Highlight 27 Induced silencing of HSP90C gene caused the upregulation of stress-responsive 28 genes and the activation of innate immune response, which resulted in the 29 chlorosis development accompanying cell death. 30 31 Abstract 32 RNA-seq analysis of a transgenic tobacco plant, i-hpHSP90C, in which 33 chloroplast HSP90C genes can be silenced in an artificially inducible manner 34 resulting in the development of chlorosis, revealed the up-and down-regulation 35 of 2746 and 3490 genes, respectively. Gene Ontology analysis of these 36 differentially expressed genes indicated the upregulation of ROS-responsive 37 genes, the activation of the innate immunity and cell death pathways, and the 38 downregulation of genes involved in photosynthesis, plastid organization, and cell 39 cycle. Cell death was confirmed by trypan blue staining and electrolyte leakage 40 assay and the H2O2 production by diaminobenzidine staining. The upregulation 41 of ER stress-responsive genes suggested the interplay between ER protein 42 quality control and chloroplast or immune response. The results collectively 43 suggest that the reduced levels of HSP90C chaperone leads the plant to develop 44 chlorosis primarily through the global downregulation of chloroplast and 45 photosynthesis-related genes and additionally through the light-dependent 46 production of ROS, followed by the activation of immune responses including the 47 cell death. 48 49 Transcriptome 52 53 Abbreviations 54 CPRGs, Chloroplast and photosynthesis-related genes; DEGs, Differentially 55 expressed genes; Dex, Dexamethasone; hp-RNA, Hairpin RNA; HSP90C, 56 Chloroplast heat shock protein 90; ROS, Reactive oxygen species; siRNA, Small 57 interfering RNA.58 3