The auxin response factor (ARF) and auxin/indole-3-acetic acid (Aux/IAA) family of genes are central components of the auxin signaling pathway and play essential roles in plant growth and development. Their large-scale analysis and evolutionary trajectory of origin are currently not known. Here, we identified the corresponding ARF and Aux/IAA family members and performed a large-scale analysis by scanning 406 plant genomes. The results showed that the ARF and Aux/IAA gene families originated from charophytes. The ARF family sequences were more conserved than the Aux/IAA family sequences. Dispersed duplications were the common expansion mode of ARF and Aux/IAA families in bryophytes, ferns, and gymnosperms; however, whole-genome duplication was the common expansion mode of the ARF and Aux/IAA families in basal angiosperms, magnoliids, monocots, and dicots. Expression and regulatory network analyses revealed that the Arabidopsis thaliana ARF and Aux/IAA families responded to multiple hormone, biotic, and abiotic stresses. The APETALA2 and serum response factor-transcription factor gene families were commonly enriched in the upstream and downstream genes of the ARF and Aux/IAA gene families. Our study provides a comprehensive overview of the evolutionary trajectories, structural functions, expansion mechanisms, expression patterns, and regulatory networks of these two gene families.

Apiaceae is a major family from Apiales and includes many important vegetable and medicinal crops. Heat shock transcription factors (Hsf) play important roles in heat tolerance during plant development. Here, we conducted systematic analyses of the Hsf gene family in three Apiaceae species, including 17 Apium graveolens (celery), 32 Coriandrum sativum (coriander), and 14 Daucus carota (carrot). A total of 73 Hsf genes were identified in three representative species, including Arabidopsis thaliana, Vitis vinifera, and Lactuca sativa. Whole-genome duplication played important roles in the Hsf gene family's expansion within Apiaceae. Interestingly, we found that coriander had more Hsf genes than celery and carrot due to greater expansion and fewer losses. Twenty-seven branches of the phylogenetic tree underwent considerable positive selection in these Apiaceae species. We also explored the expression patterns of Hsf genes in three plant organs. Collectively, this study will serve as a rich gene resource for exploring the molecular mechanisms of heat tolerance. Additionally, this is the first study to report on the Hsf gene family in Apiaceae; thus, our research will provide guidance for future comparative and functional genomic studies on the Hsf gene family and others in Apiaceae.