Abstract：
Beetles, despite their remarkable biodiversity and a long history of research, remain lacking in reference genomes annotated with structural variations in 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 colouration. 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 homologues of nine and three candidate-gene families that may be associated with the evolution of horn structure and body colouration 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.
摘要：
甲虫,尽管它们具有非凡的生物多样性和悠久的研究历史，仍然缺乏具有适应性意义的基因座结构变异的参考基因组。我们对四个Hercules甲虫的高质量染色体水平基因组进行了测序和组装，这些甲虫在雄角大小，形状和身体颜色上表现出差异。四个赫拉克勒斯甲虫基因组被组装成11个假染色体，使用纳米孔数据组装了三个基因组(Dynastesgrantii，D.hyllus和D.tityus）映射到使用PacBioHi-C数据组装的基因组（D.玛雅）。我们证明了这四个物种在基因组结构上的惊人相似性。这种保守的基因组结构可能归因于我们使用D.maya组装作为参考;然而，值得注意的是，这种保守的基因组结构是圣甲虫中反复出现的现象。我们进一步鉴定了9个和3个候选基因家族的同源物，它们可能分别与角结构和体色的进化有关。检测并讨论了Scr和Ebony2的结构变化对甲虫形态多样性的推定影响。我们还使用来自二倍体基因组的杂合性信息重建了四个Hercules甲虫的人口统计学历史。我们发现，甲虫的人口统计学历史紧密地概括了由气候变化驱动的合适森林栖息地的历史变化。
