Aux/IAA gene family in Lagerstroemia indica: Phylogeny, structural features, and roles in developmental regulation and stress adaptation

• A total of 40 Aux/IAA genes ( LiIAAs ) were identified in Lagerstroemia indica through genome-wide analysis, revealing a significant expansion in Groups III and VI. • Phylogenetic and structural analyses classified LiIAAs into six groups, showing conserved exon-intron structures but variable motif compositions, reflecting functional diversification. • Collinearity analysis demonstrated that segmental duplication events have played a significant role in the expansion of the LiIAA gene family. • Promoter analysis revealed abundant hormone-responsive and stress-related cis -elements, indicating the involvement of LiIAAs in both developmental processes and stress adaptatio. • Weighted gene co-expression network analysis (WGCNA) highlighted key LiIAAs (e.g., LiIAA1, LiIAA8 , and LiIAA15 ) associated with bud-to-branch development and salt stress responses. Auxin, primarily represented by indole-3-acetic acid (IAA), is a crucial hormone regulating plant growth, development, and stress responses. The Aux/IAA gene family plays a key role in auxin signaling by modulating downstream gene expression. Although extensively studied in model species, the roles of Aux/IAA genes in woody perennials such as Lagerstroemia indica remain poorly understood. In this study, we identified 40 Aux/IAA genes in L. indica ( LiIAAs ) through genome-wide analysis. Phylogenetic analysis classified them into six groups, with significant expansion in Groups III and VI. Structural analysis showed conserved motifs and variable exon-intron organization. Collinearity analysis identified 23 duplicated LiIAA gene pairs, suggesting that segmental duplication was the primary driver of family expansion. Comparative collinearity analysis across species revealed strong conservation of LiIAAs in dicots, whereas fewer collinearity relationships were observed with monocots. Promoter analysis revealed abundant hormone-responsive and stress-related cis -elements, suggesting roles in both development and stress adaptation. Tissue-specific expression analysis showed that LiIAAs are preferentially expression in roots, stems, leaves, and fruits, with distinct expression patterns associated with organ development. Moreover, differential expression and weighted gene co-expression network analysis (WGCNA) identified key LiIAAs , such as LiIAA1, LiIAA8 , and LiIAA15 , which are involved in bud-to-branch development and salt stress responses. The results provide insights into the molecular basis of auxin-mediated development and stress tolerance in L. indica , and offer potential genetic resources for the improvement of L. indica .