A chromosome-level reference genome for the common bed bug, <i>Cimex lectularius,</i> with identification of sex chromosomes

The common bed bug, Cimex lectularius, is a globally distributed pest insect of medical, veterinary, and economic importance. Previous reference genome assemblies for this species were generated from short-read sequencing data, resulting in a ~650 Mb composed of thousands of contigs. Here, we present a haplotype-resolved, chromosome-level reference genome, generated from an adult Harlen strain female specimen. Using PacBio long read and Omni-C proximity sequencing, we generated a 540 Mb genome with 15 chromosomes (13 autosomes and 2 sex chromosomes-X1X2) with an N50 > 30 Mb and BUSCO > 90%. Previous karyotyping efforts indicate an XY sex chromosome system, with 2n = 26 and X1X1X2X2 females and X1X2Y males; however, significant fragmentation of the X chromosome has also been reported. We further use whole genome resequencing data from males and females to identify the X1 and X2 chromosomes based on sex biases in coverage. This highly contiguous reference genome assembly provides a much-improved resource for identifying chromosomal genome architecture, and for interpreting patterns of urban outbreaks and signatures of selection linked to insecticide resistance.