Complete mitochondrial genome of Ctenophthalmus quadratus and Stenischia humilis in China provides insights into fleas phylogeny

Background: Fleas (Order Siphonaptera) are a common blood-feeding ectoparasites, which have important economic significance. Limited mitochondrial genome information has extremely impeded the study of flea biology, population genetics and phylogenetics. The Ctenophthalmus quadratus and Stenischia humilis complete mt genomes are described in this study. Methods: C. quadratus and S. humilis were collected from Jianchuan, Yunnan plague foci, China. The mt genome sequences were obtained by Illumina NovaSeq 6000 platform. The relationship between C. quadratus and S. humilis in fleas was inferred by phylogenetic analysis of mt genome sequence datasets. Results: The mt genomes of C. quadratus and S. humilis were 15,938 bp and 15,617 bp, respectively. The gene arrangement of mt genome was consistent with that of other fleas, which contain 37 genes, including 13 protein-coding genes, 22 tRNA genes and two rRNA genes. Phylogenetic analyses showed that the C. quadratus and S. humilis belonged to different species in the same family, and were closely related to Hystrichopsylla weida qinlingensis in the same family; and showed a sister relationship between the orders Siphonaptera and Mecoptera, supporting the monophyly of the order Siphonaptera. Conclusions: This study is the first to decode the complete mt genomes of the C. quadratus and S. humilis . The results demonstrate that the C. quadratus and S. humilis are distinct species, and fleas are monophyletic. Analysis of mt genome provides novel molecular data for further studying the phylogeny and evolution of fleas.