The Crucial Role of Mitochondrial/chloroplast-Related Genes in Viral Genome Replication and Host Defense: Integrative Systems Biology Analysis in Plant-Virus Interaction

Amir Ghaffar Shahriari^1*Aminallah Tahmasebi^2*Mohamad Hamed Ghodoum Parizipour³Zahra Soltani⁴Ahmad Tahmasebi⁴Muhammad Shafiq Shahid^5*

• ¹Higher Education Center of Eghlid, Eghlid, Iran
• ²Minab Higher Education Center, University of Hormozgan, Bandar Abbas, Hormozgān, Iran
• ³Agricultural Sciences and Natural Resources University of Khuzestan, Mollasani, Khuzestan, Iran
• ⁴Shiraz University, Shiraz, Fars, Iran
• ⁵Sultan Qaboos University, Muscat, Oman

Plant viruses participate as biotrophic parasites in complex interactions with their hosts, resulting through in the regulation of a diverse range of chloroplast/mitochondriamitochondrial-related genes that are essential for mediating immune responses. In this study, integrative systems biology approaches were applied to identify chloroplast/mitochondrialmitochondrion genes during viral infections caused by a wide number of viruses in Arabidopsis thaliana, tobacco (Nicotiana tabacum L.), and rice (Oryza sativa L.). TheseThe findings indicated that 1.5% of the DEGs were common between Arabidopsis/tobacco and Arabidopsis/rice, whereas 0.1% of the DEGs were shared among all species. Approximately 90% of common DEGs are uniquely associated with chloroplasts and mitochondria in the host defense against viral infection and replication. The functions of WRKY, NAC, and MYB transcription factors in imparting resistance against to viral infections could can be established. Promoter analysis revealed that the AP2/EREBP, DOF, and C2H2 zinc finger factors included the most frequent binding sites and played a more important role in plant-viral interactions. Comparative analysis revealed several miRNAs with defensive functions including miRNA156, miRNA160, and miRNA169. The PPI network revealed several key hub genes mostly related to chloroplasts/mitochondria, including