Mitogenomic architecture and phylogenetic placement of Ctenophthalmus yunnanus and Frontopsylla diqingensis: insights from comparative genomics

Shaobo Tang¹Lei Chen²Jun Wu³Bin Chen¹Shuang Liu¹Mingna Duan¹Dandan Jiang¹Wei Gu^4*Quanfu Zhang^5*Xing Yang^1*

• ¹Dali University, Dali, China
• ²The Base for control and prevention of plague and brucellosis, Chinese center for disease control and prevention. Jilin Province, China, Jilin Province, China
• ³Dali Bai Autonomous Prefecture People's Hospital Ophthalmology No.35 Renmin South Road, Xiaguan Town, Dali City, Yunnan Province, China., Dali, China
• ⁴Department of Infection of the First Affiliated Hospital of Dali University and Yunnan Provincial Department of Education Key Laboratory of Infectious Diseases, Dali, China., Dali, China
• ⁵Department of Gastroenterology, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College., Sichuan, China

This study sequenced the complete mitochondrial genomes of Ctenophthalmus yunnanus (first mitogenome reported) and Frontopsylla diqingensis from Yunnan, China, using Illumina sequencing. Comparative analyses with existing flea mitogenomes available in NCBI included nucleotide diversity and selective pressure assessments. Phylogenetic trees were reconstructed based on the PCG123 and PCG12 datasets using the Maximum Likelihood (ML) and Bayesian Inference (BI) methods, respectively. The mitogenomes of C. yunnanus (15,801 bp) and F. diqingensis (15,878 bp) are circular double-stranded. Each of two genomes comprises 37 genes. Analysis of the comparative genomic data reveals that most fleas examined in this study possess the mitochondrial genomes that are approximately 16,000 bp long, with an average AT content nearing 78%. Additionally, the values of AT skew and GC skew for most flea species are negative. Among the 13 PCGs, the codons UUA, UUU and AUU are used more frequently. Analysis of nucleotide diversity and selection pressure indicated that the cox1 gene exhibited the lowest values for both Pi and Ka/Ks. Phylogenetic analysis demonstrates that the family Ctenophthalmidae, to which C. yunnanus belongs, and the family Leptopsyllidae, to which F. diqingensis belongs, are paraphyletic. Divergence time estimation indicates that the most recent common ancestor of crown-group fleas diverged during the Cretaceous period, while the majority of extant lineages within Siphonaptera underwent diversification following the K-Pg boundary. This study expands the flea mitochondrial genome database and supports future genetic and phylogenetic research.