Accession no. KY780199), isolates of CP genes sequence in Varanasi. ToLCNDV, a begomovirus of bipartite nature was first reported to be from Tomato (Solanaceae), later affecting certain members of the Cucurbitaceae family in India and adjacent countries. The obtained DNA sequence was submitted at NCBI with the name ToLCNDV-IP (GenBank Accession no. OM777194). The phylogenetic analysis clubbed the current isolate ToLCNDV-IP with Asian isolates. All European isolates were clubbed in separate clades indicating two distinct groups of ToLCNDV isolates. ToLCNDV-IP isolate was found to be an intralineage recombinant between two Asian isolates viz ToLCNDV isolate from Papaya (India) and ToLCNDV isolate from Tomato (Pakistan). This study shows the association of recombinant ToLCNDV infection in a new host Ipomoea cairica for the first time in India.