Genome-Wide Identification and Comprehensive Characterization of the Aux/IAA Gene Family in Cucurbita moschata and Its Response Analysis to Abiotic Stress

Background Auxin is a central phytohormone involved in regulating plant growth, development, and stress responses, with the Aux/IAA gene family functioning as an essential component of the auxin signaling pathway. To elucidate the genomic features and potential functions of the Aux/IAA gene family in pumpkin ( Cucurbita moschata ), we performed a genome-wide identification and systematic characterization. Results A total of 72 CmIAA genes were identified, encoding proteins ranging from 158 to 1275 amino acids with predicted isoelectric points of 4.57 ~ 9.81. These genes were unevenly distributed across 20 chromosomes, with Chr17 harboring the highest number, while no CmIAA genes were detected on Chr3. Phylogenetic analysis classified the genes into nine subgroups (Group Ⅰ~Ⅸ), with Groups Ⅰ, Ⅳ, and Ⅵ exhibiting notable expansion. Gene structure and conserved motif analyses revealed subgroup-specific motif compositions, with motif 1 representing the core conserved domain. Intraspecific collinearity analysis identified 54 segmentally duplicated gene pairs but no tandem duplication events, whereas interspecific synteny revealed extensive orthologous relationships between pumpkin and Cucurbita pepo , Cucurbita maxima , and Arabidopsis thaliana . Promoter analysis showed that CmIAA genes contain abundant cis-elements associated with light response, hormone regulation, development, and abiotic stress. Tissue expression analysis demonstrated that many CmIAA genes were highly expressed in roots and stems, Several CmIAA genes exhibited tissue-specific and stress-type-dependent expression patterns under salt and drought treatments. Conclusions Overall, this study provides the first comprehensive characterization of the Aux/IAA gene family in pumpkin, offering fundamental insights into their structural features and expression dynamics, and providing candidate genes for future functional studies and molecular breeding applications.