Phylogeny and biogeography of the Japanese rhinoceros beetle, <i>Trypoxylus dichotomus</i> (Coleoptera: Scarabaeidae) based on SNP markers

Yang, Huan; You, Chongjuan; Tsui, Clement K. M.; Tembrock, Luke R.; Wu, Zijun; Yang, De

doi:10.1002/ece3.6982

Cited by 13 publications

(6 citation statements)

References 78 publications

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“…The rhinoceros beetle, T. dichotomus (Coleoptera: Scarabaeidae), is an ecologically important xylophagous and saprophagous insect widely distributed in China and neighboring countries [ 18 ]. In the larval stage, it can decompose recalcitrant wood material and humus efficiently in the wild [ 19–21 ], and this has been harnessed industrially to biotransform the waste substrate from mushroom production [ 22 ].…”

Section: Introductionmentioning

confidence: 99%

A chromosome-level genome assembly and intestinal transcriptome of Trypoxylus dichotomus (Coleoptera: Scarabaeidae) to understand its lignocellulose digestion ability

Wang

Liu

Zhang³

et al. 2022

GigaScience

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Lignocellulose, as the key structural component of plant biomass, is a recalcitrant structure, difficult to degrade. The traditional management of plant waste, including landfill and incineration, usually causes serious environmental pollution and health problems. Interestingly, the xylophagous beetle, Trypoxylus dichotomus, can decompose lignocellulosic biomass. However, the genomics around the digestion mechanism of this beetle remain to be elucidated. Here, we assembled the genome of T. dichotomus, showing that the draft genome size of T. dichotomus is 636.27 Mb, with 95.37% scaffolds anchored onto 10 chromosomes. Phylogenetic results indicated that a divergent evolution between the ancestors of T. dichotomus and the closely related scarabaeid species Onthophagus taurus occurred in the early Cretaceous (120 million years ago). Through gene family evolution analysis, we found 67 rapidly evolving gene families, within which there were 2 digestive gene families (encoding Trypsin and Enoyl-(Acyl carrier protein) reductase) that have experienced significant expansion, indicating that they may contribute to the high degradation efficiency of lignocellulose in T. dichotomus. Additionally, events of chromosome breakage and rearrangement were observed by synteny analysis during the evolution of T. dichotomus due to chromosomes 6 and 8 of T. dichotomus being intersected with chromosomes 2 and 10 of Tribolium castaneum, respectively. Furthermore, the comparative transcriptome analyses of larval guts showed that the digestion-related genes were more commonly expressed in the midgut or mushroom residue group than the hindgut or sawdust group. This study reports the well-assembled and annotated genome of T. dichotomus, providing genomic and transcriptomic bases for further understanding the functional and evolutionary mechanisms of lignocellulose digestion in T. dichotomus.

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Section: Introductionmentioning

confidence: 99%

A chromosome-level genome assembly and intestinal transcriptome of Trypoxylus dichotomus (Coleoptera: Scarabaeidae) to understand its lignocellulose digestion ability

Wang

Liu

Zhang³

et al. 2022

GigaScience

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“…According to the size of the control region and different gene lengths, the insect mitochondrial genomes are generally 14-20 kb in length [27]. Mitochondrial genomes with characteristics such as rare sequence recombination, maternal inheritance, gene conservation, and high evolution rate represent an essential tool for comparative studies [29,30]. A comparative study based on gene arrangement, length variation, atypical start codon, and base composition bias permits analysis of the molecular differences among species to reconstruct taxonomy [31].…”

Section: Introductionmentioning

confidence: 99%

The Mitochondrial Genomes of 18 New Pleurosticti (Coleoptera: Scarabaeidae) Exhibit a Novel trnQ-NCR-trnI-trnM Gene Rearrangement and Clarify Phylogenetic Relationships of Subfamilies within Scarabaeidae

Ayivi

Tong

Storey

et al. 2021

Insects

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The availability of next-generation sequencing (NGS) in recent years has facilitated a revolution in the availability of mitochondrial (mt) genome sequences. The mt genome is a powerful tool for comparative studies and resolving the phylogenetic relationships among insect lineages. The mt genomes of phytophagous scarabs of the subfamilies Cetoniinae and Dynastinae were under-represented in GenBank. Previous research found that the subfamily Rutelinae was recovered as a paraphyletic group because the few representatives of the subfamily Dynastinae clustered into Rutelinae, but the subfamily position of Dynastinae was still unclear. In the present study, we sequenced 18 mt genomes from Dynastinae and Cetoniinae using next-generation sequencing (NGS) to re-assess the phylogenetic relationships within Scarabaeidae. All sequenced mt genomes contained 37 sets of genes (13 protein-coding genes, 22 tRNAs, and two ribosomal RNAs), with one long control region, but the gene order was not the same between Cetoniinae and Dynastinae species. All mt genomes of Dynastinae species showed the same gene rearrangement of trnQ-NCR-trnI-trnM, whereas all mt genomes of Cetoniinae species showed the ancestral insect gene order of trnI-trnQ-trnM. Phylogenetic analyses (IQ-tree and MrBayes) were conducted using 13 protein-coding genes based on nucleotide and amino acid datasets. In the ML and BI trees, we recovered the monophyly of Rutelinae, Cetoniinae, Dynastinae, and Sericinae, and the non-monophyly of Melolonthinae. Cetoniinae was shown to be a sister clade to (Dynastinae + Rutelinae).

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“…S2 b). Genetic partitioning and divergence have been reported for T. dichotomus according to geographical distribution, with clear morphological differences 75 . Information on the structural variations identified here will be a useful source for studying the evolution of T. dichotomus through comparative genomics approaches.…”

Section: Resultsmentioning

confidence: 99%

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

Morita

Shibata

Nishiyama

et al. 2023

Sci Rep

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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.

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Phylogeny and biogeography of the Japanese rhinoceros beetle, Trypoxylus dichotomus (Coleoptera: Scarabaeidae) based on SNP markers

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 13 publications

References 78 publications

A chromosome-level genome assembly and intestinal transcriptome of Trypoxylus dichotomus (Coleoptera: Scarabaeidae) to understand its lignocellulose digestion ability

A chromosome-level genome assembly and intestinal transcriptome of Trypoxylus dichotomus (Coleoptera: Scarabaeidae) to understand its lignocellulose digestion ability

The Mitochondrial Genomes of 18 New Pleurosticti (Coleoptera: Scarabaeidae) Exhibit a Novel trnQ-NCR-trnI-trnM Gene Rearrangement and Clarify Phylogenetic Relationships of Subfamilies within Scarabaeidae

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

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