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<p><i>Papaya ringspot virus</i> (PRSV), the causal agent of ringspot disease, is one of the most destructive pathogens affecting papaya, resulting in substantial (80–90%) yield losses worldwide. A critical knowledge gap persists in understanding the molecular determinants of the host tolerance to PRSV and the antiviral role of RNA silencing. As an RNA virus, PRSV exists as a quasi-species within its host, comprising a population of closely related mutant variants which interact dynamically with the plant RNA interference (RNAi) machinery. In infected plants, viral RNA assumes multiple forms- single-stranded RNA, double-stranded RNA, encapsidated RNA, and virus-derived small interfering RNAs (vsiRNAs) that collectively influence the viral persistence and host defence. Plants often harbor co-infections by multiple viral strains or variants; a phenomenon increasingly uncovered through high-throughput sequencing technologies. In this study, we performed a comparative small RNA sequencing analysis to characterize the vsiRNA populations in PRSV infected papaya plants and non-symptomatic (healthy) counterparts of two papaya genotypes- PRSV-tolerant <i>Pusa Selection-3</i>, PRSV-susceptible <i>Pusa Majesty</i> and a wild relative, <i>Vasconcellea cauliflora</i>. High-throughput sequencing generated ~ 238 million reads, from which vsiRNAs of 21, 22, and 24 nucleotides (nt) in length were abundantly detected and mapped across the PRSV genome. Notably, 21nt vsiRNAs were predominant, constituting 35–60% of vsiRNAs in PRSV-infected samples, whereas 22nt and 24nt vsiRNAs (15–35%) were more abundant in healthy plants and the wild relative, showing a consistent sense-strand polarity bias. Analysis of the 5′-end nucleotides of the antisense strand of vsiRNAs revealed a preferential presence of Adenine (A) or Uracil (U), suggesting selective Argonaute protein loading pattern. This study provides the first comparative insight into vsiRNA dynamics across susceptible, tolerant, and wild papaya genotypes, highlighting the complexity of host-virus interactions in PRSV pathogenesis and host defense. The findings advance the understanding of the RNAi-mediated antiviral defense mechanisms underlying PRSV tolerance and lay the groundwork for developing RNAi-based resistance strategies in papaya improvement programs.</p>

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Distinct patterns of virus derived-siRNAs in response to Papaya ringspot virus infection in differentially responding genotypes of papaya (Carica papaya L.) and its wild relative

  • 期刊论文

  • 发表日期：

    2026年1月5日

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  • Madhvi Naresh,
  • Basavaprabhu L. Patil

摘要

Papaya ringspot virus (PRSV), the causal agent of ringspot disease, is one of the most destructive pathogens affecting papaya, resulting in substantial (80–90%) yield losses worldwide. A critical knowledge gap persists in understanding the molecular determinants of the host tolerance to PRSV and the antiviral role of RNA silencing. As an RNA virus, PRSV exists as a quasi-species within its host, comprising a population of closely related mutant variants which interact dynamically with the plant RNA interference (RNAi) machinery. In infected plants, viral RNA assumes multiple forms- single-stranded RNA, double-stranded RNA, encapsidated RNA, and virus-derived small interfering RNAs (vsiRNAs) that collectively influence the viral persistence and host defence. Plants often harbor co-infections by multiple viral strains or variants; a phenomenon increasingly uncovered through high-throughput sequencing technologies. In this study, we performed a comparative small RNA sequencing analysis to characterize the vsiRNA populations in PRSV infected papaya plants and non-symptomatic (healthy) counterparts of two papaya genotypes- PRSV-tolerant Pusa Selection-3, PRSV-susceptible Pusa Majesty and a wild relative, Vasconcellea cauliflora. High-throughput sequencing generated ~ 238 million reads, from which vsiRNAs of 21, 22, and 24 nucleotides (nt) in length were abundantly detected and mapped across the PRSV genome. Notably, 21nt vsiRNAs were predominant, constituting 35–60% of vsiRNAs in PRSV-infected samples, whereas 22nt and 24nt vsiRNAs (15–35%) were more abundant in healthy plants and the wild relative, showing a consistent sense-strand polarity bias. Analysis of the 5′-end nucleotides of the antisense strand of vsiRNAs revealed a preferential presence of Adenine (A) or Uracil (U), suggesting selective Argonaute protein loading pattern. This study provides the first comparative insight into vsiRNA dynamics across susceptible, tolerant, and wild papaya genotypes, highlighting the complexity of host-virus interactions in PRSV pathogenesis and host defense. The findings advance the understanding of the RNAi-mediated antiviral defense mechanisms underlying PRSV tolerance and lay the groundwork for developing RNAi-based resistance strategies in papaya improvement programs.