The genomes of Hercules beetles reveal putative adaptive loci and distinct demographic histories in pristine North American forests
Abstract
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.
README: 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
- Comparative_Genomics_Statistics:
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
- Ebony:
- 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
- BarH1:
- 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.
- coloration_genes
Sharing/access Information
This data is also available under NCBI's BioProject Accession Number PRJNA815811