Saeed Paniz Abdollahi, Ghorbani Abozar, Rostami Mahsa, Ashrafi-Dehkordi Elham
Department of Plant Protection, Faculty of Agriculture, University of Zanjan, Zanjan, Iran.
Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj, Iran.
Sci Rep. 2025 Jul 1;15(1):21025. doi: 10.1038/s41598-025-07334-6.
Bacterial leaf streak disease (BLS) is caused by Xanthomonas oryzae pv. oryzicola (Xoc), which represents a significant threat to rice (Oryza sativa) crops. The objective of the present work is to identify the genetic regions and signaling pathways that contribute to the infection process caused by Xoc. The study employs RNA-Seq data to investigate gene co-expression networks, with a particular emphasis on essential genes involved in ribosome production. Furthermore, the research investigates codon usage patterns in the context of gene expression and translation processes. The findings highlight the importance of the apoplastic pathway, which plays a crucial role in the infection of plants through the breach of the epidermis in their aerial structures. Bioinformatics tools, including STRING, KEGG, Tomtom, and GoMo, were employed to conduct differential gene expression analyses, pathway enrichment studies, and network construction, thereby facilitating the identification of essential genes involved in stress response and disease resistance. Network cluster analysis corroborated the findings of the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) survey. In total, 16 hub genes were identified through integrated PPI network and CytoHubba analysis, including RPL3B (log2FC = 4.69) and P0650C03.25 (log2FC = 4.4), both involved in ribosomal biogenesis. GO and KEGG pathway enrichment revealed significant activation of ribosome biogenesis, secondary metabolite biosynthesis, and stress-related transcription factors. Promoter motif analysis identified conserved elements associated with transcriptional regulation and water stress responses. Furthermore, key miRNAs (e.g., miR5075 and miR1848) targeting hub genes were predicted. Codon usage analysis showed that several hub genes exhibited high CAI and low ENC, indicating codon optimization under bacterial infection. These findings offer candidate targets for improving rice resistance to BLS. The objective is to furnish insights that can inform the development of efficacious preventive strategies.
细菌性条斑病（BLS）由水稻条斑病菌（Xanthomonas oryzae pv. oryzicola，Xoc）引起，对水稻（Oryza sativa）作物构成重大威胁。本研究的目的是确定导致Xoc感染过程的遗传区域和信号通路。该研究利用RNA测序数据来研究基因共表达网络，特别关注参与核糖体产生的必需基因。此外，该研究还在基因表达和翻译过程的背景下研究密码子使用模式。研究结果突出了质外体途径的重要性，该途径在植物地上结构的表皮被破坏后感染植物的过程中起着关键作用。使用包括STRING、KEGG、Tomtom和GoMo在内的生物信息学工具进行差异基因表达分析、通路富集研究和网络构建，从而有助于识别参与应激反应和抗病性的必需基因。网络聚类分析证实了基因本体论和京都基因与基因组百科全书（KEGG）调查的结果。通过整合蛋白质-蛋白质相互作用（PPI）网络和CytoHubba分析，总共鉴定出16个枢纽基因，包括RPL3B（log2倍变化=4.69）和P0650C03.25（log2倍变化=4.4），二者均参与核糖体生物合成。基因本体论和KEGG通路富集显示核糖体生物合成、次生代谢物生物合成和应激相关转录因子有显著激活。启动子基序分析确定了与转录调控和水分胁迫反应相关的保守元件。此外，还预测了靶向枢纽基因的关键微小RNA（如miR5075和miR1848）。密码子使用分析表明，几个枢纽基因表现出高密码子适应指数（CAI）和低有效密码子数（ENC），表明在细菌感染下密码子优化。这些发现为提高水稻对BLS的抗性提供了候选靶点。目的是提供可指导有效预防策略制定的见解。
