In this review, the advantages and advances in applying high-throughput sequencing (HTS) in the management of viral diseases in citrus, along with some challenges, are discussed to provide perspectives on future prospects. Since the initial implementation of HTS in citrus virology, a substantial number of citrus viruses have been identified, with a notable increase in the last 7 years. The acquisition of viral genomes and various HTS-based omics analyses serve as crucial pillars for advancing research in the etiology, epidemiology, pathology, evolution, ecology, and biotechnology of citrus viruses. HTS has notably contributed to disease diagnosis, such as the diagnoses of concave gum and impietratura, as well as to the surveillance of new virus risks and the preparation of virus-free materials. However, certain inherent defects in HTS and coupled bioinformatics analysis, such as challenges with sequence assembly and the detection of viral dark matter, require improvement to enhance practical efficiency. In addition, the utilization of HTS for the systematic management of citrus viral diseases remains limited, and drawing insights from other virus–plant pathosystems while integrating emerging compatible techniques and ideas may broaden its specific applications.

中文翻译：

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管理柑橘中的病毒病害：利用高通量测序实现多种应用


本文讨论了高通量测序 （HTS） 在柑橘病毒性疾病管理中的优势和进展，以及一些挑战，以期为未来前景提供前景。自从在柑橘病毒学中首次实施 HTS 以来，已经鉴定出大量柑橘病毒，在过去 7 年中显著增加。病毒基因组的获取和各种基于 HTS 的组学分析是推进柑橘病毒病因学、流行病学、病理学、进化、生态学和生物技术研究的重要支柱。HTS 对疾病诊断做出了重大贡献，例如凹牙龈和 impietratura 的诊断，以及监测新病毒风险和制备无病毒材料。然而，HTS 和耦合生物信息学分析中的某些固有缺陷，例如序列组装和病毒暗物质检测的挑战，需要改进以提高实际效率。此外，HTS 在柑橘病毒病害系统管理中的应用仍然有限，从其他病毒-植物病理系统中汲取见解，同时整合新兴的兼容技术和思想可能会拓宽其特定应用。