GENETIC DIVERSITY OF TOMATO LEAF CURL VIRUSES (BEGOMOVIRUS COHENI) INFECTING TOMATO

Molecular Characterization of a Novel Monopartite Begomovirus Infecting Weeds and Important Crops in Yunnan, China

The genus Begomovirus constitutes a group of devastating plant viruses causing significant economic losses in the production of agricultural crops. In the present study, conducted in Yunnan province, China, a novel monopartite begomovirus was identified from Bidens pilosa, Crassocephalum crepidioides, tomato, pepper, and common bean, showing severe disease symptoms. The complete genome of the virus shows the typical organization of monopartite begomoviruses and shares the highest nucleotide sequence identity (88.73–88.95%) with crassocephalum yellow vein virus (CraYVV). According to the species criteria of the genus Begomovirus, this virus is a novel Begomovirus species, which has since been named “bidens pilosa leaf crumple virus (BpLCrV)”. Recombination analysis revealed that the novel species is a potential recombinant begomovirus derived from CraYVV and ageratum leaf curl virus (ALCuV), and phylogenetic analysis showed that BpLCrV was clustered with tomato yellow leaf curl Thailand virus (TYLCTHV) from China. We successfully developed a BpLCrV infectious clone. Agrobacterium-mediated inoculation of the BpLCrV infectious clone could effectively infect Nicotiana benthamiana, Nicotiana glutinosa, and Datura stramonium and cause disease symptoms. Thus, in this study, BpLCrV was, for the first time, identified and characterized as a novel begomovirus that infects not only weeds but also different important crops, potentially threatening agricultural production.

Genomic insights and pathogenic potential of begomovirus infecting bitter gourd (Momordica charantia L.) in Tamil nadu, India

Virome analysis uncovers the tomato virosphere and a novel recombinant begomovirus-alphasatellite complex causing leaf curl disease in India.

BACKGROUND Begomoviruses are circular single-stranded DNA viruses transmitted by the whitefly Bemisia tabaci and are major causal agents of leaf curl disease in tomato (Solanum lycopersicum L.). The present study aimed to comprehensively characterize the virome associated with symptomatic tomato plants collected from major agro-ecological regions of Tamil Nadu, India, using high-throughput sequencing (HTS). RESULTS HTS based virome analysis of tomato plants exhibiting severe leaf curl symptoms revealed a complex viral community. The virosphere includes multiple begomoviruses, namely tomato leaf curl New Delhi virus (ToLCNDV), tomato leaf curl Bangalore virus (ToLCBaV), tomato leaf curl Karnataka virus, and chilli leaf curl virus (ChiLCV), along with associated alpha- and betasatellites. In addition, RNA viruses including pepper virus A (PepVA), chilli veinal mottle virus (ChiVMoV), and tomato chlorosis virus (ToCV) were also identified, indicating frequent occurrence of mixed infections. Full-length or coding-complete genome sequences were recovered for most viral components, whereas partial contigs were obtained for Southern tomato virus (STV) and tobacco vein distorting virus (TVDV). Notably, a novel recombinant monopartite begomovirus, tentatively named tomato leaf curl Dindigul virus (ToLCDiV), showed < 89.82% nucleotide identity with known begomovirus sequences. In addition, a distinct alphasatellite, tomato leaf curl Madurai alphasatellite (ToLCMdA) showed 86.74% nucleotide identity with known alphasatellites, supporting its distinctiveness based on ICTV species demarcation criteria. Recombination analysis suggested that ToLCDiV may have originated from parental lineages related to ToLCBaV and tomato leaf curl Gujarat virus (ToLCGV), with recombination breakpoints in the AC1, AC4, and intergenic regions. CONCLUSION This study revealed a complex tomato virome associated with leaf curl disease in Tamil Nadu, driven by mixed viral infections and recombination. The detection of the putative novel recombinant begomovirus ToLCDiV and distinct alphasatellite ToLCMdA highlights the emergence of new virus-satellite components and emphasizes the need for continued virome surveillance and integrated disease management in tomato production systems.

IDENTIFICATION OF PEDILANTHUS LEAF CURL VIRUS AND A NOVEL BETASATELLITE-INFECTING RADISH (RAPHANUS SATIVUS L.) IN PAKISTAN

Single stranded DNA viruses (Genus Begomovirus) are economically important plant pathogens that are responsible for significant yield losses in dicotyledonous plants including radish (Raphanus sativus L.). However, their distribution and diversity in certain regions of Pakistan are still not sufficiently described. During systematic field surveys conducted across six districts of Punjab province (Faisalabad, Okara, Toba Tek Singh, Multan, Lahore, and Layyah), more than 120 radish fields as well as vegetable markets were inspected, but the infected plants were detected only in six localities of Thal desert in district Layyah. The radish plants exhibiting vein thickening, leaf shortening, and enations were observed, suggestive of a geminivirus infection. Total DNA isolated from symptomatic leaves was analyzed by diagnostic PCR. Amplification using coat protein primers targeting the DNA-A component yielded a 771 bp fragment (GenBank Accession No. PV872843), while universal primers for betasatellites amplified a 1361 bp fragment (GenBank Accession No. PV872842). The sequence similarity analysis revealed that DNA-A component shared similarity with Pedilanthus leaf curl virus, whereas the associated betasatellite showed 85% nucleotides identity with radish-infecting betasatellites. According to the betasatellite species criteria established by ICTV which defines distinct species at less than 91% nucleotide sequence identity, this isolate represents a divergent species for which the name Radish leaf curl Layyah betasatellite is proposed. The phylogenetic tree for coat protein suggested its close clustering with Pedilanthus leaf curl virus and Cotton leaf curl Kokhran virus reported from the region. However, betasatellite clustered with papaya infecting betasatellite previously reported from radish crops in India. This study documents, the natural occurrence of Pedilanthus leaf curl virus and a novel Radish leaf curl Layyah betasatellite infecting radish in Pakistan. Our findings underscore the occurrence of begomovirus with new betasatellite complexes in the region and highlight the need for continuous surveillance strategies to safeguard radish cultivation. Keywords: RRadish, geminiviruses, begomoviruses, betasatellites, leaf curl disease

Molecular evidence of two begomoviruses and a novel DNA-B infecting Duranta erecta variegata in Pakistan.

Genetic Diversity and Evolutionary Dynamics of Begomoviruses Reported from Sri Lanka

Begomoviruses, members of the family Geminiviridae, pose a major challenge to crop production in Sri Lanka and globally due to their extensive host range and high evolutionary potential. This study investigated the genetic diversity and evolutionary dynamics of begomoviruses reported from Sri Lanka using publicly available genomic sequences. Viral sequences were retrieved from the NCBI database and aligned using MUSCLE. Pairwise sequence identity was assessed using SDT (v1.2), while phylogenetic relationships, nucleotide diversity, and selection pressure analyses were conducted using MEGA version 12. Recombination events were detected using RDP4 employing multiple algorithms. The analysis revealed four major begomovirus groups based on sequence identity and phylogenetic clustering: Okra enation leaf curl virus (OELCuV), Bhendi yellow vein mosaic virus (BYVMV), Sri Lankan cassava mosaic virus (SLCMV), and Tomato leaf curl Sri Lankan virus (ToLCSLV). Phylogenetic analysis supported clear species level segregation with strong bootstrap confidence. Five recombination events were identified, indicating active genetic exchange among begomovirus populations. Selection pressure analysis showed that most viral genes are under strong purifying selection, suggesting evolutionary conservation, whereas limited evidence of positive selection was observed in specific genes. Nucleotide diversity varied among populations, with OELCuV isolates exhibiting the lowest diversity, indicating a more conserved genome compared to other groups. Overall, this study highlights the significant genetic diversity and ongoing evolution of begomoviruses in Sri Lanka, emphasizing the role of recombination and selection in shaping viral populations and their potential impact on crop health and management strategies.