DOI: 10.5061/dryad.fn2z34v7f
title: Chromosome-level genome assembly of Dynastes reidi reveals structural evolution of autosomes and the sex chromosomes in Hercules Beetles

description: 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.
description: # Chromosome-level genome assembly of *Dynastes reidi* reveals structural
 evolution of autosomes and the sex chromosomes in Hercules Beetles
 [https://doi.org/10.5061/dryad.fn2z34v7f](https://doi.org/10.5061/dryad.fn2z34v7f) ## Description of the Data and file structure Files and folders (found within D.reidi.zip) ### **Braker2_results** ``` * reidi_braker.gff3: The information for gene predictions in *Dynastes reidi* genome assembly * reidi_braker.aa.fasta: The list of protein-coding genes in *Dynastes reidi* genome assembly ``` ### **BUSCO** Busco results of genome assembly and genome annotation of *D. reidi* genome assembly and annotation. ``` * busco_result_reidi_genome_assembly * busco sequences * fragmented_busco_sequences (40 files) * multi_copy_busco_sequences (76 files) * single_copy_busco_sequences (1961 files) full_table.tsv missing_busco_list.tsv short_summary.txt * busco_result_reidi_genome_annotation * busco sequences * fragmented_busco_sequences (48 files) * multi_copy_busco_sequences (338 files) * single_copy_busco_sequences (1665 files) full_table.tsv missing_busco_list.tsv short_summary.txt ``` ### **microsatellite_MISA** This folder provides the statistics for microsatellites in the *D. reidi* genome and their positions. ``` * reidi.misa (distribution of microsatellite in the D. reidi genome) * reidi_misa.statistics ``` ### **OrthoFinder_results** Gene families in the common ancestor of *D. reidi* and *D. maya* by using OrthoFinder software v2.2.7. ``` * Comparative_Genomics_Statistics: * Duplications_per_Orthogroup.tsv * Duplications_per_Species_Tree_Node.tsv * Orthogroups_SpeciesOverlaps.tsv * OrthologuesStats_many-to-many.tsv * OrthologuesStats_many-to-one.tsv * OrthologuesStats_one-to-many.tsv * OrthologuesStats_one-to-one.tsv * OrthologuesStats_Totals.tsv * Statistics_Overall.tsv * Statistics_PerSpecies.tsv * Single_Copy_Orthologue_Sequences: (8877 files) ``` ### **putative_gene_families** This folder provides fasta files for the sequences of putative gene families that are related to adaptive phenotypic variations in *D. reidi* and *D. maya*, including genes related to male horn shape and structure, and genes related to body coloration. ``` * Ebony.fa * Eyegone.fa * Laccase2.fa * optix.fa * PNR.fa * Rax_protein.fa * Scr.fa * SOX14.fa * SP8.fa * TBX20.fa * yellow.fa ``` ### **Repeat_libraries** This folder provides the library of repetitive elements with and without removing Unknown/Unclassified repeats. ``` * reidi_EDTA.TElib.classified.fa * reidi_EDTA.TElib.classified_exclude_unknown.fa ``` ## Sharing/access Information This data is also available under NCBI's BioProject Accession Number PRJNA815811