Genome-wide identification and characterization of the SaARF gene family in Solanum americanum

Auxin response factors ( ARFs ) are plant-specific transcription factors (TFs) that regulate organogenesis, vascular differentiation, and stress responses. However, the ARF family in Solanum americanum , a stress-tolerant wild relative of major Solanaceous vegetable crops, remains largely unexplored. Using the S. americanum reference genome, we identified 18 ARF genes by combining HMM profile searches with homology-based alignment. We then analyzed chromosomal distribution, physicochemical properties, gene structure, conserved protein domains and motifs, promoter cis -elements, phylogeny and collinearity, tissue-specific expression (root, stem, leaf, flower, and fruit), and transcriptional responses to cold, drought, and salt stresses. Three representative genes were further examined by transient 35S: GFP subcellular localization. Most SaARF proteins contain the canonical B3 and Auxin_resp domains, and several also harbor the C-terminal PB1 domain, which enables homotypic and heterotypic protein interactions. Phylogenetically, SaARFs cluster with ARFs from Arabidopsis and major Solanaceae crop species ( S. lycopersicum , S. melongena , S. tuberosum , and Capsicum annuum ), and exhibit extensive collinearity with Solanaceae genomes. Gene expression analyses revealed organ-preferential expression patterns and stress responsiveness; in particular, several SaARFs are enriched in reproductive organs, and multiple members are rapidly induced or repressed by salt, drought, or cold. Subcellular localization placed all three tested proteins in the nucleus. This study provides the first genome-wide characterization of the ARF family in S. americanum , refines our understanding of ARF evolution, and provides candidate genes for future functional studies on stress tolerance and fruit quality in cultivated Solanaceous vegetables.