Lagerstroemia indica is a widely used ornamental woody plant known for its summer flowering and significant ornamental and economic value. While L. indica boasts a variety of rich flower colors, the molecular mechanisms underlying this color formation remain unclear. In this study, we selected three different flower colors of L. indica—white (W), red (R), and purple (P)—for transcriptome and metabolome analysis. The metabolome analysis identified 538 flavonoids, with 22 anthocyanins highly accumulated in the red and purple flowers. RNA-seq analysis annotated a total of 35,505 genes. Furthermore, we identified 42 differentially expressed genes (DEGs) involved in anthocyanin biosynthesis, with their expression levels aligning with anthocyanin content. Correlation analysis revealed that 19 MYB and 11 bHLH transcription factors are likely involved in anthocyanin biosynthesis. Additionally, we identified 59 auxin biosynthesis and signaling-related genes that are positively correlated with anthocyanin-related genes and metabolites, suggesting that auxin may play a role in regulating anthocyanin biosynthesis in L. indica. This study provides valuable insights into the regulatory mechanisms underlying anthocyanin accumulation and color formation in L. indica petals and identifies several potential genes, laying the groundwork for further research on regulatory mechanisms and genetic improvement of L. indica.

NAC (NAM, ATAF1/2, CUC1/2) is a plant-specific transcription factor (TF) family that plays important roles in various physiological and biochemical processes of plants. However, the NAC gene family in Lagerstroemia indica and its role in anthocyanin metabolism are still unexplored. In our study, a total of 167 NACs were identified in the L. indica genome via genome-wide analysis and bioinformatics techniques. Amino acid sequence analysis showed that all 167 NAC proteins contained a conserved NAM domain. This domain primarily comprised random coils, extended strands, and alpha helices. Most NACs were found on the nucleus and dispersed over 23 of the 24 plant chromosomes. Based on phylogenetic analysis, the NACs can be categorized into ten subgroups. Furthermore, the promoter homeotropic elements predicted the cis-acting elements in the promoters of these genes related to hormones, development, environmental stress response, and other related responses, demonstrating the diverse regulatory mechanisms underlying gene functions. In addition, a co-expression network was established through RNA sequencing. This network helped identify seven key LiNACs, genes related to anthocyanin expression (CHS) and transcription factors (MYB and bHLH). To identify potential anthocyanin regulatory factors present in L. indica petals, protein interaction prediction was performed, which revealed that LiNACs might participate in anthocyanin regulation by interacting with other proteins, such as MYB, ABF, ABI, bZIP, MYC, etc. Our results provided novel insights and could help in the functional identification of LiNACs in L. indica and the regulation of anthocyanin synthesis.