The draft genome sequence of the Japanese rhinoceros beetle Trypoxylus dichotomus septentrionalis towards an understanding of horn formation

May 2023
Shinichi Morita, Tomoko F. Shibata, Tomoaki Nishiyama, Yuuki Kobayashi, Katsushi Yamaguchi, Kouhei Toga, Takahiro Ohde, Hiroki Gotoh, Takaaki Kojima, Jesse N. Weber, Marco Salvemini, Takahiro Bino, Mutsuki Mase, Moe Nakata, Tomoko Mori, Shogo Mori, Richard Cornette, Kazuki Sakura, Laura C. Lavine, Douglas J. Emlen, Teruyuki Niimi and Shuji Shigenobu

“The Japanese rhinoceros beetle Trypoxylus dichotomus is a giant beetle with distinctive exaggerated horns present on the head and prothoracic regions of the male. T. dichotomus has been used as a 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 10 × 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. We focused on the genes related to horn formation and obtained new insights into the evolution of the gene repertoire and sexual dimorphism as exemplified by the sex-specific splicing pattern of the doublesex gene. 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.”

Sage Science Products:
The SageHLS instrument was used to size select DNA between 50-80 kb for 10X Genomics Chromium linked read analysis.

Author Affiliations:
Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Okazaki, Japan
Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Japan
Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki, Japan
Division of Integrated Omics Research, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Japan
Laboratory of Evolutionary Genomics, National Institute for Basic Biology, Okazaki, Japan
Trans-Omics Facility, National Institute for Basic Biology, Okazaki, Japan
Laboratory of Sericulture and Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
URA Division, Office of Research and Academia-Government-Community Collaboration, Hiroshima University, Hiroshima, Japan
Department of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
Department of Biological Science, Faculty of Science, Shizuoka University, Shizuoka, Japan
Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
Department of Agrobiological Resources, Faculty of Agriculture, Meijo University, Nagoya, Japan
Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
Department of Biology, University of Naples Federico II, Naples, Italy
Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
Department of Entomology, Washington State University, Pullman, WA, USA
Division of Biological Sciences, The University of Montana, Missoula, MT, USA

Nature Scientific Reports

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