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

Abstract

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.

Keywords: Cimex lectularius; Hi-C; bed bug; chromosome-scale assembly; genome assembly; insecticide; resistance.

Fig. 1.

a) Hi-C contact map obtained after WenganA assembly. b) Identification of the X chromosome based on coverage information. The running medians calculated by the runmed R function (with k $=$ 1,001) are plotted for reads obtained from males or females. The different putative chromosomes are separated by vertical bars. c) Whole genome $F_{\mathrm{ST}}$ analysis between the insecticide-susceptible “LL” strain and the insecticide-resistant “LF” strain. The $F_{\mathrm{ST}}$ was computed using a sliding window of 1,000 SNPs (details in the text). The 15 chromosomes are displayed in a decreasing order from left to right and the remaining unplaced scaffolds are plotted on the right, after chromosome 15. The vertical line indicates the position of the VGSC gene and the horizontal dashed line indicates the median genome-wide $F_{\mathrm{ST}}$. d) Zoom in C, chromosome 14. The blue lines indicate the positions of 9 out of the 10 putative “resistance genes” depicted in Fig. 3 of Haberkorn et al. (2023) and the red line (around 14 Mb) indicates the position of VGSC. The bold line above the plot indicates the genomic region homologous to the four Clec_2.1 scaffolds that compose the “superlocus” as defined in Haberkorn et al. (2023) (now including a region homologous to the scaffold encoding VGSC in Clec_2.1). The continuous line was obtained using the loess function in R (span $=$ 0.15) applied on the $F_{\mathrm{ST}}$ values.

Fig. 2.

Synteny analysis for chromosome 14 of LL assembly against a) chromosome 15 of Harlan assembly H1 (haplotype 1), b) chromosome 15 of Harlan assembly H2 (haplotype 2). The position of the insecticide resistance genes identified in Fig. 3 of Haberkorn et al. (2023) and described in Supplementary Table S2 is indicated (gene ID from VGSC in bold with a star). Bold (red) lines indicate the synteny blocs overlapping with those genes.