Assembly and comparative analysis of the complete mitochondrial genome of Cardiocrinum giganteum: a primitive Liliaceae group with significant scientific research value.

Abstract

BACKGROUND : Cardiocrinum giganteum, belonging to genus Cardiocrinum of family Liliaceae, is a genus endemic to East Asia and is considered one of the more primitive groups within the Liliaceae family. C. giganteum is the largest one among all the lily species in plant and flower size, and possesses high ornamental, medicinal, and scientific research value. However, due to its long-term wild status, its value has not been fully exploited and utilized, especially regarding the mitochondrial genome, which is crucial for plant growth activities, there have been no relevant studies and reports so far. RESULTS: In this study, we sequenced and assembled the complete mitochondrial genome of C. giganteum and elucidated its evolutionary trajectory and phylogenetic relationships. The C. giganteum mitogenome has a multi-chromosomal structure containing 19 circular molecules. The assembled mitogenome has a total length of 2,066,679 bp and a GC content of 44.54%. A total of 37 unique protein-coding genes (PCGs), 16 tRNA, and three rRNA genes were annotated. Several repetitive sequences and sequence fragments homologous to chloroplasts have also been found in the C. giganteum mitogenome. To determine the evolutionary and taxonomic positions of C. giganteum, we constructed a phylogenetic tree using C. giganteum mitochondrial PCGs. Additionally, we analyzed the relatively synonymous codon usage of PCGs, identified RNA editing events, and conducted syntenic analysis with closely related species. CONCLUSIONS: This study presents the first comprehensive mitochondrial genome (mtDNA) characterization of C. giganteum (Liliaceae), revealing its unique multi-chromosomal configuration. Our findings address the knowledge gap in mitochondrial research within the Cardiocrinum genus while enriching the mitochondrial genome database of Liliaceae. The assembled mtDNA provides critical insights into the phylogenetic relationships between Cardiocrinum and its allied genera, establishing essential genomic resources for evolutionary analyses, species identification, and genetic diversity studies across Liliaceae.