Genome-Wide Discovery and Characterization of the Auxin Response Factor (ARF) Gene Family in Avicennia marina That Regulates Phytohormone Levels and Responds to Salt and Auxin Treatments

Auxin response factors (ARFs) are crucial components of auxin signaling, playing a vital role in plant growth, development, hormone regulation, and stress responses. Salinity influences plant growth and development; however, Avicennia marina exhibits remarkable salt tolerance. This study analyzed Avicennia marina ARF genes (AmARFs) and their roles in responding to salt and indole-3-acetic acid (IAA) stress. The results indicated that across 5–15 days, endogenous IAA and abscisic acid (ABA) levels in A. marina leaves showed significant, time-dependent changes under salt and IAA treatments, with IAA fluctuating around 2.0–3.3 µg g−1 FW and ABA rising sharply under combined high-salt + IAA conditions (AS25), reaching up to ~25 µg g−1 FW (p < 0.05). This is the first genome-wide identification of 41 ARF genes in Avicennia marina with expression responses to combined salt and auxin treatments. We identified 41 AmARF genes spread across 23 chromosomes. These genes are divided into four groups according to their phylogenetic relationships. Their coding regions encode amino acids from 361 to 1264, and the number of exons varies from 2 to an unspecified upper limit of 25. Examining these gene promoters revealed various hormone- and stress-response elements, with each gene containing distinct response elements. Sixteen miRNAs can inhibit various ARF genes, while protein–protein interactions and 3D structures offered valuable insights into AmARF proteins. GO enrichment analysis revealed that all 41 AmARFs are involved in the auxin-activated signaling pathway and are also involved in cell division. According to the expression experiments, 11 randomly selected genes showed predominantly upregulation in response to salt and IAA stressors compared with controls. These findings extend our understanding of the functional roles of AmARFs in stress responses. The systematic annotation of AmARF family genes offers candidate genes for future functional validation, which may help elucidate the precise roles of AmARFs in stress responses.