MicroTom Metabolic Network: Rewiring Tomato Metabolic Regulatory Network throughout the Growth Cycle

Abstract

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Ascophyllum nodosum Based Extracts Counteract Salinity Stress in Tomato by Remodeling Leaf Nitrogen Metabolism

“…Though these data are in agreement with those obtained by Flores et al [ 52 ] and Yin et al [ 53 ], they should be considered in light of the fact that MicroTom plants have not only mutations in the DWARF and self-pruning genes, but also a third mutation, responsible for internode length, which may have pleiotropic effects on metabolism of the fruits [ 52 , 54 ]. The complexity of the metabolic landscape across tissues and growth stages has been recently addressed by Li et al [ 55 ] in MicroTom, indicating that this model species is a useful resource to study metabolic regulatory networks in tomato.…”

Genome-wide characterization and expression profiling of MAPK cascade genes in Salvia miltiorrhiza reveals the function of SmMAPK3 and SmMAPK1 in secondary metabolism

“…Coexpression/coregulation cluster analysis was performed for samples from 12 different tissues or time point by MeV (Version 4.9) [87]. The normalized expression values of the genes were calculated by dividing their expression levels from different tissues or time points.…”

From Fruit Omics to Fruiting Omics: Systematic Studies of Tomato Fruiting by Metabolic Networks

“…To address these points, elucidation of the spatio-temporal metabolic shift in fleshy fruiting during the growth cycle in a whole plant is required. In the study by Li et al (2020) reported in this issue, the authors carried out a systematic integrative omics approach involving transcriptomics and metabolomics studies with 20 different types of MicroTom tomato samples in a series of developmental stages of the plant and fruit to illustrate the spatio-temporal metabolic shift. With co-efficient network analysis derived from high-resolution transcriptomic and metabolomic data, the authors succeeded in clarifying a metabolic regulatory network (MicroTom Metabolic Network, MMN) in tomato (Figure 1).…”

“…Importantly, because MMN network analysis contains all gene expressions and some part of the major primary metabolism, further metabolic regulatory networks between primary and specialized metabolism can be clarified. The study by Li et al (2020) provides novel insights from fruit omics to ''fruiting'' omics, which elucidates the spatio-temporal metabolic network during the fruiting process at plant level; these could be extremely useful in designing crop breeding of fleshy fruit crops.…”

“…However, these multi-omics data are sometimes difficult to use for detecting precise metabolic regulatory networks, because specialized metabolism is generally regulated by the plant growth cycle, organ and tissue specificity, stress induction, and nutritional limitations as well as metabolic remobilization of the primary metabolites. As presented in the work by Li et al (2020) published in this issue, metabolic regulatory networks throughout the growth cycle of plants and fruits provide systematic functional genomics of the novel transcription factors that regulate specialized metabolism in a tissue-specific manner. In addition to the current omics-integrative fruit omics approaches, this plant-wise omics approach will be a highly powerful tool for the discovery of novel insights from fruit omics to ''fruiting'' omics and elucidation of the spatio-temporal metabolic network during the fruiting process at plant level.…”