Comparative mitochondrial genomics of cultivated Sesamum indicum and its wild relative Sesamum schinzianum provides insights into structural features and organellar evolution

Introduction The genus Sesamum (Pedaliaceae) comprises a wide range of cultivated and wild species. Sesame ( Sesamum indicum ) is recognized as one of the oldest oilseed crops cultivated worldwide, whereas S. schinzianum is a wild relative closely associated with the evolutionary history of cultivated sesame. Although the nuclear and chloroplast genomes of Sesamum species have been investigated in previous studies, mitochondrial genome evolution within the genus has received relatively limited attention. Methods In this study, we assembled and comparatively analyzed the mitochondrial genomes of S. indicum and S. schinzianum by integrating BGI short-read sequencing and Oxford Nanopore long-read sequencing data. Genome assembly was performed using Flye and Unicycler, and annotation was conducted using PMGA together with manual curation. Comparative analyses were then carried out to examine genome organization, gene content, repetitive sequences, codon usage, RNA editing sites, chloroplast-derived sequences, phylogenetic relationships, and collinearity patterns. Results The mitochondrial genomes of S. indicum and S. schinzianum were assembled into one circular molecule and two major circular contigs, respectively, and both contained 36 conserved protein-coding genes. Abundant simple sequence repeats dominated by tetranucleotide motifs and notable repeat variation were detected. Codon usage showed moderate bias, and 478 and 455 RNA editing sites were predicted in S. indicum and S. schinzianum , respectively. Chloroplast-derived sequences accounted for 8.50% and 6.96% of the mitochondrial genomes, respectively. Phylogenetic and collinearity analyses supported a close relationship between the two Sesamum species and identified synteny-based structural differences between their mitogenomes. Comparative analysis of mitochondrial- and chloroplast-based phylogenies showed that the two datasets were largely congruent at the family level and consistently supported the close relationship between the two Sesamum species, although they differed in the placement of several deeper lineages. Discussion These results suggest that Sesamum mitogenomes retain conserved gene content while showing assembly- and synteny-supported structural differences. This study provides useful genomic resources for comparative and evolutionary studies of mitochondrial genomes in Pedaliaceae.