The differentiating power of mitochondrial genes: complete mitogenome sequences of 27 mosquito species present in Europe

Abstract The rapid advancement of genomic tools has revolutionised entomological research, offering new insights into insect evolution, population dynamics, and species identification. Much in line with most other insects, mitochondrial DNA has emerged as a key resource in mosquito studies, with the partial cox1 (cytochrome oxidase c subunit 1, oftentimes referred to as COI) gene commonly used for species identification. However, cox1 ’s limitations in resolving cryptic and sibling species and its challenges in metabarcoding applications underscore the need to explore alternative genetic markers. This study addresses the lack of comprehensive reference mitogenomes for mosquitoes present in Europe, by sequencing and assembling 82 mitochondrial genomes from 27 Northwest European species including 3 invasive Aedes species. Two-thirds of the species’ mitogenomes were sequenced for the first time. Our results highlight a notable variability of mitochondrial genes, highlighting the potential for development of genetic markers to improve taxonomic resolution. Notably, the nad6 and nad2 genes demonstrated more variability compared to cox1 , exhibiting higher nucleotide diversity, more variable base pairs and greater between-species variability. These genes are flanked by conserved tRNA genes, providing ideal primer sites and enabling efficient amplification for degraded or pooled samples. As such, this study presents a foundation for improved molecular identification techniques, enhancing mosquito monitoring and research across Europe by providing mitogenome sequences of 26% of the 102 European mosquito species. It also highlights the need to sequence the mitogenomes of a much larger fraction of the mosquito species community. By expanding the availability of mitogenomic data, researchers can explore novel genetic markers to improve biomonitoring and address current challenges in species identification.