DOI: 10.5061/dryad.wdbrv15t8
title: Genome evolution is associated with nutrition-responsive regulatory development in horned dung beetles

description: The Scarabaeinae, or true dung beetles, are a hyper-diverse clade of
 insects of ecological, evolutionary, and agricultural significance and
 have long served as informative models of evolutionary ecology and
 development. Perhaps the most conspicuous of their unique traits are head
 horns, novel structures that serve as secondary sexual weapons, exhibit
 extraordinary developmental plasticity, and have fueled one of the most
 dramatic morphological radiations in the animal kingdom. In this study, we
 investigate the evolutionary basis for dung beetle traits - including
 horns - via comparative genomic and developmental assays. We present
 chromosome-level genome assemblies of three dung beetle species in the
 species-rich Onthophagini tribe (&gt; 2500 extant species) including
 Onthophagus taurus, Onthophagus sagittarius, and Digitonthophagus gazella.
 Contrasting these assemblies with seven other species across the order
 Coleoptera identifies rapidly evolving gene families associated with
 metabolic regulation of developmental plasticity and metamorphosis.
 Intraspecific comparisons of chromatin accessibility in developing head
 horns of O. taurus identify distinct cis-regulatory architectures
 underlying sex- and nutrition-responsive development of this novel trait,
 including a large proportion of recently evolved regulatory elements
 sensitive to horn morph determination. Binding motifs of diverse
 developmental transcription factors are enriched in these
 nutrition-responsive open chromatin regions, including the early embryonic
 patterning gene twist. Using RNA interference (RNAi), we show twist has
 been co-opted into the beetle horn regulatory network to mediate
 differential horn morphogenesis in alternate male morphs via its
 interactions with nutrition-sensitive DNA-binding sites, highlighting the
 utility of this approach in identifying new developmental regulators of
 morphological evolution. These results demonstrate gene networks are
 highly evolvable transducers of environmental and genetic signals critical
 for the formation and diversification of developmental traits, established
 in part by condition-responsive chromatin accessibility. Further, this
 work provides new reference-quality genome assemblies of three dung
 beetles that will bolster future developmental, ecological, and
 evolutionary studies of this insect group.
description: # Genome evolution is associated with nutrition-responsive regulatory
 development in horned dung beetles This dataset includes genome annotation
 files generated for a de-novo genome assembly project of dung beetle
 genomes. This project includes de-novo genome assemblies for *Onthophagus
 taurus* (Otau), *Onthophagus sagittarius* (Osag), and *Digitonthophagus
 gazella* (Dgaz). ### FILE TYPES For each of the three dung beetle species
 (listed above), the following file eight types are available: 1.
 *.fasta.gz: (compressed) genome fasta file 2. *_masked.fasta.gz:
 (compressed) genome fasta file in which repetitive elements are
 soft-masked (lower-case) 3. *.gtf: GTF file describing the genomic
 locations of gene features identified within the assembly 4. *_repeats.fa:
 library of repetitive elements identified in each species' genome 5.
 *_repeats.gff.gz: (compressed) GFF file describing the genomic location of
 repetitive elements within the genome 6. *_nucleotides.fasta: fasta file
 of gene model sequences identified within each species' genome 7.
 *_proteins.fasta: fasta file of protein model sequences identified within
 each species' genome (translated version of file #6) 8.
 *_best_hits.txt: annotations of gene models including the best hit of each
 model to the RefSeq non-redundant Ecdysozoan protein database and NCBI
 gene models of the O. taurus v.2 protein models ### OTHER FILES
 bioinformatic_commands.txt: text file describing the primary steps for
 bioinformatic analyses carried out in this work. Corresponds to
 SupplmentaryText1 is the published manuscript.