Transcriptional and metabolomic analysis reveal different aromatic amino acid production and potential regulatory mechanisms for two kiwifruit species

Kiwifruit, as a recently domesticated horticultural fruit crop, has substantial economic and nutritional value, particularly its high vitamin C content. In this study, we investigated the different metabolites accumulation in the ripening fruit of two mainly cultivated kiwifruit species <italic>A. chinensis</italic> and <italic>A. eriantha</italic>. A total of 428 metabolites were identified, with low correlation coefficients found in amino acid metabolism, as well as in the metabolism of terpenoids and polyketides between two species, indicating the variations in taste, flavor, and nutritional properties. Furthermore, 115 items were clarified as differentially accumulated metabolites. Based on the Kyoto Encyclopedia of Genes and Genomes pathways enrichment analysis, differentially accumulated metabolites (DAMs) were majorly involved in tryptophan metabolism, biosynthesis of secondary metabolites, pyrimidine metabolism, flavonoid biosynthesis, vitamin B6 metabolism, phenylalanine, tyrosine, and tryptophan biosynthesis. Transcriptome analysis revealed 3,168 upregulated genes and 3,174 downregulated genes, we performed Gene Ontology (GO) enrichment analysis suggesting that differentially expressed genes were associated with the aromatic amino acids (AAAs) family catabolic process, which verified the results of metabolome analysis. Expression patterns of homologous genes of these two kiwifruits participating in AAAs metabolism pathway were compared, key structural genes including TSA1, TSB2, TAA, and TAT showed opposite expression profiles. Additionally, we built a co-expression network to identify multiple transcription factors involved in regulating the AAAs metabolism pathways, predominantly belonging to the MYB and MYB_related families, bHLH family, ERF family, and C2H2 family. Our research provides new perspectives on the accumulation of aromatic amino acids between different kiwifruit species. We proposed the potential transcription factors that regulate the AAAs metabolism pathway. This work offers theoretical support for inventing new more nutritional kiwifruit species by altering specific structural genes and corresponding regulatory elements.