Comparative Analysis of Tylosema esculentum Mitochondrial DNA Revealed Two Distinct Genome Structures

SIMPLE SUMMARY: Tylosema esculentum is a potential crop in southern Africa, known for its high nutritional value and ability to thrive in long-term drought conditions. To gain a better understanding of its genetic characteristics, the mitogenomes of 84 individuals from different locations in Namibia and South Africa were assembled and compared using both PacBio and Illumina sequencing data. The study revealed two distinct germplasms with significant differences in the mitogenome structure and sequence. Comparative genomics analysis was conducted to explore heteroplasmy and horizontal transfer in the marama mitogenome, providing valuable insights into cytoplasmic genetic diversity and inheritance. Additionally, evolutionary studies were performed on marama and its related legumes, indicating that the Cercidoideae subfamily tends to possess a more complete set of mitochondrial genes compared to the Faboideae species. The findings made in this study not only contribute to the germplasm selection and future marama breeding but also enhance our understanding of the inheritance and evolution of plant mitogenomes. ABSTRACT: Tylosema esculentum, commonly known as the marama bean, is an underutilized legume with nutritious seeds, holding potential to enhance food security in southern Africa due to its resilience to prolonged drought and heat. To promote the selection of this agronomically valuable germplasm, this study assembled and compared the mitogenomes of 84 marama individuals, identifying variations in genome structure, single-nucleotide polymorphisms (SNPs), insertions/deletions (indels), heteroplasmy, and horizontal transfer. Two distinct germplasms were identified, and a novel mitogenome structure consisting of three circular molecules and one long linear chromosome was discovered. The structural variation led to an increased copy number of specific genes, nad5, nad9, rrnS, rrn5, trnC, and trnfM. The two mitogenomes also exhibited differences at 230 loci, with only one notable nonsynonymous substitution in the matR gene. Heteroplasmy was concentrated at certain loci on chromosome LS1 (OK638188). Moreover, the marama mitogenome contained an over 9 kb insertion of cpDNA, originating from chloroplast genomes, but had accumulated mutations and lost gene functionality. The evolutionary and comparative genomics analysis indicated that mitogenome divergence in marama might not be solely constrained by geographical factors. Additionally, marama, as a member from the Cercidoideae subfamily, tends to possess a more complete set of mitochondrial genes than Faboideae legumes.