Mitochondrial genome of Anaphalis lactea from the Qinghai-Xizang Plateau: structural and evolutionary insights into alpine adaptation.

INTRODUCTION: Plant mitochondrial genomes exhibit remarkable structural complexity and play important roles in environmental adaptation. To investigate the evolutionary dynamics of alpine plants, this study assembled and characterized the complete mitochondrial genome of Anaphalis lactea, an endemic medicinal species native to the Qinghai-Xizang Plateau. METHODS: Using PacBio HiFi long-read sequencing data, the mitochondrial genome of A. lactea was de novo assembled and annotated. We analyzed the genomic structure, repetitive sequences, chloroplast-derived DNA transfer, RNA editing sites, and codon usage patterns. Furthermore, the evolutionary patterns were evaluated by integrating Ka/Ks ratios, PAML site models, and phylogenetic analyses. RESULTS: The complete mitochondrial genome was 297,265 bp in length, with a GC content of 44.71%, and contained 34 protein-coding genes, 20 tRNA genes, and 3 rRNA genes. A total of 271 repetitive sequences were identified, indicating substantial structural plasticity in the mitochondrial genome. Chloroplast-derived fragments accounted for 1.68% of the genome and were mainly distributed in non-coding regions. A total of 572 RNA editing sites were predicted, all of which resulted in non-synonymous amino acid substitutions. Codon usage bias was relatively weak and appeared to be primarily driven by natural selection. Ka/Ks analysis indicated that most genes evolved under purifying selection, whereas ccmFn exhibited a relatively high Ka/Ks ratio.Furthermore, PAML analysis identified positively selected sites L285A, Y303R and T378F in the ccmFc gene. Within the Asteraceae phylogenetic tree, A. lactea shows a strongly supported sister-group relationship with the tribe Anthemideae (PP = 1.00, BS = 100). Although mitochondrial DNA sequences are highly conserved, RNA editing, by altering the physicochemical properties of respiratory chain complex proteins, acts together with localized positively selected sites and may facilitate long-term adaptation to high-altitude environments through mitochondrial functional optimization. CONCLUSIONS: This study provides the first complete mitochondrial genome report for A. lactea within the tribe Gnaphalieae. These findings provide valuable genomic resources and new insights into the adaptive mechanisms of alpine plants and the evolutionary relationships within Asteraceae.