Transcriptomic analysis of changes in Citrus x microcarpa gene expression post Xanthomonas citri subsp. citri infection

Citrus canker (CC) is an economically important bacterial disease caused by Xanthomonas citri subsp. citri (Xcc). There is variability in resistance to CC among Citrus species. Previous transcriptomic studies have shown that Xcc downregulates biosynthesis of secondary metabolites at early stages of infection in susceptible citrus. However, in partially resistant calamondin (Citrus x microcarpa), increased secondary metabolite production has been reported post Xcc inoculation. We analyzed the calamondin transcriptome and discovered 3318 and 7740 differentially expressed (DE) genes between Xcc-inoculated and control samples at 2- and 5-days post inoculation (dpi), respectively. Among the DE genes, the phenylpropanoid biosynthesis (PPB) pathway, a major secondary metabolite synthesis pathway, was upregulated at early stages (2 dpi) of Xcc infection. Furthermore, in contrast to previous studies of susceptible Citrus species, pathways related to a resistance response (such as plant-pathogen interaction and MAPK signaling pathway) were upregulated whereas the pathways related to a susceptible response (such as auxin and gibberellin biosynthesis and cell wall degradation) were not significantly upregulated in calamondin. The transcriptomic regulation of plant hormone biosynthesis in calamondin was also different from the susceptible citrus. Thus, PPB may represent the principal biochemical pathway underlying CC resistance.