Chromosome-Level Sex-Specific Genome Assemblies of Onthophagus binodis Provide Insight into Scarab Sex Chromosomes

TL;DR

Researchers created detailed male and female genome maps for a scarab beetle, revealing insights into sex chromosomes and genome evolution.

Contribution

The study provides the first chromosome-level sex-specific genome assemblies for Onthophagus binodis using advanced sequencing techniques.

Findings

The male and female assemblies show a high level of completeness with over 97% BUSCO completeness scores.

Repetitive sequences make up over 75% of the genome, contributing to its large size compared to related species.

Putative Y chromosome sequences were identified in the male assembly through coverage and k-mer analysis.

Abstract

Onthophagus binodis is a coprophagous scarab beetle native to southern Africa. This species and many others in the tribe Onthophagini have been introduced to farms across multiple continents in the context of cattle pasture management efforts. The ecosystem services provided by this species, along with the amenability of comparative developmental and evolutionary studies in this clade, contribute to its role as an emerging insect model system. Here, we present sex-specific chromosomal-level genome assemblies for O. binodis generated from a combination of PacBio long reads and HiC chromatin conformation sequencing. The completeness of the 950.5 Mb female assembly and the 880.5 Mb male assembly is indicated by a contig length N50 of at least 58.6 Mb. BUSCO single-copy and duplicated completeness scores were 99.0% and 0.9% for the female assembly and 97.4% and 2.1% for the male assembly. Gene modeling identified at least 15,403 gene models in each genome with an average transcript length of 1.6 kb. Comparative analyses with other Onthophagini genomes indicated a dramatic expansion of repetitive sequences, which now comprise over 75% of this species’ genome and have driven the expansion of overall genome size to nearly twice that of close relatives. We combined the best-assembled chromosome-scale scaffolds from each sex to generate a hybrid reference assembly for this species. Comparative genomic analyses show that the nine autosomes and the X chromosome identified here in O. binodis are likely conserved throughout Onthophagini. Our sex-specific sequencing approach allowed us to identify putative Y chromosome sequences in the male assembly via coverage mapping and k-mer abundance comparisons. These genomes will be of great value to the scientific community as resources for studying insect genome evolution, development, and ecology.

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