In silico analysis of the transcriptional defense dynamics of resistant and susceptible citrus varieties against Xanthomonas citri subsp. citri

Abstract

Type A bacterial canker, caused by Xanthomonas citri subsp. citri (Xcc), affects all commercial citrus plants and threatens crops worldwide. Although kumquat (Fortunella sp.) cultivars are resistant and acid lime ‘Galego’ (Citrus aurantifolia) are susceptible to disease development, the mechanisms related to this differential tolerance are not fully understood. In this work, using a transcriptome (RNA-seq) databank and bioinformatics analysis, the transcriptional response between resistant and susceptible citrus plants infected by Xcc were compared at three different time points (24 hai, 48 hai, and 72 hai—hours after Xcc inoculation). We combined computational tools for the functional annotation and metabolic pathways analysis to transcriptome dynamics of both cultivars. Remarkable differences were found between the two groups of plants. Many genes related to pathogen recognition receptors (PRR and NLR), pathogenesis-related (PR) proteins, cell wall strengthening, oxidative burst, and enriched metabolic pathways such as plant-pathogen interaction, MAPK signaling, and phenylpropanoids biosynthesis were found to be significantly (p-value < 0.05) up-regulated at all three-time points of the kumquat samples. By contrast, the response of susceptible acid lime was delayed, with the activation genes involved in defense occurring only at 48 hai, and disappearing at 72 hai. The comprehensive analysis described here will provide a resource for improving our knowledge about the citrus defense against canker, which may help design new control methods for the disease.