Metabolomic Profiling of Citrus Grafts Challenged by <i>Phytophthora citrophthora</i> : Using the Same Samples Previously Analyzed for Epigenetic Responses

<i>Phytophthora citrophthora</i> infection severely affects citrus crops, demanding improved diagnostic and control strategies. In a previous study, epigenetic responses, including DNA methylation patterns, were analyzed in grafted citrus plants exposed to this pathogen. Here, we report a complementary metabolomic analysis using the same biological material, stored under cryogenic conditions to preserve chemical integrity. "Pera" sweet orange and "Tahiti" acid lime scions grafted onto contrasting rootstocks were inoculated and reinoculated with <i>P. citrophthora</i>. Untargeted metabolomics via LC-MS/MS and molecular networking revealed infection-induced metabolic shifts, including increased levels of coumarins, flavonoids, and alkaloids potentially involved in plant defense. Sixty-six metabolites were annotated, and their distribution varied according to graft combinations and inoculation regimes. While the chemical profiles provided insights into differential metabolic responses, they did not directly correlate with previously observed DNA methylation patterns. Nonetheless, the results support the use of metabolomics for early detection of gummosis and highlight the value of integrating molecular approaches to guide citrus breeding for disease resistance.