Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
ICAR-National Research Centre for Orchids, Pakyong, Sikkim, India.
Gene. 2021 Jun 20;786:145626. doi: 10.1016/j.gene.2021.145626. Epub 2021 Mar 31.
Viruses are abundant entities that infect almost every living organism. In recent years, Next Generation Sequencing coupled with bioinformatic analyses is widely adopted for identification of known and unknown viruses in a plant sample. In the present study, nine putative novel viruses were discovered from public domain transcriptome datasets of five endangered plant species by de novo assembly of reads using CLC and SPAdes followed by BLAST analysis. Of the identified viruses, ten coding-complete and five partial genomic segments were recovered. Based on phylogeny and BLAST analysis, the identified viruses were putatively assigned to various plant viral genera except dactylorhiza hatagirea benylike virus that probably represents a new group of plant virus. The methodology followed can be adopted for the discovery of novel viruses in plant species with little genomic information. Viral genome sequences recovered in the study will serve as a valuable resource for further characterization of identified viruses.
病毒是大量存在的实体，几乎可以感染所有生物体。近年来，下一代测序技术与生物信息学分析广泛应用于鉴定植物样本中的已知和未知病毒。在本研究中，通过 CLC 和 SPAdes 对五个濒危植物物种的公共领域转录组数据集进行从头组装，然后进行 BLAST 分析，从公开的转录组数据中发现了九个假定的新型病毒。在所鉴定的病毒中，回收了十个编码完整和五个部分基因组片段。基于系统发育和 BLAST 分析，所鉴定的病毒被推测属于各种植物病毒属，除了贝母兰似裂绵马病毒，它可能代表了一个新的植物病毒群。所采用的方法可用于具有较少基因组信息的植物物种中新病毒的发现。研究中回收的病毒基因组序列将成为进一步鉴定病毒特征的有价值资源。
