Information theory and machine learning illuminate large‐scale metabolomic responses of Brachypodium distachyon to environmental change

• DOI: 10.1111/tpj.16160
• Publication Date: 2023-03-07T08:42:57Z
• Authors: Elizabeth H. Mahood; Alexandra A. Bennett; Karyn Komatsu; Lars H. Kruse; Vincent Lau; Maryam Rahmati Ishka; Yulin Jiang; Armando Bravo; Katherine Louie; Benjamin P. Bowen; Maria J. Harrison; Nicholas J. Provart; Olena K. Vatamaniuk; Gaurav D. Moghe
• Keywords: Brachypodium distachyon; Brachypodium; Metabolome

Plant responses to environmental change are mediated via changes in cellular metabolomes. However, <5% of signals obtained from liquid chromatography tandem mass spectrometry (LC-MS/MS) can be identified, limiting our understanding how metabolomes under biotic/abiotic stress. To address this challenge, we performed untargeted LC-MS/MS leaves, roots, and other organs Brachypodium distachyon (Poaceae) 17 organ-condition combinations, including copper deficiency, heat stress, low phosphate, arbuscular mycorrhizal symbiosis. We found that both leaf root were significantly affected by the growth medium. Leaf more diverse than metabolomes, but latter specialized responsive change. 1 week deficiency shielded root, not metabolome, perturbation due Machine learning (ML)-based analysis annotated approximately 81% fragmented peaks versus 6% using spectral matches alone. one most extensive validations ML-based peak annotations plants thousands authentic standards, analyzed 37% based on these assessments. Analyzing responsiveness each predicted metabolite class revealed significant perturbations glycerophospholipids, sphingolipids, flavonoids. Co-accumulation further identified condition-specific biomarkers. make results accessible, developed a visualization platform Bio-Analytic Resource for Biology website (https://bar.utoronto.ca/efp_brachypodium_metabolites/cgi-bin/efpWeb.cgi), where perturbed classes readily visualized. Overall, study illustrates emerging chemoinformatic methods applied reveal novel insights into dynamic plant metabolome stress adaptation.