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Background   Ananas comosus  var.  bracteatus  is a colorful plant used as a cut flower or landscape ornamental. The unique foliage color of this plant includes both green and red leaves and, as a trait of interest, deserves investigation. In order to explore the pigments behind the red section of the chimeric leaves, the green and red parts of chimeric leaves of  Ananas comosus  var.  bracteatus  were sampled and analyzed at phenotypic, cellular and molecular levels in this study.    Results  The CIELAB results indicated that the a* values and L* values samples had significant differences between two parts. Freehand sections showed that anthocyanin presented limited accumulation in the green leaf tissues but obviously accumulation in the epidermal cells of red tissues. Transcriptomic and metabolomic analyses were performed by RNA-seq and LC-ESI-MS/MS. Among the 508 identified metabolites, 10 kinds of anthocyanins were detected, with 6 significantly different between the two samples. The cyanidin-3,5-O-diglucoside content that accounts for nearly 95.6% in red samples was significantly higher than green samples. RNA-Seq analyses showed that 11 out of 40 anthocyanin-related genes were differentially expressed between the green and red samples. Transcriptome and metabolome correlations were determined by nine quadrant analyses, and 9 anthocyanin-related genes, including  MYB5  and  MYB82 , were correlated with 7 anthocyanin-related metabolites in the third quadrant in which genes and metabolites showing consistent change. Particularly, the PCCs between these two MYB genes and cyanidin-3,5-O-diglucoside were above 0.95.    Conclusion  Phenotypic colors are closely related to the tissue structures of different leaf parts of  Ananas comosus  var.  bracteatus , and two MYB transcription factors might contribute to differences of anthocyanin accumulation in two parts of  Ananas comosus  var.  bracteatus  chimeric leaves. This study lay a foundation for further researches on functions of MYBs in  Ananas comosus  var.  bracteatus  and provides new insights to anthocyanin accumulation in different parts of chimeric leaves.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07642-x.

Metabolome and transcriptome profiling reveals anthocyanin contents and anthocyanin-related genes of chimeric leaves in Ananas comosus var. bracteatus