Abstract
BACKGROUND: Phlomoides rotata, an endemic Tibetan medicinal plant adapted to extreme alpine environments, faces conservation challenges due to habitat degradation and overharvesting. Despite its ecological and medicinal importance, its mitochondrial genome remains uncharacterized, limiting insights into its evolutionary adaptations and genomic architecture. RESULTS: We present the initial de novo assembly and annotation of the P. rotata mitochondrial genome, a circular molecule with a GC content of 45.06% and a length of 377,312 bp. A total of 32 protein-coding genes (PCGs), three ribosomal RNA (rRNA) genes, and 12 transfer RNA (tRNA) genes were identified through genome annotation. These genes include multicopy genes (trnM-CAU, matR). Analysis of codon usage bias indicated a preference for A/U ending synonymous codons, aligning with trends observed in other angiosperms. RNA editing research revealed 445 C-to-U transitions, predominantly at the second codon position, with nonsynonymous alterations (71%) surpassing synonymous changes, indicating potential functional adaptive roles. Repetitive sequence analysis uncovered 81 simple sequence repeats (SSRs) and a large palindromic repeat (13,075 bp), linked to genomic rearrangements. Homologous alignments identified 12 chloroplast-derived fragments in the mitogenome, including intact tRNA and rpl23 genes, evidencing interorganellar gene transfer. Phylogenetic analysis using 27 conserved PCGs positioned P. rotata within a well-supported Lamiales clade, closely related to Leonurus japonicus, corroborating its taxonomic placement and providing a framework for evolutionary studies. CONCLUSIONS: The P. rotata mitogenome exhibits structural complexity and adaptive features, including codon bias, RNA editing, and repetitive sequences, underscoring its role in high-altitude adaptation. These findings provide critical genomic resources for conservation, breeding, and understanding the molecular mechanisms of organellar evolution in extreme environments.