Genome-wide characterization of the AP2/ERF gene family in Scutellaria baicalensis Georgi reveals root-preferential and MeJA-responsive candidate genes

Abstract

APETALA2/ethylene-responsive factor (AP2/ERF) transcription factors play central roles in plant growth, development and environmental responses. Scutellaria baicalensis is a medicinal plant that predominantly accumulates pharmacologically important flavones in its roots, and methyl jasmonate (MeJA) induced these flavones accumulation. However, the AP2/ERF family has not been systematically characterized in S. baicalensis, and members showing root-preferential expression and MeJA responsiveness remain unknown. Here, we identified 137 SbAP2/ERF genes at the genome-wide level and investigated their phylogenetic relationships, conserved motifs, domain architectures, gene structures, chromosomal distribution, duplication patterns, interspecific collinearity, promoter cis-acting elements, and expression profiles. The identified 137 genes were classified into the ERF (68), DREB (40), AP2 (24), RAV (3), and Soloist (2) subfamilies. Most members within each subfamily shared similar structural features, whereas marked differences were observed among subfamilies. Of the 63 nonredundant duplicated gene pairs, 54 were segmental and nine were tandem duplicates. Promoter analysis identified 4,491 predicted cis-acting element sites associated mainly with light, hormone, and stress responses, and MeJA-responsive motifs co-occurred in 95 promoters. Analysis of publicly available RNA sequencing (RNA-seq) datasets revealed diverse organ-preferential expression patterns and time-dependent transcriptional responses to MeJA. Combining the RNA-seq profiles and qRT-PCR measurements identified eight candidate genes which were preferentially expressed in roots and significantly upregulated by MeJA including SbAP2-13, SbAP2-14, SbAP2-27, SbAP2-40, SbAP2-59, SbAP2-117, SbAP2-130, and SbAP2-137. These results provide a comprehensive resource for the SbAP2/ERF family and prioritize candidate genes for investigating MeJA-responsive transcriptional processes and the potential regulation of root-specific flavones biosynthesis in S. baicalensis.