University of Virginia, Charlottesville, VA, USA.
Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India.
Methods Mol Biol. 2022;2408:71-84. doi: 10.1007/978-1-0716-1875-2_4.
The current era of high-throughput sequencing (HTS) technology has expedited the detection and diagnosis of viruses and viroids in the living system including plants. HTS data has become vital to study the etiology of the infection caused by both known as well as novel viral elements in planta, and their impact on overall crop health and productivity. Viral-derived small interfering RNAs are generated as a result of defence response by the host via RNAi machinery. They are immensely exploited for performing exhaustive viral investigations in plants using bioinformatics as well as experimental approaches.This chapter briefly presents the basics of virus-derived small interfering RNAs (vsiRNAs ) biology in plants and their applications in plant genomics and highlights in silico strategies exploited for virus/viroid detection. It gives a systematic pipeline for vsiRNAs identification using currently available bioinformatics tools and databases. This will surely work as a quick beginner's recipe for the in silico revelation of plant vsiRNAs as well as virus/viroid diagnosis using high-throughput sequencing data.
高通量测序（HTS）技术的当前时代加速了包括植物在内的活体系统中病毒和类病毒的检测和诊断。HTS 数据对于研究由植物中已知和新型病毒元件引起的感染的病因及其对整体作物健康和生产力的影响至关重要。病毒衍生的小干扰 RNA 是宿主通过 RNAi 机制产生的防御反应的结果。它们被广泛用于使用生物信息学和实验方法对植物中的病毒进行详尽的研究。本章简要介绍了植物中小干扰 RNA（vsiRNA）的生物学基础及其在植物基因组学中的应用，并重点介绍了用于病毒/类病毒检测的计算策略。它提供了一种使用当前可用的生物信息学工具和数据库识别 vsiRNA 的系统流程。这对于使用高通量测序数据进行植物 vsiRNA 的计算揭示以及病毒/类病毒诊断来说，无疑是一个快速的入门指南。
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