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

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 one male and two 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.