Exploiting Natural Variation in Tomato to Define Pathway Structure and Metabolic Regulation of Fruit Polyphenolics in the Lycopersicum Complex

Mol Plant. 2020 Jul 6;13(7):1027-1046. doi: 10.1016/j.molp.2020.04.004. Epub 2020 Apr 16.


While the structures of plant primary metabolic pathways are generally well defined and highly conserved across species, those defining specialized metabolism are less well characterized and more highly variable across species. In this study, we investigated polyphenolic metabolism in the lycopersicum complex by characterizing the underlying biosynthetic and decorative reactions that constitute the metabolic network of polyphenols across eight different species of tomato. For this purpose, GC-MS- and LC-MS-based metabolomics of different tissues of Solanum lycopersicum and wild tomato species were carried out, in concert with the evaluation of cross-hybridized microarray data for MapMan-based transcriptomic analysis, and publicly available RNA-sequencing data for annotation of biosynthetic genes. The combined data were used to compile species-specific metabolic networks of polyphenolic metabolism, allowing the establishment of an entire pan-species biosynthetic framework as well as annotation of the functions of decoration enzymes involved in the formation of metabolic diversity of the flavonoid pathway. The combined results are discussed in the context of the current understanding of tomato flavonol biosynthesis as well as a global view of metabolic shifts during fruit ripening. Our results provide an example as to how large-scale biology approaches can be used for the definition and refinement of large specialized metabolism pathways.

Keywords: Solanum lycopersicum; gene discovery; natural diversity; pathway elucidation; secondary metabolism; wild accessions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatography, Liquid
  • Flavonoids / metabolism
  • Fruit / growth & development
  • Fruit / metabolism*
  • Gas Chromatography-Mass Spectrometry
  • Gene Expression Profiling
  • Genetic Variation
  • Glycosyltransferases / metabolism
  • Lycopersicon esculentum / genetics
  • Lycopersicon esculentum / metabolism*
  • Mass Spectrometry
  • Metabolic Networks and Pathways
  • Metabolomics
  • Molecular Sequence Annotation
  • Polyphenols / metabolism*
  • Species Specificity


  • Flavonoids
  • Polyphenols
  • Glycosyltransferases