Pear (Pyrus spp.) is an important perennial fruit crop of India. During May 2022, pear leaf samples were collected from the orchard of ICAR-Indian Agricultural Research Institute, Regional Station, Dhanda, Shimla, Himachal Pradesh, India. RNA sequencing of two pooled samples, Pe1 and Pe2, was done using NovaSeq 6000. Host unaligned reads were de novo assembled into contigs and annotated through BLAST using the virus database. Near complete genome sequences of apple rubbery wood virus 1 (ARWV-1), apple necrotic mosaic virus (ApNMV), citrus virus A (CiVA), apple stem grooving virus (ASGV), apple stem pitting virus (ASPV), apple chlorotic leaf spot virus (ACLSV), and a genetic variant of ASGV named as ASGV-Shimla, and a partial sequence of apple scar skin viroid (ASSVd) were assembled. ARWV-1 and ApNMV belong to the genus Rubodvirus and Ilarvirus having tripartite negative sense and positive sense single stranded RNA genomes, respectively, and their presence in pear trees was observed for the first time indicating the host expansion. Presence of CiVA, ASGV and ACLSV in pear in India was also recorded for the first time in India. The fragments per kilobase of transcript per million reads mapped estimation showed the dominance of ASPV and CiVA in Pe1 and Pe2, respectively. Single nucleotide variants (SNVs) analysis revealed that ASPV had the highest number of SNVs (477), while ACLSV had the lowest number of SNVs (1). The presence of ARWV-1, ApNMV, CiVA, ASPV, ASGV, ACLSV, ASGV-Shimla, and ASSVd was also confirmed in pear samples through Sanger sequencing. The present study widens our understanding of the pear virome and host range expansion of viruses in the genus Rubodvirus and Ilarvirus. This information will be useful in biological study of these viruses and virus indexing programs in pear.

梨（Pyrus spp.）是印度重要的多年生水果作物。2022 年 5 月，从印度喜马偕尔邦西姆拉丹达地区站 ICAR-印度农业研究所的果园采集了梨叶样本。使用 NovaSeq 6000 对两个合并样本 Pe1 和 Pe2 进行 RNA 测序。宿主未比对的读数从头组装成重叠群，并使用病毒数据库通过 BLAST 进行注释。苹果橡胶木病毒 1 (ARWV-1)、苹果坏死花叶病毒 (ApNMV)、柑橘病毒 A (CiVA)、苹果茎沟病毒 (ASGV)、苹果茎点蚀病毒 (ASPV)、苹果褪绿叶病毒的近乎完整基因组序列组装了斑点病毒（ACLSV）、ASGV的遗传变种（命名为ASGV-Shimla）以及苹果疤痕类病毒（ASSVd）的部分序列。ARWV-1和ApNMV分别属于红病毒属和伊拉病毒属，分别具有三重负义和正义单链RNA基因组，并且首次观察到它们在梨树中的存在，表明宿主扩张。印度梨中也首次记录到 CiVA、ASGV 和 ACLSV 的存在。每百万读段每千碱基转录本的片段映射估计显示 ASPV 和 CiVA 分别在 Pe1 和 Pe2 中占主导地位。单核苷酸变异 (SNV) 分析显示，ASPV 的 SNV 数量最多 (477)，而 ACLSV 的 SNV 数量最少 (1)。通过桑格测序也证实了梨样品中存在 ARWV-1、ApNMV、CiVA、ASPV、ASGV、ACLSV、ASGV-Shimla 和 ASSVd。本研究拓宽了我们对红病毒属和伊拉病毒属病毒的梨病毒组和宿主范围扩展的理解。这些信息将有助于这些病毒的生物学研究和梨中的病毒索引程序。