Genome-Wide Identification and Species-Specific Expression Analysis of SQE Genes in Lonicera japonica

Squalene epoxidase (SQE) is a crucial enzyme limiting triterpene saponin biosynthesis rate. As an important plant secondary metabolite, triterpene saponins have pharmacological effects like anticancer, antiviral, and cholesterol-lowering. Moreover, it is the active ingredient of genus Lonicera medicinal plants, and the index for distinguishing Flos Lonicerae Confusae from honeysuckle and controlling their quality. In this study, seven LjSQE genes were identified from the Lonicera japonica genome and analyzed for gene structure, chromosomal distribution, phylogeny, cis-acting elements, synteny, and expression patterns. The analysis revealed that the exon-intron structure and motifs of LjSQEs were highly conserved, and these genes were distributed on four chromosomes. LjSQE1–4 belong to angiosperms’ conserved lineage; LjSQE5–7 are products of recent Lonicera lineage replication, with tandem replication driving early LjSQEs family expansion. LjSQEs promoters are enriched with cis-acting elements related to light response, phytohormone response, anaerobic induction, and drought stress. LjSQE3 and LjSQE5 expression is significantly lower in L. japonica than in L. macrantha, directly relating to lower triterpene saponins in L. japonica. In conclusion, this study provides comprehensive knowledge of the L. japonica LjSQEs family and molecular clues for analyzing saponin composition differences between L. japonica and L. macrantha. It also provides a theoretical basis and candidate genes for developing molecular breeding to improve L. japonica’s medicinal quality.