Abstract
BACKGROUND: Houttuynia cordata is a well-known medicinal and edible plant with important economic value. It belongs to the magnoliid clade, a basal lineage of angiosperms. Currently, the limited number of reported mitochondrial genomes from magnoliids severely restricts our understanding of early mitochondrial genome evolution. To address this gap, we present the complete mitochondrial genome of H. cordata. RESULTS: The H. cordata mitochondrial genome spans 534,194 bp, and predominantly adopts a bicyclic structure among four possible configurations. It encodes 45 protein-coding genes (PCGs) (40 unique), 29 transfer RNAs (21 unique), and 3 ribosomal RNAs. Repeat analysis revealed significant differences in tandem repeats, dispersed repeats, and simple sequence repeat (SSR) types and densities between the two chromosomes, with Chromosome 1 exhibiting higher repeat density and diversity. Additionally, the H. cordata mitochondrial genome harbors 18 potential mitochondrial plastid DNAs (MTPTs), most of which originate from the inverted repeats (IR) regions of the plastid genome. Variant detection at the individual-level revealed significant heteroplasmy across most regions, while large repeat regions and MTPTs regions exhibited relative conservation. Phylogenetic and collinearity analyses further indicated substantial differences between the mitochondrial genome structure of H. cordata and 15 other magnoliid species, while conserved regions were maintained. CONCLUSION: This study elucidates the unique evolutionary characteristics of the H. cordata mitochondrial genome and provides valuable insights into its genetics and evolution. Comparative analysis with other magnoliid species reveals both dynamic evolutionary changes and the conservation of mitochondrial genome structure and gene content in early angiosperms.