The genomes of Hercules beetles reveal putative adaptive loci and distinct demographic histories in pristine North American forests

Beetles, despite their remarkable biodiversity and a long history of research, remain lacking in reference genomes annotated with structural variations of loci of adaptive significance. We sequenced and assembled high-quality chromosome-level genomes of four Hercules beetles which exhibit divergence in male horn size and shape, and body coloration. The four Hercules beetle genomes were assembled to 11 pseudo-chromosomes, where the three genomes assembled using Nanopore data (Dynastes grantii, D. hyllus, and D. tityus) were mapped to the genome assembled using PacBio + Hi-C data (D. maya). We demonstrated a striking similarity in genome structure among the four species. This conservative genome structure may be attributed to our use of the D. maya assembly as the reference; however, it is worth noting that such a conservative genome structure is a recurring phenomenon among scarab beetles. We further identified homologs of nine and three candidate-gene families that may be associated with the evolution of horn structure and body coloration, respectively. Structural variations in Scr and Ebony2 were detected and discussed for their putative impacts on generating morphological diversity in beetles. We also reconstructed the demographic histories of the four Hercules beetles using heterozygosity information from the diploid genomes. We found that the demographic histories of the beetles closely recapitulated historical changes in suitable forest habitats driven by climate shifts.

甲虫尽管具有极高的生物多样性且研究历史悠久，但目前仍缺乏带有适应性位点结构变异注释的参考基因组。本研究对4种雄性角大小、形态及体色存在分化的犀金龟（Hercules beetles）进行测序，并组装获得高质量染色体级基因组。该4个犀金龟基因组均组装至11条假染色体水平，其中3个基于纳米孔测序（Nanopore）数据组装的基因组（Dynastes grantii、D. hyllus与D. tityus）均被比对至采用PacBio+Hi-C技术组装的玛雅犀金龟（D. maya）参考基因组。本研究发现，这4个物种的基因组结构具有极高的相似性。这种保守的基因组结构可能源于我们以D. maya组装体作为参考基因组；但值得注意的是，此类基因组结构保守性在金龟子（scarab beetles）类群中是一种普遍存在的现象。本研究进一步分别鉴定出9个与角结构演化相关、3个与体色演化相关的候选基因家族同源物。研究人员检测到Scr基因与Ebony2基因的结构变异，并就其对甲虫形态多样性产生的潜在影响展开了讨论。本研究还利用二倍体基因组的杂合性信息，重构了该4种犀金龟的种群历史。研究发现，这些甲虫的种群历史与气候变化驱动的适宜森林栖息地的历史变化高度吻合。