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

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. EmlenTeruyuki Niimi, Shuji Shigenobu

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish
Article number8735
Pages (from-to)8735
JournalScientific Reports
Volume13
Issue number1
DOIs
StatePublished - May 30 2023

Keywords

  • Animals
  • Female
  • Male
  • Coleoptera/genetics
  • Phenotype
  • Sex Characteristics

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