This study aimed to elucidate the mitochondrial genome organization of
Chlorogomphus papilio and the phylogenetic relationships of Chlorogomphidae. We used the Illumina MiSeq sequencing platform to sequence the mitochondrial genome of
C. papilio, which was subsequently assembled, annotated, and analyzed. Bayesian inference,
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This study aimed to elucidate the mitochondrial genome organization of
Chlorogomphus papilio and the phylogenetic relationships of Chlorogomphidae. We used the Illumina MiSeq sequencing platform to sequence the mitochondrial genome of
C. papilio, which was subsequently assembled, annotated, and analyzed. Bayesian inference, maximum likelihood, and maximum parsimony methods were employed to construct the mitochondrial phylogenetic tree of 25 species of Chlorogomphidae based on
16S rRNA and
cox1 genes. We observed that the mitochondrial genome of
C. papilio is 15,251 bp in length and includes 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a non-coding control region. All PCGs start with a typical ATN codon. While
cox1,
cox2,
cox3, and
nad5 end with an incomplete termination codon (T), the remaining PCGs terminate with TAG. The secondary structure of the 22 tRNAs showed that only the
trnS1 gene lacked the dihydrouracil arm (DHU arm), whereas the rest formed a typical cloverleaf structure. Additionally, 32 G-U mismatches were observed in the secondary structure. Phylogenetic analyses indicated that
C. papilio and
C. magnificus are sister species. Divergence time analyses indicated that Chlorogomphidae originated around 111.04 Ma, with
C. papilio diverging from the common ancestor shared with
C. magnificus approximately 58.51 Ma. This divergence is likely linked to the Paleocene–Eocene Thermal Maximum (PETM) and the tectonic uplift of the Himalayas, which created warm, humid habitats and contributed to geographic isolation. This study contributes to a better understanding of the mitochondrial genome and phylogeny of
C. papilio, providing valuable molecular markers for further genetic studies.
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