The first mitochondrial genome in Zingiber: Structural and evolutionary characterization of ginger (Zingiber officinale)

The genus Zingiber possesses substantial economic and medicinal value, yet its mitochondrial genome (mitogenome) has remained entirely unexplored. Here, we present the first complete mitogenome assembly of ginger ( Zingiber officinale ), obtained through a hybrid sequencing (Illumina and PacBio) strategy. The genome features a complex, multi-branched structure totaling 8,977,507 bp and a GC content of 45.27%. It harbors 40 protein-coding genes (PCGs), 31 tRNAs, and three rRNAs. We identified abundant repetitive sequences, including 2954 SSRs and 54,887 dispersed repeats driving this genomic expansion, alongside widespread evidence of intracellular DNA transfer, with 273 plastid-derived fragments integrated into the mitogenome. Codon usage analysis revealed a pronounced bias toward A/U-ending synonymous codons. Importantly, Deepred-Mt predictions of extensive C-to-U RNA editing sites were experimentally corroborated via Sanger sequencing, confirming their critical role in maintaining the hydrophobicity of respiratory chain genes. Comparative analyses revealed a striking evolutionary decoupling: highly conserved nucleotide substitution rates contrasting with extreme structural rearrangements relative to related Curcuma species, and phylogenetic reconstruction strongly supported the sister relationship between Z. officinale and the Curcuma clade. This study provides a foundational genomic resource for further research on cytoplasmic inheritance, genome gigantism, molecular breeding, and the links between mitogenomic variation and key agronomic or medicinal traits in Z. officinale . • The first mitochondrial genome in the genus Zingiber was assembled for ginger ( Zingiber officinale ). • The mitogenome exhibits multi-branched structure with 13 contigs. • Extensive intracellular gene transfer was identified, with 273 plastid-derived DNA fragments. • RNA editing prediction shows a preference for respiratory genes. • Phylogenetic analysis resolved Z. officinale as sister to the Curcuma clade.