Comparative transcriptome and co-expression analysis reveal key genes involved in leaf margin serration in Perilla frutescens

OBJECTIVE: In this study, we aimed to identify the genes involved in leaf margin serration in Perilla frutescens. P. frutescens (Family: Lamiaceae) is widely grown in Asian countries. Perilla leaf is the medicinal part stipulated in the Chinese Pharmacopoeia. There are mainly two types of perilla leaves: one with serrated leaf margin which is the phenotype described in the pharmacopoeia and the other with smooth leaf margin. METHODS: Transcriptome sequencing, co-expression analysis, and qRT-PCR analysis of six perilla tissues sampled from two different phenotypes (serrated and smooth leaves) were performed. RESULTS: Forty-three differentially expressed genes (DEGs), which may potentially regulate leaf shape, were identified through de novo transcriptome sequencing between the two groups. Genes involved in leaf shape regulation were identified. Simultaneously, we validated five DEGs by qRT-PCR, and the results were consistent with the transcriptome data. In addition, 1186 transcription factors (TFs) belonging to 45 TF families were identified. Moreover, the co-expression network of DEGs was constructed. CONCLUSION: The study identified the key genes that control leaf shape by comparing the transcriptomes. Our findings also provide basic data for further exploring P. frutescens, which can help study the mechanism of leaf shape development and molecular breeding.