Supplemental Material for Haberkorn et al., 2025

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 QTL analysis. However, the exact gene content of this locus is still unclear, in particular regarding the inclusion of the Voltage-Gated Sodium Channel (VGSC) 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 VGSC 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.温带臭虫（Cimex lectularius）的种群密度近期在全球范围内呈现爆发式增长。此次种群爆发主要源于抗药性演化，而该物种的抗药性主要由一个常染色体基因座驱动，这一结论通过数量性状基因座（Quantitative Trait Locus, QTL）分析得以确定。然而，该基因座的确切基因组成仍不明确，尤其是关于电压门控钠通道（Voltage-Gated Sodium Channel, VGSC）基因是否包含其中，这是因为现有早期基因组组装结果存在不确定性。为解决这一歧义，同时更为广泛地提供对抗这种吸血人类寄生虫的实用资源，本研究结合短读长、长读长及Hi-C测序数据，构建了该物种的染色体级基因组组装。本研究采用了三种不同的组装策略，最终均得到包含13条常染色体与2条X染色体的组装结果，与此前细胞学研究及近期发表的染色体级组装结果一致。最优组装的总长度为507 Mb，N50值为35 Mb，覆盖了98%的完整通用单拷贝同源基准基因集（Benchmarking Universal Single-Copy Orthologs, BUSCO）基因，且覆盖了此前参考基因组99%的序列。该染色体级组装结果显示，主要抗药性基因座确实包含VGSC基因，以及其他可能与抗药性相关的基因。此外，群体基因组学分析表明，这个7.65 Mb的基因座在抗药性与敏感品系间存在高度分化，验证了此前的研究结果。我们期望这份高质量、完整且已注释的温带臭虫（C. lectularius）基因组，能够成为理解抗药性演化机制的实用资源，并更为广泛地助力臭虫种群的防控工作。