Comprehensive Analysis of the AP2/ERF Transcription Factor Family in Schisandra chinensis and Its Implications for secondary metabolism

The AP2/ERF transcription factor superfamily is integral to plant secondary metabolism; however, its comprehensive genomic characterization in Schisandra chinensis-a medicinal plant esteemed for its dibenzocyclooctadiene (DBCOD) lignans with a wide range of pharmacological properties-has not yet been conducted. In this study, we identified a total of 144 ScAP2/ERF genes from the high-quality, chromosome-level genome of S. chinensis. These genes were categorized into five subfamilies (ERF, DREB, AP2, RAV, and Soloist) through phylogenetic analysis with Arabidopsis thaliana. Conserved motif analysis confirmed the presence of the characteristic AP2 domain in all ScAP2/ERF proteins, with members of the AP2 subfamily containing two AP2 domains and RAV members featuring both AP2 and B3 domains. Chromosomal localization analysis revealed an uneven distribution of these genes across 14 chromosomes, with clusters identified on chromosomes 1, 2, 6, 10, 11, and 13. Cis-acting element analysis demonstrated an enrichment of light-responsive, MeJA-responsive, ABA-responsive, and anaerobic induction elements in the promoters of ScAP2/ERF genes. Synteny analysis identified 26 pairs of segmentally duplicated genes within the S. chinensis genome and 39 orthologous pairs with A. thaliana. Expression profiling across roots, stems, leaves, and fruits revealed distinct tissue-specific expression patterns. Of the 144 identified genes, 122 (84.7%) were detectably expressed in at least one tissue; among them, ten exhibited notably high expression in fruit tissues, suggesting their potential regulatory roles in the accumulation of pharmacologically active compounds in the medicinal fruit. This study represents a comprehensive genome-wide identification of the AP2/ERF family in S. chinensis, thereby establishing a foundational framework for understanding its evolutionary history and functional diversification. Furthermore, it offers candidate genes for subsequent functional validation in the regulation of their potential roles in regulating secondary metabolism.