First complete genome sequences and transcript expression profiling of tea plant necrotic ring blotch virus isolates from Iran

Abstract

Tea plant necrotic ring blotch virus (TPNRBV), a highly prevalent and damaging pathogen in tea plantations. In 2021, TPNRBV was detected in Iran, where its molecular and biological properties were subsequently characterized. Despite the growing recognition of TPNRBV, there is a notable lack of complete genome sequences for this virus. In the recent research, High-throughput sequencing (HTS) was performed using the Illumina HiSeq 2000 platform. In silico analyses, including genome assembly, differential expression of TPNRBV open reading frames (ORFs), identification of intra-population single-nucleotide variants (SNVs), as well as phylogenetic and recombination analyses, were performed on the HTS data using CLC Genomics Workbench. The complete genome sequences of two Iranian TPNRBV isolates were obtained using HTS. Analysis of the transcript expression levels for TPNRBV ORFs revealed a significant increase in the expression of the P22 gene, followed by the P24 and P14 genes. Polymorphism analysis identified 93 single-nucleotide polymorphisms (SNVs) across the TPNRBV genome, which were highly concentrated in the RNA1 and RNA2 segments. Phylogenetic analysis based on RNA1 to RNA4 revealed that the Iranian TPNRBV isolates share a close evolutionary relationship with Chinese isolates. In this study, the complete genome sequences of two TPNRBV isolates from Iran are reported for the first time. While the function of P22 remains unclear, its elevated expression in both samples suggests the need for further investigation into its potential role. The identification of amino acid-changing SNVs in the coding regions highlights their evolutionary significance, underscoring the need for further research to understand the impact of these mutations on the virus’s life cycle and pathogenicity. Given that TPNRBV SNVs were identified from pooled samples, a high degree of sequence variation and abundant SNVs were anticipated. This study represents the first comprehensive investigation of tea plant virome in Iran and provides important insights into this field. Additionally, it marks the first report on the population-level expression profile of TPNRBV viral transcripts and the prediction of SNVs, offering a foundation for future research focused on the control and management of this virus.