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<p>Cherry virus&#xa0;A (CVA; <i>Capillovirus alphavii</i>), a&#xa0;member of the genus <i>Capillovirus</i> in the family <i>Betaflexiviridae</i>, is an economically significant plant virus that infects <i>Prunus</i> species, including sweet cherry (<i>Prunus avium</i>). This study presents the first comprehensive genomic characterization of an Iranian isolate of CVA (CVA-Ir) from cherry orchards in West Azarbaijan Province, Iran. Using high-throughput RNA sequencing (RNA-Seq), the complete genome of CVA-Ir was sequenced, revealing a&#xa0;7434-nucleotide positive-sense single-stranded RNA genome with two open reading frames (ORFs). ORF1 encodes a&#xa0;polyprotein with conserved domains, including methyltransferase, helicase, RNA-dependent RNA polymerase, and coat protein, while RF2 encodes a&#xa0;movement protein. Phylogenetic analysis clustered CVA-Ir with isolates obtained from cherry in Canada, forming a&#xa0;distinct subclade within the <i>Capillovirus</i> genus, and highlighted the genetic diversity of CVA isolates across different hosts. The Iranian isolate exhibited high nucleotide identity (99%) with Canadian isolates, suggesting potential evolutionary and transmission pathways. Virus-specific primers designed from the CVA-Ir genome successfully validated the RNA-Seq results through reverse transcription polymerase chain reaction (RT-PCR). This study underscores the utility of RNA-Seq in plant virology for identifying and characterizing viral pathogens and provides critical insights into the genetic diversity and phylogenetic relationships of CVA.</p>

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Complete Genome Characterization of an Iranian Isolate of Cherry Virus A (Capillovirus alphavii) Based on RNA-Seq Analysis

  • 期刊论文

  • 发表日期：

    2025年9月29日

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  • Parsa Golabi,
  • Ahmad Hosseini,
  • Mina Rastgou

摘要

Cherry virus A (CVA; Capillovirus alphavii), a member of the genus Capillovirus in the family Betaflexiviridae, is an economically significant plant virus that infects Prunus species, including sweet cherry (Prunus avium). This study presents the first comprehensive genomic characterization of an Iranian isolate of CVA (CVA-Ir) from cherry orchards in West Azarbaijan Province, Iran. Using high-throughput RNA sequencing (RNA-Seq), the complete genome of CVA-Ir was sequenced, revealing a 7434-nucleotide positive-sense single-stranded RNA genome with two open reading frames (ORFs). ORF1 encodes a polyprotein with conserved domains, including methyltransferase, helicase, RNA-dependent RNA polymerase, and coat protein, while RF2 encodes a movement protein. Phylogenetic analysis clustered CVA-Ir with isolates obtained from cherry in Canada, forming a distinct subclade within the Capillovirus genus, and highlighted the genetic diversity of CVA isolates across different hosts. The Iranian isolate exhibited high nucleotide identity (99%) with Canadian isolates, suggesting potential evolutionary and transmission pathways. Virus-specific primers designed from the CVA-Ir genome successfully validated the RNA-Seq results through reverse transcription polymerase chain reaction (RT-PCR). This study underscores the utility of RNA-Seq in plant virology for identifying and characterizing viral pathogens and provides critical insights into the genetic diversity and phylogenetic relationships of CVA.