Complete mitochondrial genome of Perilla frutescens (Lamiaceae) insights into structure, Codon usage, repeats, and RNA editing

Abstract

Perilla frutescens (L.) Britton, a member of the Lamiaceae family, is a versatile plant highly valued for its unique aroma and medicinal properties. Additionally, P. frutescens seeds are rich in α-linolenic acid, holding significant economic importance. While the nuclear and chloroplast genomes of P. frutescens have already been documented, the complete Mitochondrial genome sequence has yet to be reported. In this investigation, we conducted the sequencing, annotation, and assembly of the entire Mitochondrial genome of P. frutescens using a combination of Illumina and PacBio data. The resulting assembled P. frutescens Mitochondrial genome spans 299,551 bp and exhibits a typical circular structure, with a GC content of 45.23%. Within the genome, a total of 59 unique genes were identified, encompassing 37 protein-coding genes, 20 tRNA genes, and 2 rRNA genes, with 18 introns present in 8 protein-coding genes. Notably, the codons of the P. frutescens Mitochondrial genome display a notable A/T bias. Our analysis also revealed 293 dispersed repeat sequences, 77 simple sequence repeats (SSRs), and 6 tandem repeat sequences. Additionally, RNA editing sites exhibited a preference for the formation of leucine at amino acid editing sites. Furthermore, we identified 70 sequence fragments (12,680 bp) that have been transferred from the chloroplast to the Mitochondrial genome, accounting for 4.23% of the entire Mitochondrial genome. Phylogenetic analysis indicated that among Lamiaceae plants, P. frutescens is most closely related to Salvia miltiorrhiza and Platostoma chinense. Inter-species Ka/Ks results suggested that Ka/Ks <1 for 28 PCGs, indicating that these genes will continue to evolve under purifying selection pressure. The findings of this study will contribute to the enrichment of Mitochondrial genome data for P. frutescens and provide a theoretical foundation for future molecular breeding research on P. frutescens.