The complex and dynamic mitochondrial genome of garlic (Allium sativum): Insights from structural and evolutionary analysis

Garlic (Allium sativum) is an important crop with significant value in both agriculture and medicine, yet its mitochondrial genome remains uncharacterized. This gap has limited the understanding of organellar evolution and genomic diversity. The mitogenome was assembled with Illumina and PacBio revealed a complex, multipartite architecture spanning 548,160 bp with six contigs, a size that is within the common range for angiosperm mitochondrial genomes. The structure demonstrated considerable plasticity, and was characterized by abundant repetitive sequences. Annotation identified 25 protein-coding genes, 14 tRNAs, and three rRNAs, representing a conserved gene set. Extensive chloroplast-to-mitochondrion DNA transfer was observed, with 38 homologous fragments totaling 33.6 kb that included functionally intact genes. Codon usage analysis revealed a pronounced A/U-ending preference in synonymous codons. Additionally, 494C-to-U RNA editing sites were predicted, indicating significant concentrations in NADH dehydrogenase genes. Phylogenetic analysis based on 23 conserved mitochondrial genes robustly resolved A. sativum as sister to Allium fistulosum. This study presents the first complete mitochondrial genome of A. sativum, which reveals substantial structural complexity and dynamic evolution. This genome provides a foundational resource for further investigation into organellar genome evolution within the Allium genus.