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<p>Dragon fruit (<i>Selenicereus</i> spp.) is an emerging high-value tropical fruit crop grown extensively in India. However, very limited information is available on viruses associated with its cultivation. Hence, we conducted virome profiling of dragon fruit cladodes collected from major growing regions of southern and western India using high-throughput sequencing (HTS), followed by validation through RT-PCR and RT-loop-mediated isothermal amplification. The survey conducted across Karnataka, Maharashtra, and Andhra Pradesh revealed moderate to high disease incidence (15–45%), with symptoms including mosaic, mottling, chlorotic streaks, and necrotic lesions. The meta-transcriptome analysis of the RNA isolated from infected cladodes revealed the presence of seven viruses; tobacco streak virus (TSV), groundnut bud necrosis virus (GBNV), pitaya virus X (PiVX), cactus virus X (CVX), cucumber mosaic virus (CMV), tomato mosaic virus (ToMV), and tomato brown rugose fruit virus (ToBRFV). However, the complete/near-complete genome sequences were successfully reconstructed for TSV, GBNV, PiVX, and CVX. Relative abundance analysis indicated GBNV as the dominant virus, followed by CVX, PiVX, and TSV. The phylogenetic analysis showed close clustering of GBNV, TSV, PiVX, and CVX isolates with previously reported Indian and global isolates, indicating high genetic conservation and probable regional dissemination through shared agroecosystems and planting materials. Recombination analysis identified statistically significant recombination events in TSV (RNA1 and RNA2), GBNV (L segment), and PiVX (RdRp region), suggesting ongoing genetic reshuffling and adaptive evolution. In contrast, CVX showed no evidence of recombination. RT-LAMP assays developed for the identified viruses enabled rapid, sensitive, and field-deployable detection, confirming widespread mixed infections across surveyed regions. This study represents the first comprehensive HTS-based virome profiling of dragon fruit in India and highlights the complexity of viral infections in this crop. The integration of HTS with RT-LAMP provides a robust framework for early diagnosis, quarantine surveillance, and the production of virus-free planting material, which is essential for the sustainable expansion of dragon fruit cultivation in India.</p>

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Comprehensive high-throughput sequence-based detection and RT-LAMP confirmation of RNA viruses associated with dragon fruit (Selenicereus spp.) in India

  • 期刊论文

  • 发表日期：

    2026年3月14日

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  • G. S. Madhu,
  • V. Venkataravanappa,
  • Mantesh Muttappagol,
  • C. N. Lakshminarayana Reddy,
  • Shridhar Hiremath

摘要

Dragon fruit (Selenicereus spp.) is an emerging high-value tropical fruit crop grown extensively in India. However, very limited information is available on viruses associated with its cultivation. Hence, we conducted virome profiling of dragon fruit cladodes collected from major growing regions of southern and western India using high-throughput sequencing (HTS), followed by validation through RT-PCR and RT-loop-mediated isothermal amplification. The survey conducted across Karnataka, Maharashtra, and Andhra Pradesh revealed moderate to high disease incidence (15–45%), with symptoms including mosaic, mottling, chlorotic streaks, and necrotic lesions. The meta-transcriptome analysis of the RNA isolated from infected cladodes revealed the presence of seven viruses; tobacco streak virus (TSV), groundnut bud necrosis virus (GBNV), pitaya virus X (PiVX), cactus virus X (CVX), cucumber mosaic virus (CMV), tomato mosaic virus (ToMV), and tomato brown rugose fruit virus (ToBRFV). However, the complete/near-complete genome sequences were successfully reconstructed for TSV, GBNV, PiVX, and CVX. Relative abundance analysis indicated GBNV as the dominant virus, followed by CVX, PiVX, and TSV. The phylogenetic analysis showed close clustering of GBNV, TSV, PiVX, and CVX isolates with previously reported Indian and global isolates, indicating high genetic conservation and probable regional dissemination through shared agroecosystems and planting materials. Recombination analysis identified statistically significant recombination events in TSV (RNA1 and RNA2), GBNV (L segment), and PiVX (RdRp region), suggesting ongoing genetic reshuffling and adaptive evolution. In contrast, CVX showed no evidence of recombination. RT-LAMP assays developed for the identified viruses enabled rapid, sensitive, and field-deployable detection, confirming widespread mixed infections across surveyed regions. This study represents the first comprehensive HTS-based virome profiling of dragon fruit in India and highlights the complexity of viral infections in this crop. The integration of HTS with RT-LAMP provides a robust framework for early diagnosis, quarantine surveillance, and the production of virus-free planting material, which is essential for the sustainable expansion of dragon fruit cultivation in India.