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.

虽然植物的主要代谢途径的结构通常在物种间得到很好的定义和高度保守，但是定义专门代谢的那些结构的特征却不那么清晰，并且在物种间变化更大。在这项研究中，我们通过表征潜在的生物合成和装饰性反应，构成了八种不同番茄中多酚的代谢网络，研究了番茄白果复合物中的多酚代谢。为此，番茄和野番茄物种不同组织的基于GC-MS和LC-MS的代谢组学与交叉杂交微阵列数据的评估（用于基于MapMan的转录组分析）和公开可用的RNA测序数据（用于注释生物合成基因）协同进行。合并后的数据用于编译多酚代谢的物种特异性代谢网络，从而可以建立整个泛物种生物合成框架，并注释涉及类黄酮途径代谢多样性的装饰酶的功能。在对番茄黄酮生物合成的当前理解以及果实成熟过程中新陈代谢变化的整体观点的背景下讨论了合并的结果。