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

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## Description of the Data and file structure

Files and folders (found within data.zip)

* **Braker2_results**
* grantii_braker.gff3: The information for gene predictions in *Dynastes grantii* genome assembly
* hyllus_braker.gff3: The information for gene predictions in *Dynastes hyllus* genome assembly
* maya_braker.gff3: The information for gene predictions in *Dynastes maya* genome assembly
* tityus_braker.gff3: The information for gene predictions in *Dynastes tityus* genome assembly
* **BUSCO:** Busco results of genome assembly and genome annotation of four Hercules beetle species. Accordingly, there are 4 folders inside the BUSCO folder. Within each folder, we provide the identified busco sequences from genome assembly (using option -m geno) and from the predicted protein of braker2 results (using option -m protein...