The draft genome sequence of Japanese rhinoceros beetle Trypoxylus dichotomus

Abstract

Beetles are the largest insect order and one of the most successful animal groups in terms of number of species. The Japanese rhinoceros beetle Trypoxylus dichotomus (Coleoptera, Scarabaeidae, Dynastini) is a giant beetle with distinctive exaggerated horns present on the head and prothoracic regions of the male. T. dichotomus has been used as research model in various fields such as evolutionary developmental biology, ecology, ethology, biomimetics, and drug discovery. In this study, de novo assembly of 615 Mb, representing 80% of the genome estimated by flow cytometry, was obtained using the 10x Chromium platform. The scaffold N50 length of the genome assembly was 8.02 Mb, with repetitive elements predicted to comprise 49.5% of the assembly. In total, 23,987 protein-coding genes were predicted in the genome. In addition, de novo assembly of the mitochondrial genome yielded a contig of 20,217 bp. We also analyzed the transcriptome by generating 16 RNA-seq libraries from a variety of tissues of both sexes and developmental stages, which allowed us to identify 13 co-expressed gene modules. The detailed genomic and transcriptomic information of T. dichotomus is the most comprehensive among those reported for any species of Dynastinae. This genomic information will be an excellent resource for further functional and evolutionary analyses, including the evolutionary origin and genetic regulation of beetle horns and the molecular mechanisms underlying sexual dimorphism.

Genome evolution and divergence in cis-regulatory architecture is associated with condition-responsive development in horned dung beetles

“…Comparative genome analyses included the three newly assembled dung beetle genomes presented in this study alongside seven other high-quality beetle genomes representing a diverse PLOS GENETICS set of families across the Coleoptera. These genomes include the common eastern firefly Photinus pyralis [56], emerald ash borer Agrilus planipennis, red flour beetle Tribolium castaneum [57], mountain pine beetle Dendroctonus ponderosae [58], Asian longhorned beetle Anoplophora glabripennis [59], Colorado potato beetle Leptinotarsa decemlineata [60], and the Japanese rhinoceros beetle Trypoxylus dichotomus [61]. For all analyses of gene content between species, only the longest isoform of each species' gene was used.…”