Multi-Omics-Based Discovery of Plant Signaling Molecules

Abstract

Plants produce numerous structurally and functionally diverse signaling metabolites, yet only relatively small fractions of which have been discovered. Multi-omics has greatly expedited the discovery as evidenced by increasing recent works reporting new plant signaling molecules and relevant functions via integrated multi-omics techniques. The effective application of multi-omics tools is the key to uncovering unknown plant signaling molecules. This review covers the features of multi-omics in the context of plant signaling metabolite discovery, highlighting how multi-omics addresses relevant aspects of the challenges as follows: (a) unknown functions of known metabolites; (b) unknown metabolites with known functions; (c) unknown metabolites and unknown functions. Based on the problem-oriented overview of the theoretical and application aspects of multi-omics, current limitations and future development of multi-omics in discovering plant signaling metabolites are also discussed.

Multiomics Analysis Reveals the Genetic Basis of Volatile Terpenoid Formation in Oolong Tea

“…Previous studies using weighted gene coexpression network analysis (WGCNA) have aimed to identify transcription factors (TFs) that may regulate the expression of genes involved in biosynthetic pathways of plant secondary metabolites. However, these studies have often overlooked whether these TFs can bind to the promoter regions of genes involved in metabolite biosynthesis. ,, Our PanTFBS tool allowed us to identify TFBS variations in gene modules in WGCNA based on the pangenome.…”

Making small molecules in plants: A chassis for synthetic biology‐based production of plant natural products

“…Considering the tight endogenous regulation in plants, both plant native and artificially synthesized regulators are in urgent need of being identified or designed. An integrative approach to combine multiomics (genomic, transcriptomic, metabolomics) data, and applying machine-learning approaches can aid in uncovering novel genes encoding enzymes, transporters, and regulators involved in plant specialized metabolism (Luo et al, 2022). Metabolome genome-wide association study (mGWAS) targeting large populations, linking global metabolites changes to genetic variants (single-nucleotide polymorphisms (SNPs)), could also enable the discovery of key genes in the biosynthetic pathway.…”

“…With more bioactive compounds and associated genes being characterized using multiomics techniques (Luo et al, 2022), the scope for plants as a unique platform for engineering and the production of high-value compounds will expand gradually. The discovery of bioactive phytochemicals in plants and their functions in promoting plant health can potentially contribute to sustainable agriculture in many different aspects, especially in terms of weathering biotic and abiotic stresses.…”

Functions and biosynthesis of plant signaling metabolites mediating plant–microbe interactions

“…The attention is gradually shifting from understanding their impacts on plant–microbe interactions at isolated single species level to more systematic multispecies and population levels, partially as a result of the advancement of multiomics techniques. 301 After all, plants grown in the fields encounter an enormous number of microbes and the way they interact with the microbiota is closely associated with plant fitness. 7 What the functions of microbiota are in maintaining plant health and how plant natural products contribute to the establishment of a beneficial plant microbiota are emerging questions that lay ahead.…”