Integrated metabolomic and transcriptomic analysis revealed the capsanthin biosynthesis and sequestration in processing type red pepper (Capsicum annuum var. conoides)

Fruit color is a key quality trait in processing-type red pepper. This study investigated the metabolic and transcriptional mechanisms underlying capsanthin accumulation and pigment sequestration in Yanjiao pepper cultivars of Capsicum annuum var. conoides. Ten Yanjiao cultivars were evaluated using colorimetric phenotyping and targeted carotenoid metabolomics, and four representative cultivars, Yj425, Yj485, Yj518, and Yj666, were selected for comparative transcriptome analysis. The transcriptomic data were used to identify differentially expressed genes related to carotenoid biosynthesis, carotenoid cleavage, ABA metabolism, and transcriptional regulation. Processed RNA-seq data, including gene count and FPKM expression matrices and downstream analysis results, are provided to support the study of capsanthin biosynthesis, carotenoid esterification, and pigment sequestration in red pepper fruits.