Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran.
Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute, Karaj, Iran.
BMC Genomics. 2024 Jul 30;25(1):736. doi: 10.1186/s12864-024-10649-9.
Rice black-streaked dwarf virus (RBSDV) is an etiological agent of a destructive disease infecting some economically important crops from the Gramineae family in Asia. While RBSDV causes high yield losses, genetic characteristics of replicative viral populations have not been investigated within different host plants and insect vectors. Herein, eleven publicly available RNA-Seq datasets from Chinese RBSDV-infected rice, maize, and viruliferous planthopper (Laodelphax striatellus) were obtained from the NCBI database. The patterns of SNP and RNA expression profiles of expected RBSDV populations were analyzed by CLC Workbench 20 and Geneious Prime software. These analyses discovered 2,646 mutations with codon changes in RBSDV whole transcriptome and forty-seven co-mutated hotspots with high variant frequency within the crucial regions of S5-1, S5-2, S6, S7-1, S7-2, S9, and S10 open reading frames (ORFs) which are responsible for some virulence and host range functions. Moreover, three joint mutations are located on the three-dimensional protein of P9-1. The infected RBSDV-susceptible rice cultivar KTWYJ3 and indigenous planthopper datasets showed more co-mutated hotspot numbers than others. Our analyses showed the expression patterns of viral genomic fragments varied depending on the host type. Unlike planthopper, S5-1, S2, S6, and S9-1 ORFs, respectively had the greatest read numbers in host plants; and S5-2, S9-2, and S7-2 were expressed in the lowest level. These findings underscore virus/host complexes are effective in the genetic variations and gene expression profiles of plant viruses. Our analysis revealed no evidence of recombination events. Interestingly, the negative selection was observed at 12 RBSDV ORFs, except for position 1015 in the P1 protein, where a positive selection was detected. The research highlights the potential of SRA datasets for analysis of the virus cycle and enhances our understanding of RBSDV's genetic diversity and host specificity.
水稻黑条矮缩病毒（RBSDV）是亚洲禾本科一些重要经济作物毁灭性病害的病原体。虽然 RBSDV 导致了高产量损失，但在不同的宿主植物和昆虫介体中，复制病毒群体的遗传特征尚未得到研究。在此，从 NCBI 数据库中获得了 11 个来自中国受 RBSDV 感染的水稻、玉米和带毒飞虱（Laodelphax striatellus）的公开可用的 RNA-Seq 数据集。通过 CLC Workbench 20 和 Geneious Prime 软件分析了预期 RBSDV 群体的 SNP 和 RNA 表达谱模式。这些分析发现，在 RBSDV 全转录本中，有 2646 个具有密码子变化的突变，并且在 S5-1、S5-2、S6、S7-1、S7-2、S9 和 S10 开放阅读框（ORF）的关键区域内有 47 个共突变热点，这些区域负责一些毒力和宿主范围功能。此外，三个联合突变位于 P9-1 的三维蛋白上。受感染的 RBSDV 敏感水稻品种 KTWYJ3 和本地飞虱数据集显示出比其他数据集更多的共突变热点数量。我们的分析表明，病毒基因组片段的表达模式因宿主类型而异。与飞虱不同，S5-1、S2、S6 和 S9-1 ORF 分别在宿主植物中具有最大的读取数；而 S5-2、S9-2 和 S7-2 的表达水平最低。这些发现强调了病毒/宿主复合物在植物病毒的遗传变异和基因表达谱中是有效的。我们的分析没有发现重组事件的证据。有趣的是，除了 P1 蛋白的 1015 位，在 12 个 RBSDV ORF 中观察到了负选择，而在该位置检测到了正选择。该研究强调了 SRA 数据集在分析病毒周期方面的潜力，并增强了我们对 RBSDV 遗传多样性和宿主特异性的理解。
