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Background  Anthocyanin, chlorophyll, and carotenoid pigments are widely distributed in plants, producing various colors. Ornamental kale ( Brassica oleracea var. acephala  DC) which has colorful inner leaves is an ideal plant to explore how these three pigments contribute to leaf color. The molecular mechanisms of the coloration in ornamental kale could provide reference for exploring the mechanisms of pigmentation in other plants.    Results  In this study, we sequenced the transcriptome and determined the pigment contents of an unusual cultivar of ornamental kale with three different types of leaf coloration: pink (C3), light pink (C2), and variegated pink–green (C1). A total of 23,965 differentially expressed genes were detected in pairwise comparisons among the three types of leaves. The results indicate that  Bo9g058630  coding dihydroflavonol 4–reductase (DFR) and  Bo3g019080  coding shikimate O–hydroxycinnamoyltransferase (HCT) acted in anthocyanin biosynthesis in pink leaves.  Bo1g053420  coding pheophorbidase (PPD) and  Bo3g012430  coding 15–cis–phytoene synthase (crtB) were identified as candidate genes for chlorophyll metabolism and carotenoid biosynthesis, respectively. The transcription factors TT8, MYBL2, GATA21, GLK2, and RR1 might participate in triggering the leaf color change in ornamental kale. Anthocyanin content was highest in C3 and lowest in C1. Chlorophyll and carotenoid contents were lowest in C2 and highest in C1.    Conclusions  Based on these findings, we suspected that the decrease in anthocyanin biosynthesis and the increase in chlorophyll and carotenoid biosynthesis might be the reason for the leaf changing from pink to variegate pink–green in this unusual cultivar. Our research provides insight into the molecular mechanisms of leaf coloration in ornamental kale, contributing to a theoretical foundation for breeding new varieties.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07785-x.

Simultaneous changes in anthocyanin, chlorophyll, and carotenoid contents produce green variegation in pink–leaved ornamental kale