Comprehensive DNA methylation analysis of the Culex pipiens complex genome

The Culex pipiens complex, comprising subspecies like Culex pipiens pallens, Culex pipiens quinquefasciatus, and Culex pipiens molestus, serves as the vector for numerous mosquito-borne diseases, posing a global public health threat. Despite subtle morphological differences, these subspecies display significant variations in environmental and host preferences, as well as autogeny. This study aimed to elucidate interspecific differences within the Culex pipiens complex through DNA methylation analysis, employing Whole-genome bisulfite sequencing technology. Overall, the Culex pipiens complex exhibited low genome-wide methylation levels (0.6%), with CHH sites showing significantly higher methylation than CpG and CHG (p<0.001). Notably, 56 hypermethylated sites were identified, with the majority belonging to CHH and located within introns. Additionally, 178/209/215 differentially methylated sites and 4/8/11 differentially methylated regions were identified through comparisons between subspecies. GO pathway analysis highlighted impacts on protein binding, response to light stimuli, and abiotic stimuli, suggesting their involvement in subspecies differences. Numerous differentially methylated regions linked to energy metabolism and protein binding were identified, providing a novel perspective to comprehend distinctions within the Culex pipiens complex.This research not only enhances our understanding of interspecific variations in the Culex pipiens complex but also offers insights that could aid in the control of mosquito-borne diseases.