First report of tomato leaf curl Gujarat virus (Begomovirus solanumgujaratense) causing leaf curl disease on Xanthium strumarium in India

"Xanthium strumarium, often regarded as a major weed but known for its medicinal properties, was observed exhibiting symptoms of leaf curl, yellowing, and shortened internodes in six locations across Salem, Dindigul, and Madurai districts of Tamil Nadu, India, during 2023–2024 (Supplementary Fig. 1). Symptomatic and asymptomatic leaves were collected for analysis. Detection of begomoviruses was performed using primer pairs PAL1c1960/PAR1v772 and GKToLCV-F/GKToLCV-R (Rojas et al. 1993; Nagendran et al. 2014), producing amplicons of approximately 1200 bp and 900 bp, respectively, in all symptomatic samples. Based on the sequences amplified by the above primer pairs, specific primers, ToGUVF/ToGUVR, were designed to amplify the complete DNA-A genome, producing amplicons of approximately 1400 bp (Supplementary Table 1). DNA-B specific degenerate primer pair, PBL1v2040/PCRc1 (Rojas et al. 1993) was used to screen samples for the presence of DNA-B, but no amplification was detected, confirming the monopartite nature of the virus. Primers UN101/UN102 and beta01/beta02 (Sattar et al. 2022) were employed to identify the presence of alpha and beta satellites. While alphasatellites were not detected, betasatellites were successfully amplified in all symptomatic samples, yielding ~ 1400 bp amplicons. Amplicons generated using the primer pairs PAL1c1960/ PAR1v772 (~ 1200 bp), GKToLCV-F/GKToLCV-R (~ 900 bp), ToGUVF/ToGUVR (~ 1400 bp), and betasatellite-specific primers beta01/beta02 (~ 1400 bp) were purified, sequenced bidirectionally, trimmed and aligned. One consensus sequence of begomovirus (2760 bp) and betasatellite (1349 bp) were submitted to the NCBI GenBank (PV021314 and PV021315, respectively). BLASTn search revealed that the investigated begomovirus sequence (PV021314) shared 97.39% nucleotide identity with the Begomovirus solanumgujaratense (tomato leaf curl Gujarat virus, ToLCGUV; AY234383) reported in tomato from Nepal. Similarly, the betasatellite sequence (PV021315) exhibited 94.30% nucleotide identity with the tomato leaf curl Gujarat betasatellite (ToLCGUB; KF964647) reported in tomato from Andhra Pradesh, India. Species-specific primers targeting tomato leaf curl viruses, including Begomovirus solanumdelhiense (tomato leaf curl New Delhi virus, ToLCNDV), Begomovirus solanumkarnatakaense (tomato leaf curl Karnataka virus, ToLCKV), Begomovirus solanumbangalorense (tomato leaf curl Bangalore virus, ToLCBV), and ToLCGUV (Reddy et al. 2005), were tested. Amplification was observed only with the ToLCGUV-specific primer set. Phylogenetic analysis of the full-length genomes of DNA-A and betasatellites further confirmed that the begomovirus and betasatellite sequences from X. strumarium clustered closely with the ToLCGUV and ToLCGUB sequences, respectively, previously reported in tomato (Supplementary Figs. 2 and 3). ToLCGUV, a monopartite begomovirus, is transmitted by the polyphagous insect pest Bemisia tabaci Gennadius (Hemiptera: Aleyrodidae). B. tabaci is capable of disseminating viruses from the Begomovirus, Ipomovirus, Crinivirus, Carlavirus, and Torradovirus families to crops and weeds. Moreover, ToLCGUV has been reported from crops like tomato, papaya, cotton, common beans and chilli. Thus, the detection of ToLCGUV in X. strumarium, a widespread weed in southern India, highlights its role as a potential reservoir host, facilitating the spread of the virus to neighboring crops through B. tabaci. This finding underscores the importance of weed management in controlling outbreaks of begomoviruses. To our knowledge, this is the first report of ToLCGUV and ToLCGUB infecting X. strumarium in India."