Comparative Analysis of the Mitochondrial Genomes of the endangered Notopterygium Species in the Qinghai-Tibetan Plateau

Background Notopterygium species are perennial medicinal herbaceous plants native to the Qinghai-Tibet Plateau and surrounding regions, valued for their antioxidant, antiviral, and antitumor properties. However, the complete mitochondrial genome sequences of this genus have not yet been characterised.Results This study assembled the complete mitogenomes of eight individuals from four Notopterygium species using a hybrid strategy integrating Illumina, HiFi, and ONT data. Results showed that most species displayed a single “master circle” structure, while N. franchetii exhibited both circular and branched configurations. The mitochondrial genomes range from 284,004 bp to 339,028 bp, containing 36-40 protein-coding genes, 24-30 tRNA genes, and 3 rRNA genes. Chloroplast-derived sequences varied from 29 bp to 8,931 bp, with significantly higher transfer frequency in N. franchetii and N. oviforme. Phylogenetic reconstruction revealed interspecific relationships consistent with plastid and nuclear data. The divergence times of Notopterygium species closely correspond with the second (13-15 Mya) and third (7-8 Mya) uplift events of the Qinghai-Tibet Plateau (QTP), suggesting that geographic isolation driven by QTP uplift served as a major evolutionary driver for speciation.Conclusions This study provides the first Notopterygium mitochondrial genomes, offering crucial biological insights into the evolutionary history, adaptive mechanisms, and phylogenetic relationships of this genus.