Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
Institute of Biological Sciences, Faculty of Natural and Applied Sciences, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan 64200, Pakistan.
Viruses. 2023 Feb 9;15(2):486. doi: 10.3390/v15020486.
Cassava mosaic disease (CMD) is caused by several divergent species belonging to the genus () transmitted by the whitefly cryptic species group. In India and other parts of Asia, the Indian cassava mosaic virus-Kerala (ICMV-Ker) is an emergent begomovirus of cassava causing damage that results in reduced yield loss and tuber quality. Double-stranded RNA-mediated interference (RNAi) is an evolutionary conserved mechanism in eukaryotes and highly effective, innate defense system to inhibit plant viral replication and/or translation. The objective of this study was to identify and characterize cassava genome-encoded microRNAs (mes-miRNA) that are predicted to target ICMV-Ker ssDNA-encoded mRNAs, based on four in silico algorithms: miRanda, RNA22, Tapirhybrid, and psRNA. The goal is to deploy the predicted miRNAs to trigger RNAi and develop cassava plants with resistance to ICMV-Ker. Experimentally validated mature cassava miRNA sequences ( = 175) were downloaded from the miRBase biological database and aligned with the ICMV-Ker genome. The miRNAs were evaluated for base-pairing with the cassava miRNA seed regions and to complementary binding sites within target viral mRNAs. Among the 175 locus-derived mes-miRNAs evaluated, one cassava miRNA homolog, mes-miR1446a, was identified to have a predicted miRNA target binding site, at position 2053 of the ICMV-Ker genome. To predict whether the cassava miRNA might bind predicted ICMV-Ker mRNA target(s) that could disrupt viral infection of cassava plants, a cassava locus-derived miRNA-mRNA regulatory network was constructed using Circos software. The in silico-predicted cassava locus-derived mes-miRNA-mRNA network corroborated interactions between cassava mature miRNAs and the ICMV-Ker genome that warrant in vivo analysis, which could lead to the development of ICMV-Ker resistant cassava plants.
木薯花叶病（CMD）是由几种属于 （）属的不同种引起的，由粉虱隐种组传播。在印度和亚洲其他地区，印度木薯花叶病毒-喀拉拉邦（ICMV-Ker）是一种新兴的木薯曲叶病毒，会造成损害，导致产量下降和薯块质量降低。双链 RNA 介导的干扰（RNAi）是真核生物中进化保守的机制，是一种高效的先天防御系统，可抑制植物病毒的复制和/或翻译。本研究的目的是根据四个计算机算法：miRanda、RNA22、Tapirhybrid 和 psRNA，鉴定和表征预测靶向 ICMV-Ker ssDNA 编码 mRNA 的木薯基因组编码 microRNAs（mes-miRNA）。目标是利用预测的 miRNAs 触发 RNAi，并开发对 ICMV-Ker 具有抗性的木薯植物。从 miRBase 生物数据库中下载了经实验验证的成熟木薯 miRNA 序列（n = 175），并与 ICMV-Ker 基因组进行了比对。评估了 miRNA 与木薯 miRNA 种子区域的碱基配对情况，以及与靶病毒 mRNA 内互补结合位点的情况。在所评估的 175 个基因座衍生的 mes-miRNAs 中，鉴定出一个木薯 miRNA 同源物 mes-miR1446a，在 ICMV-Ker 基因组的 2053 位有一个预测的 miRNA 靶结合位点。为了预测木薯 miRNA 是否可能与预测的 ICMV-Ker mRNA 靶标结合，从而破坏木薯植物的病毒感染，使用 Circos 软件构建了一个基于木薯基因座的 miRNA-mRNA 调控网络。计算机预测的木薯基因座衍生的 mes-miRNA-mRNA 网络证实了木薯成熟 miRNA 与 ICMV-Ker 基因组之间的相互作用，这需要进行体内分析，这可能导致开发出对 ICMV-Ker 具有抗性的木薯植物。
