Genomics-based annotations help unveil the molecular composition of edible plants

Given the important role food plays in health and well-being, the past decades have seen considerable experimental efforts dedicated to mapping the chemical composition of food ingredients. As the composition of raw food is genetically predetermined, here we ask, to what degree can we rely on genome-associated metabolic annotations to predict the chemical composition of natural ingredients? To that end, we developed an approach to unveil the chemical composition of 75 edible plants genomes, finding that genome-associated functional annotations substantially increase the number of compounds linked to specific plants. To account for the gap between the metabolic potential represented by functional annotations and the compounds likely to be accumulated and detected experimentally, we employed a predictive thermodynamic feasibility approach to systematically identify compounds that are likely to accumulate in plants. To quantify the accuracy of our predictions, we performed untargeted metabolomics on 13 plants, allowing us to experimentally confirm the detectability of the predicted compounds. For example, we observed 59 potentially novel compounds predicted and experimentally detected in corn. Our study shows that the application of genome-associated functional annotations can lead to an integrated metabologenomics platform capable of unveiling the chemical composition of edible plants and the biochemical pathways responsible for the observed compounds. Author SummaryNutrition and well-being take a central role in todays high pace life, but how much do we really know about the food we eat? Here, we harness existing metabolic knowledge encrypted in staple food ingredients genome to help us explore the composition of raw edible plants. We first show the benefit and value of looking into genome-associated functional annotations on a wide scale. Next, we rely on new experimental data to develop a framework that helps us reveal new, potentially bioactive compounds in staple food ingredients. This has significance in, first, extending current food composition knowledge and second in discovering newly detected bioactive compounds, shedding light on the potential impacts of common food ingredients beyond their nutritional value as described in food labels. Finally, we show that staple foods that are already included in our daily diets might have the potential to contribute to our well-being.