Exploration of the Donors and Specific Genes of B Subgenome in Perilla frutescens Based on Genomic Analysis

<i>Perilla frutescens</i> is an important medicinal and edible plant in Asia and was introduced in Europe and North America mainly as a spice plant. The commonly cultivated species is an allotetraploid (AABB). While the identity of its AA diploid donor has been preliminarily clarified, the other donor, BB, has not been discovered yet, and the taxonomic status and characteristics of the BB donor remain unresolved. Based on the published genomes of <i>Perilla</i> spp., we employed a collinearity analysis, gene structure similarity assessment, and multi-level functional annotation to infer the genomic and phenotypic features of the B subgenome. Results suggest that the protein sequences of the B and A subgenomes exhibit the highest similarity, while the protein sequences of <i>Lavandula angustifolia</i> or <i>Ocimum basilicum</i> are less similar to the B subgenome, and two subgenomes also possess the largest number of homologous genes and have similar gene structures. A total of 90 BB progenitor-specific genes were significantly enriched in pathways related to secondary metabolite biosynthesis and environmental stress response. Among these genes, the terpene synthase genes constitute the main genetic basis for the diversity of bioactive components in perilla. The discovery of a homologous gene containing the NB-ARC domain, associated with resistance to late blight, suggests that BB may contribute to key disease-resistant traits. Further gene family analysis revealed that compared with the A subgenome, the B subgenome exhibited fewer genes and lower diversity in the <i>TPS</i> and <i>NB-ARC</i> families. These findings indicate that BB may have originated from an unfound or extinct species within the <i>Perilla</i> spp. The BB donor might be less diversified than AA, possibly adapting to a narrow geographic and climatic range.