Objective To systematically identify the R2R3-MYB transcription factor family in Xuanmugua(Chaenomeles speciose) based on transcriptomic and metabolomic data, and to screen key candidate genes potentially involved in the regulation of flavonoid biosynthesis. Methods Transcriptome and metabolome databases were constructed using different tissues of C. speciosa. The R2R3-MYB transcription factor family was systematically identified based on full-length transcriptome data. Subsequently, the sequence characteristics, phylogenetic relationships, and tissue-specific expression patterns of these genes were analyzed. Results A total of 31 R2R3-type CsMYB genes were identified from the transcriptome data of C. speciosa. Based on phylogenetic analysis with Ninanjie(Arabidopsis thaliana) and Yueji (Rosa chinensis), we classified these genes into 11 subfamilies. Members within the same subfamily showed similar conserved motifs and gene structures. Flavonoids, including catechin and epicatechin, were significantly enriched in the pulp and peel. The 31 CsMYB genes exhibited differential expression patterns across various tissues of C. speciosa, among which 14 CsMYB genes, such as CsMYB1, CsMYB21, and CsMYB25, were highly expressed in the peel or pulp. Further correlation analysis revealed that six candidate genes, including CsMYB1, CsMYB2, and CsMYB14, were significantly and positively correlated with the accumulation of multiple flavonoids, such as catechin and epicatechin. These results were further validated by RT-qPCR. Conclusion This study provides the first systematic identification of the R2R3-MYB transcription factor family in C. speciosa and screens key CsMYB genes potentially involved in the regulation of flavonoid biosynthesis. These findings provide a reference for subsequent functional verification of candidate genes and lay a foundation for elucidating the molecular mechanisms underlying the quality formation of C. speciosa.

Chaenomeles speciose (Sweet) Nakai  /  R2R3-MYB transcription factor  /  transcriptomics  /  metabolomics  /  catechin  /  epicatechin