Virome analysis deciphered the infection of American plum line pattern virus, little cherry virus 1 and plum bark necrosis stem pitting-associated virus in plum from India

IF 1.7 3区农林科学 Q2 AGRONOMY European Journal of Plant Pathology Pub Date : 2024-07-04 DOI:10.1007/s10658-024-02912-2

Zainul A. Khan, Pooja Thapa, Damini Diksha, Yazing S. Mailem, Susheel K. Sharma, Sajad U. Nabi, Sumiah Wani, Mehraj D. Shah, Mahendra K. Verma, Nitika Gupta, Virendra K. Baranwal

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Abstract

As very limited information is available on viruses and viroids infecting plum in India, virome analysis was undertaken to determine the virus and viroid spectrum infecting plum. High throughput sequencing (HTS) analysis of five plum samples (PM1-PM5) revealed the presence of near complete genome sequences of prunus necrotic ringspot virus (PNRSV), American plum line pattern virus (APLPV), apple chlorotic leaf spot virus (ACLSV) and hop stunt viroid (HSVd) in PM1; little cherry virus 1 (LChV-1), plum bark necrosis stem pitting-associated virus (PBNSPaV), ACLSV and HSVd in PM2. No virus or viroid sequence was obtained in PM3, PM4 and PM5. Near complete genome sequences of these viruses were obtained using different assemblers. APLPV, LChV-1, PBNSPaV and HSVd are being reported here for the first time from plum in India. The presence of these viruses was also confirmed by reverse transcription polymerase chain reaction and Sanger sequencing in HTS samples as well as in additional 36 plum samples (PM6-PM41) collected from the same orchard from where PM1 and PM2 samples were obtained. The validation test in an additional 36 samples indicated predominance of APLPV and PNRSV which were detected in all the samples, while other viruses were present only in some of the samples. Moreover, fragments per kilobase of transcript per million reads mapped and virus accumulation studies showed dominance of PNRSV RNA3 in PM1 and LChV-1 in PM2. Analysis of single nucleotide variants (SNVs) showed that PNRSV RNA3 had the highest SNVs (99) and PBNSPaV had the lowest SNVs (1). The phylogenetic analysis revealed that these viruses are phylogenetically related to viruses from different countries. These findings advance our knowledge of the viral pathogens of plum, and would help in virus indexing and certification of clean plant for commercial plum cultivars.

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病毒组分析破译了印度李子感染的美国李子线纹病毒、小樱桃病毒 1 和李子树皮坏死茎点病相关病毒的情况

摘要由于有关感染印度李子的病毒和病毒病的信息非常有限，因此进行了病毒组分析，以确定感染李子的病毒和病毒病谱。PM2 中的小樱桃病毒 1（LChV-1）、李树皮坏死茎点状相关病毒（PBNSPaV）、ACLSV 和 HSVd。在 PM3、PM4 和 PM5 中没有获得病毒或病毒体序列。这些病毒的近乎完整的基因组序列是通过不同的组装器获得的。这里首次报告了印度李子中的 APLPV、LChV-1、PBNSPaV 和 HSVd。通过反转录聚合酶链反应和 Sanger 测序，在 HTS 样品以及从获得 PM1 和 PM2 样品的同一果园采集的另外 36 个李子样品（PM6-PM41）中证实了这些病毒的存在。对另外 36 个样本的验证测试表明，所有样本中都检测到了 APLPV 和 PNRSV，而其他病毒只出现在部分样本中。单核苷酸变异（SNVs）分析表明，PNRSV RNA3 的 SNVs 最高（99），而 PBNSPaV 的 SNVs 最低（1）。系统进化分析表明，这些病毒与不同国家的病毒存在系统进化关系。这些研究结果增进了我们对李子病毒病原体的了解，并将有助于李子商业栽培品种的病毒索引和洁净植物认证。

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来源期刊

European Journal of Plant Pathology 农林科学-农艺学

CiteScore

4.20

自引率

5.60%

发文量

183

审稿时长

3 months

期刊介绍： The European Journal of Plant Pathology is an international journal publishing original articles in English dealing with fundamental and applied aspects of plant pathology; considering disease in agricultural and horticultural crops, forestry, and in natural plant populations. The types of articles published are :Original Research at the molecular, physiological, whole-plant and population levels; Mini-reviews on topics which are timely and of global rather than national or regional significance; Short Communications for important research findings that can be presented in an abbreviated format; and Letters-to-the-Editor, where these raise issues related to articles previously published in the journal. Submissions relating to disease vector biology and integrated crop protection are welcome. However, routine screenings of plant protection products, varietal trials for disease resistance, and biological control agents are not published in the journal unless framed in the context of strategic approaches to disease management.