Genome-wide identification and comprehensive characterization of the Aux/IAA gene family in Cucurbita moschata and its responses analysis to abiotic stresses
TL;DR
This study systematically characterized the Aux/IAA gene family in pumpkin, highlighting its evolutionary diversity, structural conservation, and distinct regulatory features and inform the potential roles of CmIAA genes in abiotic stress responses.
Abstract
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. 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 (Groups Ⅰ–Ⅸ), with Groups Ⅰ, Ⅵ, and Ⅸ exhibiting relative 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 and Cucurbita maxima . Promoter analysis showed that CmIAA genes contain multiple cis-elements associated with hormone responses and abiotic stress responses, including ABRE, MBS, and DRE. Tissue expression analysis demonstrated that many CmIAA genes exhibited tissue-preferential expression patterns. Under abiotic stress conditions, CmIAA 69 showed a salt-specific expression pattern, whereas CmIAA 39 and CmIAA 58 responded to both salt and drought treatments, indicating that these CmIAA genes play distinct roles in pumpkin responses to different abiotic stresses. This study systematically characterized the Aux/IAA gene family in pumpkin, highlighting its evolutionary diversity, structural conservation, and distinct regulatory features. These findings provide valuable genetic resources for further functional studies and inform the potential roles of CmIAA genes in abiotic stress responses.