Genome-wide analysis of the Ehretia macrophylla AUX/IAA family under drought and SiO₂ nanoparticle treatment

Abstract Auxin/indole-3-acetic acid (AUX/IAA) proteins are central transcriptional repressors in auxin signaling and are increasingly implicated in plant responses to water deficit. However, AUX/IAA family organization and drought-responsive expression remain poorly characterized in woody plants, and the transcriptional response to silicon dioxide nanoparticles (SiO₂ NPs) is still largely unexplored. In this study, we identified 42 EmAUX/IAA genes in Ehretia macrophylla Wall. and analyzed their chromosomal distribution, gene structures, conserved motifs, promoter cis-elements, phylogenetic relationships, and evolutionary constraints. RNA-seq analysis under control (CK), severe drought (SD), and SiO₂ NP-treated drought (NPs-SD) conditions showed treatment-associated changes in EmAUX/IAA expression. EmAUX/IAA13, EmAUX/IAA28, and EmAUX/IAA33 were induced under drought, and several drought-responsive patterns were attenuated or redirected after SiO₂ NP treatment. qRT-PCR analysis of eight selected genes, including these three candidates, supported the principal expression trends. GO and KEGG enrichment highlighted photosynthesis, ribosome biogenesis, carbon metabolism, secondary metabolism, and hormone-related stress responses. These results provide a genome-wide catalog of the EmAUX/IAA family and prioritize candidates for functional analysis. Because physiological, hormone, and genetic evidence was not obtained, the proposed links among SiO₂ NPs, auxin signaling, and drought responses should be regarded as preliminary associations requiring further validation.