Abbas Zahid Khorshid, Singh Anjana, Noorani Md Salik, Baig Mirza Sarwar, Alharbi Sulaiman Ali, Mahrous Yussri Moh'd Y, Alnefiei Naif Abdulrhman Zabin, Hassan Mo'awia Mukhtar, Siddiqui Zahid Hameed
Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia.
Plant Molecular Virology Lab, Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard (A Deemed-to-Be University), New Delhi 110062, India.
ACS Omega. 2025 Jul 17;10(29):32433-32443. doi: 10.1021/acsomega.5c04600. eCollection 2025 Jul 29.
Small RNA deep sequencing (sRNA-seq) is a powerful tool for detecting known and novel plant viruses by analyzing virus-derived small RNAs (vsRNAs). In this study, the complete genome of Broad Bean Wilt Virus 2 (BBWV-2) was recovered from leaf samples using sRNA-seq, followed by bioinformatics analysis. The Genome Detective Tool, an online bioinformatics platform, identified both RNA1 (5.952 kb) and RNA2 (3.509 kb) of the BBWV-2 form raw data. RNA1 and RNA2 showed 78.8% and 78.1% nucleotide identity, and 88.2% and 87.4% amino acid identity, respectively, with their corresponding reference sequences. Comparative sequence analysis identified multiple mutations, comprising 8 and 6 indels distributed across the full-length sequences of RNA1 and RNA2, respectively, along with 1027 and 690 single-nucleotide substitutions localized within their coding regions. Analysis of the 5' untranslated regions (UTRs) identified five distinct motifs from both RNAs. Structural modeling suggested that RNA2 exhibits greater flexibility than RNA1, which may influence its biological functions. Phylogenetic analysis placed the Indian isolate within Group I, clustering with isolates from South Korea, China, the USA, and Germany, without clear host or geographic clustering. This study provides the first complete sequences of BBWV-2 RNA1 and RNA2 from India and represents the first global report of its occurrence in . Further, these findings enhance our understanding of the molecular diversity and evolutionary dynamics of BBWV-2.
小RNA深度测序（sRNA-seq）是一种通过分析病毒衍生的小RNA（vsRNAs）来检测已知和新型植物病毒的强大工具。在本研究中，利用sRNA-seq从叶片样本中获得了蚕豆萎蔫病毒2（BBWV-2）的完整基因组，随后进行了生物信息学分析。在线生物信息学平台Genome Detective Tool从原始数据中鉴定出了BBWV-2的RNA1（5.952 kb）和RNA2（3.509 kb）。RNA1和RNA2与其相应参考序列的核苷酸同一性分别为78.8%和78.1%，氨基酸同一性分别为88.2%和87.4%。比较序列分析鉴定出多个突变，其中RNA1和RNA2全长序列分别有8个和6个插入/缺失，其编码区域内分别有1027个和690个单核苷酸替换。对5'非翻译区（UTRs）的分析从两种RNA中鉴定出五个不同的基序。结构建模表明，RNA2比RNA1具有更大的灵活性，这可能会影响其生物学功能。系统发育分析将印度分离株置于第一组，与来自韩国、中国、美国和德国的分离株聚类，没有明显的宿主或地理聚类。本研究提供了来自印度的BBWV-2 RNA1和RNA2的首个完整序列，并首次在全球范围内报道了其在印度的出现情况。此外，这些发现增强了我们对BBWV-2分子多样性和进化动态的理解。
