Chromosome-scale genome assembly of the bed bug Cimex lectularius sheds light on a key insecticide resistance locus

The population densities of the common bed bug, Cimex lectularius, have recently exploded worldwide. This demographic boom is mostly due to the evolution of insecticide resistance, which appears to be mainly driven by one autosomal locus in this species, identified by a Quantitative Trait Loci analysis. However, the exact gene content of this locus is still unclear, in particular regarding the inclusion of the voltage-gated sodium channel gene, due to uncertainty in previous assemblies available. To resolve this ambiguity, and more generally to provide useful resources to fight this hematophagous human parasite, we combined short, long, and Hi-C reads to produce a chromosome-scale assembly for this species. Three competing assembly strategies were used, all of which resulted in 13 autosomes plus two X chromosomes, consistent with previous cytological studies and a very recent chromosome-scale assembly. The best assembly had a total length of 507 Mb, an N50 of 35 Mb, encoded 98% of complete BUSCO genes, and covered 99% of the previous reference genome. This chromosome-scale assembly revealed that the main insecticide-resistance locus does indeed contain the voltage-gated sodium channel gene, as well as other genes possibly involved in insecticide resistance. Additionally, a population genomics analysis showed that this 7.65 Mb locus is highly differentiated between insecticide-resistant and susceptible strains, confirming previous results. We hope this high-quality, complete, and annotated genome of C. lectularius will serve as a useful resource to understand the mechanisms of insecticide resistance evolution and, more generally, better control bed bug populations.