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<p>Metabolomic analyses of chilli genotypes revealed significant metabolic shifts during fruit ripening and pigmentation. Metabolite profiling identified 1137 compounds from the different metabolite classes. Ripening was characterized by increased fatty acyls and sugars while decreased alkaloids. The metabolites chlorophyll-a, chlorophyllide b, erucic acid and pyrophaeophorbide-a identified as biomarker for vegetative phase while fucosterol, terpinolene, stachyose, agrimoniin and camphene for ripening phase. Each pigmented chilli exhibited unique enrichments in specific metabolites: green chillies in alkaloids (16-Hydroxytabersonine) and steroids (6-Deoxoteasterone); red chillies in terpenoids (solavetione), orange chillies in amino acids (proline and tryptophan) and flavonoids (naringin); and black chillies in vitamins (alpha-tocopherol and retinol). Carotenoid composition of chilli differed with fruit color: green chilli with capsicoside C2, red chilli with capsanthin, orange chilli with capsanthin-3,6-epoxide and black chilli with zeinoxanthin.Transcriptome analysis identified 4606 differentially expressed genes during ripening, involved in cell wall degradation, carotenoids, abscisic acid and ethylene synthesis. Key transcription factor <i>RIN</i> (NCBI gene ID 107847473), encoded by MADS-box protein04g005320, was found to be expressed in ripening, regulating ripening-related genes. KEGG pathway analysis indicate that ripening phase characterized by upregulation of genes related to the biosynthesis of secondary metabolites, cutin, suberine and wax biosynthesis, tropane, piperidine and pyridine alkaloid biosynthesis, porphyrin metabolism, carotenoid biosynthesis, and monoterpenoid biosynthesis. Integrated transcriptome-metabolome identified involvement of genes in carotenoid biosynthesis, flavonoid biosynthesis and porphyrin and chlorphyll metabolism regulating ripining and pigmentation in chilli.</p> Graphical Abstract <p></p>

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Integrated Transcriptome and Metabolome Identifies Novel Genes and Metabolites Associated With Ripening and Pigmentation in Chilli Pepper (Capsicum Annuum L.)

  • 期刊论文

  • 发表日期：

    2026年1月28日

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  • Anil A. Hake,
  • Partha Saha,
  • B. K. Singh,
  • Prabhakara Rao Kudupudi,
  • Madhavilatha Kommana,
  • Sarala Kesamsetty,
  • Sheshu Madhav Maganti

摘要

Metabolomic analyses of chilli genotypes revealed significant metabolic shifts during fruit ripening and pigmentation. Metabolite profiling identified 1137 compounds from the different metabolite classes. Ripening was characterized by increased fatty acyls and sugars while decreased alkaloids. The metabolites chlorophyll-a, chlorophyllide b, erucic acid and pyrophaeophorbide-a identified as biomarker for vegetative phase while fucosterol, terpinolene, stachyose, agrimoniin and camphene for ripening phase. Each pigmented chilli exhibited unique enrichments in specific metabolites: green chillies in alkaloids (16-Hydroxytabersonine) and steroids (6-Deoxoteasterone); red chillies in terpenoids (solavetione), orange chillies in amino acids (proline and tryptophan) and flavonoids (naringin); and black chillies in vitamins (alpha-tocopherol and retinol). Carotenoid composition of chilli differed with fruit color: green chilli with capsicoside C2, red chilli with capsanthin, orange chilli with capsanthin-3,6-epoxide and black chilli with zeinoxanthin.Transcriptome analysis identified 4606 differentially expressed genes during ripening, involved in cell wall degradation, carotenoids, abscisic acid and ethylene synthesis. Key transcription factor RIN (NCBI gene ID 107847473), encoded by MADS-box protein04g005320, was found to be expressed in ripening, regulating ripening-related genes. KEGG pathway analysis indicate that ripening phase characterized by upregulation of genes related to the biosynthesis of secondary metabolites, cutin, suberine and wax biosynthesis, tropane, piperidine and pyridine alkaloid biosynthesis, porphyrin metabolism, carotenoid biosynthesis, and monoterpenoid biosynthesis. Integrated transcriptome-metabolome identified involvement of genes in carotenoid biosynthesis, flavonoid biosynthesis and porphyrin and chlorphyll metabolism regulating ripining and pigmentation in chilli.

Graphical Abstract