DOI: 10.5061/dryad.6wwpzgn33
title: The genomes of Hercules beetles reveal putative adaptive loci and distinct demographic histories in pristine North American forests

description: 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 with the
 evolution of horn structure and body coloration, 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.
description: # The genomes of Hercules beetles reveal putative adaptive loci and
 distinct demographic histories in pristine North American forests --- ##
 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 proteins), the table of completed busco
 sequences (full_table.tsv), missing busco sequences
 (missing_busco_list.tsv), and a summary (short_summary.txt). In addition,
 there are three folders inside each busco_sequences folder including
 fragmented busco sequences, multi-copy busco sequences, and single-copy
 busco sequences. The detailed structure of each folder are listed below: *
 ***D_grantii*** * busco_result_grantii_genome_annotation * busco sequences
 * fragmented_busco_sequences (84 files) * multi_copy_busco_sequences (243
 files) * single_copy_busco_sequences (1638 files) full_table.tsv
 missing_busco_list.tsv short_summary.txt *
 busco_result_grantii_genome_assembly * busco sequences *
 fragmented_busco_sequences (67 files) * multi_copy_busco_sequences (18
 files) * single_copy_busco_sequences (1943 files) full_table.tsv
 missing_busco_list.tsv short_summary.txt * ***D_hyllus*** *
 busco_result_hyllus_genome_annotation * busco sequences *
 fragmented_busco_sequences (229 files) * multi_copy_busco_sequences (186
 files) * single_copy_busco_sequences (1362 files) full_table.tsv
 missing_busco_list.tsv short_summary.txt *
 busco_result_hyllus_genome_assembly * busco sequences *
 fragmented_busco_sequences (145 files) * multi_copy_busco_sequences (12
 files) * single_copy_busco_sequences (1666 files) full_table.tsv
 missing_busco_list.tsv short_summary.txt * ***D_maya*** *
 busco_result_maya_genome_annotation * busco sequences *
 fragmented_busco_sequences (40 files) * multi_copy_busco_sequences (275
 files) * single_copy_busco_sequences (1764 files) full_table.tsv
 missing_busco_list.tsv short_summary.txt *
 busco_result_maya_genome_assembly * busco sequences *
 fragmented_busco_sequences (49 files) * multi_copy_busco_sequences (19
 files) * single_copy_busco_sequences (2034 files) full_table.tsv
 missing_busco_list.tsv short_summary.txt * ***D_tityus*** *
 busco_result_tityus_genome_annotation * busco sequences *
 fragmented_busco_sequences (53 files) * multi_copy_busco_sequences (244
 files) * single_copy_busco_sequences (1772 files) full_table.tsv
 missing_busco_list.tsv short_summary.txt *
 busco_result_tityus_genome_assembly * busco sequences *
 fragmented_busco_sequences (45 files) * multi_copy_busco_sequences (25
 files) * single_copy_busco_sequences (2021 files) full_table.tsv
 missing_busco_list.tsv short_summary.txt * **OrthoFinder_results:** gene
 families in the common ancestor of four Dynastes beetle species that were
 clustered 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: (8133 files)
 * Species_Tree: * Orthogroups_for_concatenated_alignment.txt *
 SpeciesTree_rooted.txt * SpeciesTree_rooted_node_labels.txt *
 SpeciesTree_single_orthologues.txt * **putative_gene_families:** This
 folder provides fasta files for the sequences of putative gene families
 that related to adaptive phenotypic variations in Hercules beetles,
 including genes related to male horn shape and structure, and genes
 related to body coloration. * coloration_genes * Ebony: *
 Ebony2_1_OG0010274.fa * Ebony2_1_OG0010274_aln.fa * Ebony2_2_OG0010275.fa
 * Ebony2_2_OG0010275_aln.fas * Laccase2: * Laccase2_1_OG0010398.fa *
 Laccase2_1_OG0010398_aln.fas * Laccase2_2_OG0010399.fa *
 Laccase2_2_OG0010399_aln.fas * Yellow: * Yellow_OG0001480.fa *
 Yellow_OG0001480_aln.fas * Yellow_OG0007698.fa * Yellow_OG0007698_aln.fas
 * Yellow_OG0008341.fa * Yellow_OG0008341_aln.fas * Yellow_OG0008412.fa *
 Yellow_OG0008412_aln.fas * Yellow_OG0010074.fa * Yellow_OG0010074_aln.fas
 * Yellow_OG0012504.fa * Yellow_OG0012504_aln.fas * Yellow_OG0012505.fa *
 Yellow_OG0012505_aln.fas * Yellow_OG0012507.fa * Yellow_OG0012507_aln.fas
 * horn_shape_genes * BarH1: * BarH1_1_OG0003503.fa *
 BarH1_1_OG0003503_aln.fas * BarH1_2_OG0009440.fa *
 BarH1_2_OG0009440_aln.fas * Eyegone: * Eyegone_1_OG0005897.fa *
 Eyegone_1_OG0005897_aln.fas * Eyegone_2_OG0017256.fa *
 Eyegone_2_OG0017256_aln.fas * PNR: * PNR_OG0004876.fa *
 PNR_OG0004876_aln.fas * Rax: * RAX_OG0000654.fa * RAX_OG0000654_aln.fas *
 Rx1: * Rx1_1_OG0006301.fa * Rx1_1_OG0006301_aln.fas * Rx1_2_OG0006303.fa *
 Rx1_2_OG0006303_aln.fas * Rx_like: * Rxlike_OG0006304.fa *
 Rxlike_OG0006304_aln.fas * Sex_combs_reduced: * Scr_OG0002354.fa *
 Scr_OG0002354_aln.fas * Sox14: * SOX14_1_OG0004487.fa *
 SOX14_1_OG0004487_aln.fas * SOX14_2_OG0004490.fa *
 SOX14_2_OG0004490_aln.fas * SOX14_3_OG0012931.fa *
 SOX14_3_OG0012931_aln.fas * TBX20: * TBX20_1_OG0002187.fa *
 TBX20_1_OG0002187_aln.fas * TBX20_2_OG0005089.fa *
 TBX20_2_OG0005089_aln.fas * TBX20_3_OG0013115.fa *
 TBX20_3_OG0013115_aln.fas * TBX20_4_OG0015527.fa *
 TBX20_4_OG0015527_aln.fas * putative_genes_positions.xlsx: this is a xlsx
 file that provide the information distribution of all candidate genes that
 related to coloration and horn shape in the four Hercules beetle genomes.
 The results are visualized and discussed more detail in our paper. ##
 Sharing/access Information This data is also available under NCBI's
 BioProject Accession Number PRJNA815811