Comparative mitogenome assembly and structural variation across Perilla frutescens and closely related taxa using whole-genome sequencing data

Abstract Background Perilla frutescens (L.) Britton is an economically important aromatic industrial crop in East Asia and an increasingly important target for genomic resource development and germplasm improvement. Research has focused largely on metabolomics, nuclear genomes, and plastomes, and the published P. frutescens mitogenome has not been compared systematically with those of close relatives. Results We assembled, annotated, and compared mitogenomes from five sampled representatives: P. frutescens , Keiskea sinensis Diels, Mosla soochouensis Matsuda, M. chinensis Maxim., and the M. chinensis cultivar ‘Jiangxiangru’. The analysis used PacBio HiFi reads for P. frutescens and K. sinensis , together with publicly available PacBio reads for the three sampled Mosla representatives. The assembled mitochondrial genomes ranged in size from 299,551 to 347,981 bp, whereas GC content varied narrowly (44.8–45.2%). Gene content was broadly similar among the sampled representatives, whereas structural features were more variable. Dispersed repeats occupied 6.65–17.77% of the mitogenomes. In pairwise comparisons with the other four sampled mitogenomes, collinear blocks covered 39–68% of the sampled P. frutescens mitogenome. Candidate mitochondrial plastid DNA sequences (MTPTs) were detected in all five mitogenomes but differed in number, length, and sequence identity to the corresponding plastome. We predicted 282–374 candidate RNA-editing sites per sampled mitogenome, most involving C-to-U changes. Plastid and mitochondrial trees agreed for the focal representatives but differed at broader taxonomic levels. Conclusions These reference assemblies place the P. frutescens mitogenome in a close-relative context and document structural differences among the sampled representatives. They provide a comparative organellar resource for future validation in broader accession panels.