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<p>Begomoviruses are major pathogens of chilli, causing significant yield losses and posing a serious threat to Indian agriculture. This study examined the genetic diversity and evolutionary relationships of begomoviruses associated with chilli leaf curl disease in Uttar Pradesh, Haryana, Chhattisgarh and Delhi. Symptomatic leaf samples collected during the 2020–2021 growing season were analysed using rolling-circle amplification, cloning and sequencing of 25 DNA-A and betasatellite molecules, along with four alphasatellite components. Sequence analysis revealed that <i>Begomoviruscapsici</i> (Chilli leaf curl virus, ChiLCV) predominated (16 isolates), followed by <i>B. delhiensis</i> (ToLCNDV) and <i>B. multaniensis</i> (Cotton Leaf Curl Multan Virus) (three each), and <i>B. tomatopyralis</i> (TYLCV) and <i>B. indicapsici</i> (two each). Phylogenetic analysis showed TYLCV_Deo_RVA/IN/23 and ToLCNDV_RE_RVA/IN/23 clustering with isolates from Saudi Arabia and Pakistan. Recombination breakpoints were most common in low-GC regions, with the AC1 gene showing the highest frequency. ChiLCV_GKP_RVA/IN/23 had the highest substitution rate for AC1, while AC3 and AV2 of ChiLCINV_GZB_RVA/IN/23 showed substantial positive selection. The data indicate significant genetic heterogeneity among ten begomoviruses that infect chilli in northern and Central-East India, highlighting their potential as inoculum sources and contributors to the formation of novel begomovirus strains.</p>

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Genetic diversity and recombination of begomoviruses associated with chilli leaf curl disease in northern and Central-East India

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年7月28日

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  • Vineeta Pandey,
  • Aarshi Srivastava,
  • Ali Akhtar,
  • Ramwant Gupta,
  • R. K. Gaur

摘要

Begomoviruses are major pathogens of chilli, causing significant yield losses and posing a serious threat to Indian agriculture. This study examined the genetic diversity and evolutionary relationships of begomoviruses associated with chilli leaf curl disease in Uttar Pradesh, Haryana, Chhattisgarh and Delhi. Symptomatic leaf samples collected during the 2020–2021 growing season were analysed using rolling-circle amplification, cloning and sequencing of 25 DNA-A and betasatellite molecules, along with four alphasatellite components. Sequence analysis revealed that Begomoviruscapsici (Chilli leaf curl virus, ChiLCV) predominated (16 isolates), followed by B. delhiensis (ToLCNDV) and B. multaniensis (Cotton Leaf Curl Multan Virus) (three each), and B. tomatopyralis (TYLCV) and B. indicapsici (two each). Phylogenetic analysis showed TYLCV_Deo_RVA/IN/23 and ToLCNDV_RE_RVA/IN/23 clustering with isolates from Saudi Arabia and Pakistan. Recombination breakpoints were most common in low-GC regions, with the AC1 gene showing the highest frequency. ChiLCV_GKP_RVA/IN/23 had the highest substitution rate for AC1, while AC3 and AV2 of ChiLCINV_GZB_RVA/IN/23 showed substantial positive selection. The data indicate significant genetic heterogeneity among ten begomoviruses that infect chilli in northern and Central-East India, highlighting their potential as inoculum sources and contributors to the formation of novel begomovirus strains.