Chromosome-level genome assembly of Dynastes reidi reveals structural evolution of autosomes and the sex chromosomes in Hercules beetles

Abstract The Hercules beetles have long been iconic symbols of evolutionary diversification, sexual selection, and systematics. Despite their rapid phenotypic evolution and a rich history of inspiring evolutionary biologists, genomic resources for these charismatic beetles remain limited, especially for the Giant Hercules beetles. We present the first chromosome-level genome assembly of a Giant Hercules beetle from the Lesser Antilles. The assembled genome is approximately 837 Mb in size, with a scaffold N50 of 66.68 Mb, which can be anchored to 11 pseudochromosomes with a BUSCO completeness score of 95.9%. An estimate of 55.5% of the genome can be attributed to repetitive elements. Additionally, we detected candidate sex-linked chromosomes by comparing sequencing read depths between 1 male and 2 females using Illumina short reads. The chromosome-level genome assembly of Dynastes reidi not only provides critical insights into evolutionary and functional genomics but also supports informed conservation and management efforts. In addition, this genomic resource will enable future pangenome analyses aimed at understanding the genetic basis of species divergence and morphological innovation in beetles. Our study also marks the emergence of a new model system to investigate the origin and diversification of phenotypic novelty by leveraging genomic resources across diverse domesticated beetle breeds.