Conserved Changes in the Dynamics of Metabolic Processes during Fruit Development and Ripening across Species      

Abstract

Computational analyses of molecular phenotypes traditionally aim at identifying biochemical components that exhibit differential expression under various scenarios (e.g. environmental and internal perturbations) in a single species. High-throughput metabolomics technologies allow the quantification of (relative) metabolite levels across developmental stages in different tissues, organs, and species. Novel methods for analyzing the resulting multiple data tables could reveal preserved dynamics of metabolic processes across species. The problem we address in this study is 2-fold. (1) We derive a single data table, referred to as a compromise, which captures information common to the investigated set of multiple tables containing data on different fruit development and ripening stages in three climacteric (i.e. peach [Prunus persica] and two tomato [Solanum lycopersicum] cultivars, Ailsa Craig and M82) and two nonclimacteric (i.e. strawberry [Fragaria 3 ananassa] and pepper [Capsicum chilense]) fruits; in addition, we demonstrate the power of the method to discern similarities and differences between multiple tables by analyzing publicly available metabolomics data from three tomato ripening mutants together with two tomato cultivars. (2) We identify the conserved dynamics of metabolic processes, reflected in the data profiles of the corresponding metabolites that contribute most to the determined compromise. Our analysis is based on an extension to principal component analysis, called STATIS, in combination with pathway overenrichment analysis. Based on publicly available metabolic profiles for the investigated species, we demonstrate that STATIS can be used to identify the metabolic processes whose behavior is similarly affected during fruit development and ripening. These findings ultimately provide insights into the pathways that are essential during fruit development and ripening across species.

NMR fingerprinting as a tool to evaluate post-harvest time-related changes of peaches, tomatoes and plums

“…Inappropriate post-harvest storage could reduce greatly shelf life, which is not beneficial for the market (Ansari & Tuteja, 2014). Information on metabolic profiles, derived from different time points (TPs) during post-harvest phase of fruit and vegetables, offers an excellent opportunity to investigate which metabolic processes change and to monitor the transformations due to dynamic processes that involve a complex series of molecular and biochemical pathways (Klie et al, 2014).…”

Biochemical Parameters in Tomato Fruits from Different Cultivars as Functional Foods for Agricultural, Industrial, and Pharmaceutical Uses

“…Therefore, in order to speed up the ripening of fruit, ethylene gas is employed. The action of ethylene helps to ripen tomatoes within 4-6 days, under the same conditions without ethylene gas fruit maturation time is nearly three times longer [73,74].…”

Applying the Solanaceae Strategies to Strawberry Crop Improvement

“…To cite just a few examples: tomato fruit imports sucrose while strawberry fruit imports both sucrose and sorbitol, sugars can be transiently stored as starch in tomato but not in strawberry, and profiles of volatile organic compounds differ markedly between the two species. To cope with these discrepancies, new computational analyses, such as STATIS, which combines principal component analysis and pathway over-enrichment analysis [63], have been successfully used to identify the metabolic processes whose behavior is similarly affected during fruit development and ripening in tomato and strawberry.…”