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Weber JN, Kojima W, Boisseau RP, Niimi T, Morita S, Shigenobu S, Gotoh H, Araya K, Lin CP, Thomas-Bulle C, Allen CE, Tong W, Lavine LC, Swanson BO, Emlen DJ. Evolution of horn length and lifting strength in the Japanese rhinoceros beetle Trypoxylus dichotomus. Curr Biol 2023; 33:4285-4297.e5. [PMID: 37734374 DOI: 10.1016/j.cub.2023.08.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/28/2023] [Accepted: 08/23/2023] [Indexed: 09/23/2023]
Abstract
What limits the size of nature's most extreme structures? For weapons like beetle horns, one possibility is a tradeoff associated with mechanical levers: as the output arm of the lever system-the beetle horn-gets longer, it also gets weaker. This "paradox of the weakening combatant" could offset reproductive advantages of additional increases in weapon size. However, in contemporary populations of most heavily weaponed species, males with the longest weapons also tend to be the strongest, presumably because selection drove the evolution of compensatory changes to these lever systems that ameliorated the force reductions of increased weapon size. Therefore, we test for biomechanical limits by reconstructing the stages of weapon evolution, exploring whether initial increases in weapon length first led to reductions in weapon force generation that were later ameliorated through the evolution of mechanisms of mechanical compensation. We describe phylogeographic relationships among populations of a rhinoceros beetle and show that the "pitchfork" shaped head horn likely increased in length independently in the northern and southern radiations of beetles. Both increases in horn length were associated with dramatic reductions to horn lifting strength-compelling evidence for the paradox of the weakening combatant-and these initial reductions to horn strength were later ameliorated in some populations through reductions to horn length or through increases in head height (the input arm for the horn lever system). Our results reveal an exciting geographic mosaic of weapon size, weapon force, and mechanical compensation, shedding light on larger questions pertaining to the evolution of extreme structures.
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Affiliation(s)
- Jesse N Weber
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Wataru Kojima
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8511, Japan
| | - Romain P Boisseau
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
| | - Teruyuki Niimi
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka Myodaiji, Okazaki 444-8585, Japan
| | - Shinichi Morita
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka Myodaiji, Okazaki 444-8585, Japan
| | - Shuji Shigenobu
- Trans-Scale Biology Center, National Institute for Basic Biology, 38 Nishigonaka Myodaiji, Okazaki 444-8585, Japan
| | - Hiroki Gotoh
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Oya, Suruga Ward, Shizuoka, Japan
| | - Kunio Araya
- Faculty of Social and Cultural Studies, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka-city Fukuoka 819-0395, Japan
| | - Chung-Ping Lin
- Department of Life Science, National Taiwan Normal University, No.88 Sec. 4, Tingzhou Rd, Taipei 11677, Taiwan
| | - Camille Thomas-Bulle
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA; Department of Biological Sciences, University of Denver, Denver, CO 80208, USA
| | - Cerisse E Allen
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
| | - Wenfei Tong
- Cornell Laboratory of Ornithology, Ithaca, NY 14850, USA
| | - Laura Corley Lavine
- Department of Entomology, Washington State University, Pullman, WA 99164, USA
| | - Brook O Swanson
- Department of Biology, Gonzaga University, 502 East Boone Avenue, Spokane, WA 99258-0102, USA
| | - Douglas J Emlen
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA.
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Morita S, Shibata TF, Nishiyama T, Kobayashi Y, Yamaguchi K, Toga K, Ohde T, Gotoh H, Kojima T, Weber JN, Salvemini M, Bino T, Mase M, Nakata M, Mori T, Mori S, Cornette R, Sakura K, Lavine LC, Emlen DJ, Niimi T, Shigenobu S. The draft genome sequence of the Japanese rhinoceros beetle Trypoxylus dichotomus septentrionalis towards an understanding of horn formation. Sci Rep 2023; 13:8735. [PMID: 37253792 DOI: 10.1038/s41598-023-35246-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 05/15/2023] [Indexed: 06/01/2023] Open
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.
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Grants
- 23128505, 25128706, 16H01452, 18H04766, 20H04933, 20H05944, 17H06384, 22128008, 19K16181, 21K15135 Japan Society for the Promotion of Science
- 23128505, 25128706, 16H01452, 18H04766, 20H04933, 20H05944, 17H06384, 22128008, 19K16181, 21K15135 Japan Society for the Promotion of Science
- 23128505, 25128706, 16H01452, 18H04766, 20H04933, 20H05944, 17H06384, 22128008, 19K16181, 21K15135 Japan Society for the Promotion of Science
- 23128505, 25128706, 16H01452, 18H04766, 20H04933, 20H05944, 17H06384, 22128008, 19K16181, 21K15135 Japan Society for the Promotion of Science
- IOS-1456133 National Science Foundation
- IOS-1456133 National Science Foundation
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Affiliation(s)
- Shinichi Morita
- 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
| | - Tomoko F Shibata
- Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki, Japan
| | - Tomoaki Nishiyama
- Division of Integrated Omics Research, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Japan
| | - Yuuki Kobayashi
- Laboratory of Evolutionary Genomics, National Institute for Basic Biology, Okazaki, Japan
| | - Katsushi Yamaguchi
- Trans-Omics Facility, National Institute for Basic Biology, Okazaki, Japan
| | - Kouhei Toga
- 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
| | - Takahiro Ohde
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Okazaki, Japan
- Laboratory of Sericulture and Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Department of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hiroki Gotoh
- Laboratory of Sericulture and Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Department of Biological Science, Faculty of Science, Shizuoka University, Shizuoka, Japan
| | - Takaaki Kojima
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Department of Agrobiological Resources, Faculty of Agriculture, Meijo University, Nagoya, Japan
| | - Jesse N Weber
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Marco Salvemini
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Takahiro Bino
- Trans-Omics Facility, National Institute for Basic Biology, Okazaki, Japan
| | - Mutsuki Mase
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Okazaki, Japan
- Laboratory of Sericulture and Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Moe Nakata
- Laboratory of Sericulture and Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Tomoko Mori
- Trans-Omics Facility, National Institute for Basic Biology, Okazaki, Japan
| | - Shogo Mori
- Trans-Omics Facility, National Institute for Basic Biology, Okazaki, Japan
| | - Richard Cornette
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Kazuki Sakura
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Okazaki, Japan
| | - Laura C Lavine
- Department of Entomology, Washington State University, Pullman, WA, USA
| | - Douglas J Emlen
- Division of Biological Sciences, The University of Montana, Missoula, MT, USA
| | - Teruyuki Niimi
- 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.
- Laboratory of Sericulture and Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan.
| | - Shuji Shigenobu
- Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Japan.
- Laboratory of Evolutionary Genomics, National Institute for Basic Biology, Okazaki, Japan.
- Trans-Omics Facility, National Institute for Basic Biology, Okazaki, Japan.
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Wang Q, Liu L, Zhang S, Wu H, Huang J. A chromosome-level genome assembly and intestinal transcriptome of Trypoxylus dichotomus (Coleoptera: Scarabaeidae) to understand its lignocellulose digestion ability. Gigascience 2022; 11:giac059. [PMID: 35764601 PMCID: PMC9239855 DOI: 10.1093/gigascience/giac059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/30/2022] [Accepted: 05/27/2022] [Indexed: 12/15/2022] Open
Abstract
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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Affiliation(s)
- Qingyun Wang
- National Joint Local Engineering Laboratory for High-Efficient Preparation of Biopesticide, Zhejiang A&F University, 666 Wusu Street, Lin'an, Hangzhou, Zhejiang 311300, China
| | - Liwei Liu
- National Joint Local Engineering Laboratory for High-Efficient Preparation of Biopesticide, Zhejiang A&F University, 666 Wusu Street, Lin'an, Hangzhou, Zhejiang 311300, China
- Zhejiang Museum of Natural History, No. 6 West Lake Cultural Square, Hangzhou, Zhejiang 310014, China
| | - Sujiong Zhang
- Dapanshan Insect Institute of Zhejiang, Pan'an, Zhejiang 322300, China
| | - Hong Wu
- National Joint Local Engineering Laboratory for High-Efficient Preparation of Biopesticide, Zhejiang A&F University, 666 Wusu Street, Lin'an, Hangzhou, Zhejiang 311300, China
| | - Junhao Huang
- National Joint Local Engineering Laboratory for High-Efficient Preparation of Biopesticide, Zhejiang A&F University, 666 Wusu Street, Lin'an, Hangzhou, Zhejiang 311300, China
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Jiang Q, Han Z, Li W, Ji T, Yuan Y, Zhang J, Zhao C, Cheng Z, Wang S. Adsorption properties of heavy metals and antibiotics by chitosan from larvae and adult Trypoxylus dichotomus. Carbohydr Polym 2022; 276:118735. [PMID: 34823771 DOI: 10.1016/j.carbpol.2021.118735] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/26/2021] [Accepted: 10/04/2021] [Indexed: 12/20/2022]
Abstract
Chitosan was prepared by hydrothermal deacetylation from multi-step protein purification chitin based on Trypoxylus dichotomus, for treating heavy metals and antibiotics. Chitosan with higher deacetylation degree and lower molecular weight were synthesized. The adult chitosan was composed of nanofibers arranged more evenly, showing higher yield, thermal stabilities and antimicrobial properties. The adsorption capacities of Cu2+ and Fe3+ were 462 and 270 mg/g, lower than 934 mg/g of Pb2+. Levofloxacin and tetracycline hydrochloride adsorption capacity were 26 and 22 mg/g, lower than 67 mg/g of sulfamethoxazole. In addition, compared with single pollutants, the adsorption of sulfamethoxazole and Pb2+ can increase by 6% and 5% when they act as composite contaminants. The adsorption procedure can be well described by pseudo-second-order kinetics and Langmuir isothermal model, indicating it a homogeneous monolayer chemisorption. Therefore, the Trypoxylus dichotomus source chitosan prepared by hydrothermal deacetylation has potential applications in the adsorption of complex pollutants.
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Affiliation(s)
- Qiushi Jiang
- College of Resources and Environment, Jilin Agricultural University, Changchun 130118, People's Republic of China
| | - Zhaolian Han
- College of Resources and Environment, Jilin Agricultural University, Changchun 130118, People's Republic of China
| | - Weiping Li
- College of Resources and Environment, Jilin Agricultural University, Changchun 130118, People's Republic of China
| | - Tingxu Ji
- College of Plant protection, Jilin Agricultural University, Changchun 130118, People's Republic of China
| | - Yafeng Yuan
- College of Resources and Environment, Jilin Agricultural University, Changchun 130118, People's Republic of China
| | - Junjie Zhang
- Jilin Province Technology Research Center of Biological Control Engineering, Jilin Agricultural University, Changchun 130118, People's Republic of China
| | - Chunli Zhao
- College of Horticulture, Jilin Agricultural University, Changchun 130118, People's Republic of China
| | - Zhiqiang Cheng
- College of Resources and Environment, Jilin Agricultural University, Changchun 130118, People's Republic of China.
| | - Song Wang
- Urology department of the first hospital of Jilin University, 71# Xinmin street, Changchun 130000, People's Republic of China.
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5
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OUP accepted manuscript. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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6
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Ayivi SPG, Tong Y, Storey KB, Yu DN, Zhang JY. 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. INSECTS 2021; 12:1025. [PMID: 34821825 PMCID: PMC8622766 DOI: 10.3390/insects12111025] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/07/2021] [Accepted: 11/09/2021] [Indexed: 12/24/2022]
Abstract
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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Affiliation(s)
- Sam Pedro Galilee Ayivi
- Department of Biology, College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (S.P.G.A.); (Y.T.)
| | - Yao Tong
- Department of Biology, College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (S.P.G.A.); (Y.T.)
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada;
| | - Dan-Na Yu
- Department of Biology, College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (S.P.G.A.); (Y.T.)
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Jia-Yong Zhang
- Department of Biology, College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (S.P.G.A.); (Y.T.)
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
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