Main conclusionNicotiana tabacumexhibits recovery response towards tomato leaf curl Gujarat virus. Transcriptome analysis revealed the differential expression of defense-related genes. Genes encoding for cysteine protease inhibitor, hormonal- and stress-related to DNA repair mechanism are found to be involved in the recovery process.AbstractElucidating the role of host factors in response to viral infection is crucial in understanding the plant host–virus interaction.Begomovirus, a genus in the familyGeminiviridae,is reported throughout the globe and is known to cause serious crop diseases. Tomato leaf curl Gujarat virus (ToLCGV) infection inNicotiana tabacumresulted in initial symptom expression followed by a quick recovery in the systemic leaves. Transcriptome analysis using next-generation sequencing (NGS) revealed a large number of differentially expressed genes both in symptomatic as well as recovered leaves when compared to mock-inoculated plants. The virus infectedN. tabacumresults in alteration of various metabolic pathways, phytohormone signaling pathway, defense related protein, protease inhibitor, and DNA repair pathway. RT-qPCR results indicated thatGermin-like protein subfamily T member 2(NtGLPST), Cysteine protease inhibitor 1-like (NtCPI), Thaumatin-like protein(NtTLP), Kirola-like(NtKL), andEthylene-responsive transcription factor ERF109-like(NtERTFL) were down-regulated in symptomatic leaves when compared to recovered leaves of ToLCGV-infected plants. In contrast, theAuxin-responsive protein SAUR71-like(NtARPSL) was found to be differentially down-regulated in recovered leaves when compared to symptomatic leaves and the mock-inoculated plants. Lastly,Histone 2X protein like(NtHH2L) gene was found to be down-regulated, whereasUncharacterized(NtUNCD) was up-regulated in both symptomatic as well as recovered leaves compared to the mock-inoculated plants. Taken together, the present study suggests potential roles of the differentially expressed genes that might govern tobacco’s susceptibility and/or recovery response towards ToLCGV infection.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00425-023-04182-4.