Evolutionary and Characteristic Analyses of the ARF Gene Family in Dendrobium lindleyi and Their Response to Exogenous IAA Treatment

Auxin response factors (ARFs) are core transcription factors in auxin signaling, yet their evolution and transcriptional responses in Dendrobium lindleyi remain unclear. In this study, 21 ARF genes were identified in D. lindleyi. They were distributed across six subfamilies (Class I–VI), with Class III containing nine members. Phylogenetic analysis indicated that Classes I, II, and IV were detected in Physcomitrella patens (mosses) and Selaginella kraussiana (lycophytes), Classes III and V were first detected in Ceratopteris richardii (ferns), and Class VI was first detected in Ginkgo biloba. The number of syntenic ARF gene pairs between D. lindleyi and other orchids far exceeded that between D. lindleyi and external lineages. Orthology analysis revealed eight retained ARF ortholog groups; OGARF1 contained eight copies, and core and expanded copies underwent strong purifying selection. Promoter regions were rich in MeJA-, ABA-, and light-responsive elements but relatively scarce in auxin-responsive elements. Compared with the 0 h mock control, DlinARF9 was downregulated in stems at 6 h IAA treatment, while DlinARF4 and DlinARF6 were downregulated and upregulated in leaves at 12 h. ARF genes showed tissue-specific expression; RNA-seq differentially expressed genes were all Class III, and qRT-PCR detected significant upregulation of DlinARF5 (Class VI). DlinARF4 and DlinARF6 localized to the nucleus, supporting their roles as nuclear transcriptional regulators. This study provides foundational data for elucidating ARF evolution and divergent transcriptional responses in D. lindleyi.