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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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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Kobayashi Y, Shibata TF, Hirakawa H, Nishiyama T, Yamada A, Hasebe M, Shigenobu S, Kawaguchi M. The genome of Lyophyllum shimeji provides insight into the initial evolution of ectomycorrhizal fungal genomes. DNA Res 2023; 30:6969780. [PMID: 36610744 PMCID: PMC9896470 DOI: 10.1093/dnares/dsac053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/29/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Mycorrhizae are one of the most fundamental symbioses between plants and fungi, with ectomycorrhizae being the most widespread in boreal forest ecosystems. Ectomycorrhizal fungi are hypothesized to have evolved convergently from saprotrophic ancestors in several fungal clades, especially members of the subdivision Agaricomycotina. Studies on fungal genomes have identified several typical characteristics of mycorrhizal fungi, such as genome size expansion and decreases in plant cell-wall degrading enzymes (PCWDEs). However, genomic changes concerning the evolutionary transition to the ectomycorrhizal lifestyle are largely unknown. In this study, we sequenced the genome of Lyophyllum shimeji, an ectomycorrhizal fungus that is phylogenetically related to saprotrophic species and retains some saprotroph-like traits. We found that the genome of Ly. shimeji strain AT787 lacks both incremental increases in genome size and reduced numbers of PCWDEs. Our findings suggest that the previously reported common genomic traits of mycorrhizal fungi are not essential for the ectomycorrhizal lifestyle, but are a result of abolishing saprotrophic activity. Since Ly. shimeji is commercially consumed as an edible mushroom, the newly available genomic information may also impact research designed to enhance the cultivation of this mushroom.
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Affiliation(s)
- Yuuki Kobayashi
- To whom correspondence should be addressed. Tel.: +81-0564-55-7672, (Y.K.)
| | - Tomoko F Shibata
- Division of Evolutionary Biology, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Tomoaki Nishiyama
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Ishikawa 920-0934, Japan
| | - Akiyoshi Yamada
- Faculty of Agriculture, Shinshu University, Kamiina, Nagano 399-4598, Japan
| | - Mitsuyasu Hasebe
- Division of Evolutionary Biology, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan,Department of Basic Biology, SOKENDAI, Okazaki, Aichi 444-8585, Japan
| | - Shuji Shigenobu
- Laboratory of Evolutionary Genomics, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan,Department of Basic Biology, SOKENDAI, Okazaki, Aichi 444-8585, Japan,Trans-omics Facility, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
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3
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Konno D, Sugino S, Shibata TF, Misawa K, Imamura-Kawasawa Y, Suzuki J, Kido K, Nagasaki M, Yamauchi M. Antiemetic effects of baclofen in a shrew model of postoperative nausea and vomiting: Whole-transcriptome analysis in the nucleus of the solitary tract. CNS Neurosci Ther 2022; 28:922-931. [PMID: 35238164 PMCID: PMC9062569 DOI: 10.1111/cns.13823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 11/28/2022] Open
Abstract
Aims The molecular genetic mechanisms underlying postoperative nausea and vomiting (PONV) in the brain have not been fully elucidated. This study aimed to determine the changes in whole transcriptome in the nucleus of the solitary tract (NTS) in an animal model of PONV, to screen a drug candidate and to elucidate the molecular genetic mechanisms of PONV development. Methods Twenty‐one female musk shrews were assigned into three groups: the Surgery group (shrew PONV model, n = 9), the Sham group (n = 6), and the Naïve group (n = 6). In behavioral studies, the main outcome was the number of emetic episodes. In genetic experiments, changes in the transcriptome in the NTS were measured. In a separate study, 12 shrews were used to verify the candidate mechanism underlying PONV. Results A median of six emetic episodes occurred in both the Sham and Surgery groups. Whole‐transcriptome analysis indicated the inhibition of the GABAB receptor‐mediated signaling pathway in the PONV model. Baclofen (GABAB receptor agonist) administration eliminated emetic behaviors in the shrew PONV model. Conclusions Our findings suggest that the GABAB receptor‐mediated signaling pathway is involved in emesis and that baclofen may be a novel therapeutic or prophylactic agent for PONV.
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Affiliation(s)
- Daisuke Konno
- Department of Anesthesiology and Perioperative Medicine, Tohoku University School of Medicine, Sendai, Japan.,Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan
| | - Shigekazu Sugino
- Department of Anesthesiology and Perioperative Medicine, Tohoku University School of Medicine, Sendai, Japan
| | - Tomoko F Shibata
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan
| | - Kazuharu Misawa
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yuka Imamura-Kawasawa
- Department of Pharmacology, Biochemistry and Molecular Biology, Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, USA
| | - Jun Suzuki
- Department of Anesthesiology and Perioperative Medicine, Tohoku University School of Medicine, Sendai, Japan
| | - Kanta Kido
- Department of Anesthesiology, Kanagawa Dental University Graduate School of Dentistry, Yokosuka, Japan
| | - Masao Nagasaki
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan
| | - Masanori Yamauchi
- Department of Anesthesiology and Perioperative Medicine, Tohoku University School of Medicine, Sendai, Japan
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4
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Li Y, Omori A, Flores RL, Satterfield S, Nguyen C, Ota T, Tsurugaya T, Ikuta T, Ikeo K, Kikuchi M, Leong JCK, Reich A, Hao M, Wan W, Dong Y, Ren Y, Zhang S, Zeng T, Uesaka M, Uchida Y, Li X, Shibata TF, Bino T, Ogawa K, Shigenobu S, Kondo M, Wang F, Chen L, Wessel G, Saiga H, Cameron RA, Livingston B, Bradham C, Wang W, Irie N. Author Correction: Genomic insights of body plan transitions from bilateral to pentameral symmetry in Echinoderms. Commun Biol 2021; 4:459. [PMID: 33824400 PMCID: PMC8024292 DOI: 10.1038/s42003-021-02005-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A Correction to this paper has been published: https://doi.org/10.1038/s42003-021-02005-4
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Affiliation(s)
- Yongxin Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Akihito Omori
- Sado Island Center for Ecological Sustainability, Niigata University, Niigata, Japan
| | - Rachel L Flores
- Dept. of Biological Sciences, California State Univesity, Long Beach, CA, USA
| | - Sheri Satterfield
- Dept. of Biological Sciences, California State Univesity, Long Beach, CA, USA
| | - Christine Nguyen
- Dept. of Biological Sciences, California State Univesity, Long Beach, CA, USA
| | | | | | - Tetsuro Ikuta
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa, Japan.,Tokyo Metropolitan University, Yokosuka, Tokyo, Japan
| | | | | | - Jason C K Leong
- Dept. of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Adrian Reich
- Providence Institute of Molecular Oogenesis, Brown University, Providence, RI, USA
| | - Meng Hao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wenting Wan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yang Dong
- Yunnan Agricultural University, Kunming, China
| | - Yaondong Ren
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Si Zhang
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Tao Zeng
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Masahiro Uesaka
- RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo, Japan
| | - Yui Uchida
- Dept. of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Universal Biology Institute, University of Tokyo, Tokyo, Japan
| | - Xueyan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Tomoko F Shibata
- Dept. of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Takahiro Bino
- NIBB Core Research Facilities, National Institute of Basic Biology, Okazaki, Aichi, Japan
| | - Kota Ogawa
- Faculty of Social and Cultural Studies, Kyushu University, Fukuoka, Japan
| | - Shuji Shigenobu
- NIBB Core Research Facilities, National Institute of Basic Biology, Okazaki, Aichi, Japan
| | - Mariko Kondo
- Dept. of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Fayou Wang
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Luonan Chen
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.,Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China
| | - Gary Wessel
- Providence Institute of Molecular Oogenesis, Brown University, Providence, RI, USA
| | - Hidetoshi Saiga
- Tokyo Metropolitan University, Yokosuka, Tokyo, Japan.,Dept. of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Chuo University, Tokyo, Japan
| | - R Andrew Cameron
- Beckman Institute, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Brian Livingston
- Dept. of Biological Sciences, California State Univesity, Long Beach, CA, USA
| | | | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. .,School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China.
| | - Naoki Irie
- Dept. of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan. .,Universal Biology Institute, University of Tokyo, Tokyo, Japan.
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5
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Yano H, Alam MZ, Rimbara E, Shibata TF, Fukuyo M, Furuta Y, Nishiyama T, Shigenobu S, Hasebe M, Toyoda A, Suzuki Y, Sugano S, Shibayama K, Kobayashi I. Corrigendum: Networking and Specificity-Changing DNA Methyltransferases in Helicobacter pylori. Front Microbiol 2020; 11:596598. [PMID: 33072061 PMCID: PMC7537328 DOI: 10.3389/fmicb.2020.596598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 11/18/2022] Open
Affiliation(s)
- Hirokazu Yano
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.,Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Md Zobaidul Alam
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Emiko Rimbara
- Department of Bacteriology II, National Institute of Infectious Diseases (NIID), Musashimurayama, Japan
| | | | | | - Yoshikazu Furuta
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.,Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tomoaki Nishiyama
- Advanced Science Research Center, Kanazawa University, Kanazawa, Japan
| | | | - Mitsuyasu Hasebe
- National Institute for Basic Biology (NIBB), Okazaki, Japan.,Department of Basic Biology, School of Life Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Sumio Sugano
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.,Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Keigo Shibayama
- Department of Bacteriology II, National Institute of Infectious Diseases (NIID), Musashimurayama, Japan
| | - Ichizo Kobayashi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.,Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Department of Infectious Diseases, School of Medicine, Kyorin University, Mitaka, Japan.,Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France.,Research Center for Micro-Nano Technology, Hosei University, Koganei, Japan
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6
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Cui S, Kubota T, Nishiyama T, Ishida JK, Shigenobu S, Shibata TF, Toyoda A, Hasebe M, Shirasu K, Yoshida S. Ethylene signaling mediates host invasion by parasitic plants. Sci Adv 2020; 6:6/44/eabc2385. [PMID: 33115743 PMCID: PMC7608805 DOI: 10.1126/sciadv.abc2385] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 09/10/2020] [Indexed: 05/18/2023]
Abstract
Parasitic plants form a specialized organ, a haustorium, to invade host tissues and acquire water and nutrients. To understand the molecular mechanism of haustorium development, we performed a forward genetics screening to isolate mutants exhibiting haustorial defects in the model parasitic plant Phtheirospermum japonicum. We isolated two mutants that show prolonged and sometimes aberrant meristematic activity in the haustorium apex, resulting in severe defects on host invasion. Whole-genome sequencing revealed that the two mutants respectively have point mutations in homologs of ETHYLENE RESPONSE 1 (ETR1) and ETHYLENE INSENSITIVE 2 (EIN2), signaling components in response to the gaseous phytohormone ethylene. Application of the ethylene signaling inhibitors also caused similar haustorial defects, indicating that ethylene signaling regulates cell proliferation and differentiation of parasite cells. Genetic disruption of host ethylene production also perturbs parasite invasion. We propose that parasitic plants use ethylene as a signal to invade host roots.
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Affiliation(s)
- Songkui Cui
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
- Institute for Research Initiatives, Division for Research Strategy, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Tomoya Kubota
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Tomoaki Nishiyama
- Advanced Science Research Center, Kanazawa University, Kanazawa 920-0934, Japan
| | | | - Shuji Shigenobu
- National Institute for Basic Biology, Okazaki 444-8585, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Okazaki 444-8585, Japan
| | | | - Atsushi Toyoda
- Comparative Genomics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Mitsuyasu Hasebe
- National Institute for Basic Biology, Okazaki 444-8585, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Okazaki 444-8585, Japan
| | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Satoko Yoshida
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.
- Institute for Research Initiatives, Division for Research Strategy, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
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7
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Yano H, Alam MZ, Rimbara E, Shibata TF, Fukuyo M, Furuta Y, Nishiyama T, Shigenobu S, Hasebe M, Toyoda A, Suzuki Y, Sugano S, Shibayama K, Kobayashi I. Networking and Specificity-Changing DNA Methyltransferases in Helicobacter pylori. Front Microbiol 2020; 11:1628. [PMID: 32765461 PMCID: PMC7379913 DOI: 10.3389/fmicb.2020.01628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022] Open
Abstract
Epigenetic DNA base methylation plays important roles in gene expression regulation. We here describe a gene expression regulation network consisting of many DNA methyltransferases each frequently changing its target sequence-specificity. Our object Helicobacter pylori, a bacterium responsible for most incidence of stomach cancer, carries a large and variable repertoire of sequence-specific DNA methyltransferases. By creating a dozen of single-gene knockout strains for the methyltransferases, we revealed that they form a network controlling methylome, transcriptome and adaptive phenotype sets. The methyltransferases interact with each other in a hierarchical way, sometimes regulated positively by one methyltransferase but negatively with another. Motility, oxidative stress tolerance and DNA damage repair are likewise regulated by multiple methyltransferases. Their regulation sometimes involves translation start and stop codons suggesting coupling of methylation, transcription and translation. The methyltransferases frequently change their sequence-specificity through gene conversion of their target recognition domain and switch their target sets to remodel the network. The emerging picture of a metamorphosing gene regulation network, or firework, consisting of epigenetic systems ever-changing their specificity in search for adaptation, provides a new paradigm in understanding global gene regulation and adaptive evolution.
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Affiliation(s)
- Hirokazu Yano
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.,Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Md Zobaidul Alam
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Emiko Rimbara
- Department of Bacteriology II, National Institute of Infectious Diseases (NIID), Musashimurayama, Japan
| | | | | | - Yoshikazu Furuta
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.,Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tomoaki Nishiyama
- Advanced Science Research Center, Kanazawa University, Kanazawa, Japan
| | | | - Mitsuyasu Hasebe
- National Institute for Basic Biology (NIBB), Okazaki, Japan.,Department of Basic Biology, School of Life Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Sumio Sugano
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.,Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Keigo Shibayama
- Department of Bacteriology II, National Institute of Infectious Diseases (NIID), Musashimurayama, Japan
| | - Ichizo Kobayashi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.,Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Department of Infectious Diseases, School of Medicine, Kyorin University, Mitaka, Japan.,Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France.,Research Center for Micro-Nano Technology, Hosei University, Koganei, Japan
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8
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Li Y, Omori A, Flores RL, Satterfield S, Nguyen C, Ota T, Tsurugaya T, Ikuta T, Ikeo K, Kikuchi M, Leong JCK, Reich A, Hao M, Wan W, Dong Y, Ren Y, Zhang S, Zeng T, Uesaka M, Uchida Y, Li X, Shibata TF, Bino T, Ogawa K, Shigenobu S, Kondo M, Wang F, Chen L, Wessel G, Saiga H, Cameron RA, Livingston B, Bradham C, Wang W, Irie N. Genomic insights of body plan transitions from bilateral to pentameral symmetry in Echinoderms. Commun Biol 2020; 3:371. [PMID: 32651448 PMCID: PMC7351957 DOI: 10.1038/s42003-020-1091-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 06/19/2020] [Indexed: 12/13/2022] Open
Abstract
Echinoderms are an exceptional group of bilaterians that develop pentameral adult symmetry from a bilaterally symmetric larva. However, the genetic basis in evolution and development of this unique transformation remains to be clarified. Here we report newly sequenced genomes, developmental transcriptomes, and proteomes of diverse echinoderms including the green sea urchin (L. variegatus), a sea cucumber (A. japonicus), and with particular emphasis on a sister group of the earliest-diverged echinoderms, the feather star (A. japonica). We learned that the last common ancestor of echinoderms retained a well-organized Hox cluster reminiscent of the hemichordate, and had gene sets involved in endoskeleton development. Further, unlike in other animal groups, the most conserved developmental stages were not at the body plan establishing phase, and genes normally involved in bilaterality appear to function in pentameric axis development. These results enhance our understanding of the divergence of protostomes and deuterostomes almost 500 Mya. Li et al. investigate the evolution and genetic basis of the adult pentameral body plan in echinoderms using genomic, transcriptomic, and proteomic data. They determine that the last common ancestor of echinoderms contained an organized Hox cluster and endoskeleton genes, and suggest that cooption of bilateral development genes was involved in evolution of the pentameric body plan.
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Affiliation(s)
- Yongxin Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Akihito Omori
- Sado Island Center for Ecological Sustainability, Niigata University, Niigata, Japan
| | - Rachel L Flores
- Dept. of Biological Sciences, California State Univesity, Long Beach, CA, USA
| | - Sheri Satterfield
- Dept. of Biological Sciences, California State Univesity, Long Beach, CA, USA
| | - Christine Nguyen
- Dept. of Biological Sciences, California State Univesity, Long Beach, CA, USA
| | | | | | - Tetsuro Ikuta
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa, Japan.,Tokyo Metropolitan University, Yokosuka, Tokyo, Japan
| | | | | | - Jason C K Leong
- Dept. of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Adrian Reich
- Providence Institute of Molecular Oogenesis, Brown University, Providence, RI, USA
| | - Meng Hao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wenting Wan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yang Dong
- Yunnan Agricultural University, Kunming, China
| | - Yaondong Ren
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Si Zhang
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Tao Zeng
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Masahiro Uesaka
- RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo, Japan
| | - Yui Uchida
- Dept. of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Universal Biology Institute, University of Tokyo, Tokyo, Japan
| | - Xueyan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Tomoko F Shibata
- Dept. of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Takahiro Bino
- NIBB Core Research Facilities, National Institute of Basic Biology, Okazaki, Aichi, Japan
| | - Kota Ogawa
- Faculty of Social and Cultural Studies, Kyushu University, Fukuoka, Japan
| | - Shuji Shigenobu
- NIBB Core Research Facilities, National Institute of Basic Biology, Okazaki, Aichi, Japan
| | - Mariko Kondo
- Dept. of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Fayou Wang
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Luonan Chen
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.,Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China
| | - Gary Wessel
- Providence Institute of Molecular Oogenesis, Brown University, Providence, RI, USA
| | - Hidetoshi Saiga
- Tokyo Metropolitan University, Yokosuka, Tokyo, Japan.,Dept. of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Chuo University, Tokyo, Japan
| | - R Andrew Cameron
- Beckman Institute, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Brian Livingston
- Dept. of Biological Sciences, California State Univesity, Long Beach, CA, USA
| | | | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. .,School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China.
| | - Naoki Irie
- Dept. of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan. .,Universal Biology Institute, University of Tokyo, Tokyo, Japan.
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Omori A, Shibata TF, Akasaka K. Gene expression analysis of three homeobox genes throughout early and late development of a feather star Anneissia japonica. Dev Genes Evol 2020; 230:305-314. [PMID: 32671457 DOI: 10.1007/s00427-020-00665-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 07/08/2020] [Indexed: 11/26/2022]
Abstract
Crinoids are considered as the most basal extant echinoderms. They retain aboral nervous system with a nerve center, which has been degraded in the eleutherozoan echinoderms. To investigate the evolution of patterning of the nervous systems in crinoids, we examined temporal and spatial expression patterns of three neural patterning-related homeobox genes, six3, pax6, and otx, throughout the development of a feather star Anneissia japonica. These genes were involved in the patterning of endomesodermal tissues instead of the ectodermal neural tissues in the early planktonic stages. In the stages after larval attachment, the expression of these genes was mainly observed in the podia and the oral nervous systems instead of the aboral nerve center. Our results indicate the involvement of these three genes in the formation of oral nervous system in the common ancestor of the echinoderms and suggest that the aboral nerve center is not evolutionally related to the brain of other bilaterians.
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Affiliation(s)
- Akihito Omori
- Marine Biological Station, Sado Island Center for Ecological Sustainability, Niigata University, 87 Tassha, Sado, Niigata, 952-2135, Japan.
- Misaki Marine Biological Station, School of Science, The University of Tokyo, 1024 Koajiro, Misaki, Miura, Kanagawa, 238-0225, Japan.
| | - Tomoko F Shibata
- Misaki Marine Biological Station, School of Science, The University of Tokyo, 1024 Koajiro, Misaki, Miura, Kanagawa, 238-0225, Japan
| | - Koji Akasaka
- Misaki Marine Biological Station, School of Science, The University of Tokyo, 1024 Koajiro, Misaki, Miura, Kanagawa, 238-0225, Japan
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10
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Palfalvi G, Hackl T, Terhoeven N, Shibata TF, Nishiyama T, Ankenbrand M, Becker D, Förster F, Freund M, Iosip A, Kreuzer I, Saul F, Kamida C, Fukushima K, Shigenobu S, Tamada Y, Adamec L, Hoshi Y, Ueda K, Winkelmann T, Fuchs J, Schubert I, Schwacke R, Al-Rasheid K, Schultz J, Hasebe M, Hedrich R. Genomes of the Venus Flytrap and Close Relatives Unveil the Roots of Plant Carnivory. Curr Biol 2020; 30:2312-2320.e5. [PMID: 32413308 PMCID: PMC7308799 DOI: 10.1016/j.cub.2020.04.051] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/16/2020] [Accepted: 04/21/2020] [Indexed: 12/20/2022]
Abstract
Most plants grow and develop by taking up nutrients from the soil while continuously under threat from foraging animals. Carnivorous plants have turned the tables by capturing and consuming nutrient-rich animal prey, enabling them to thrive in nutrient-poor soil. To better understand the evolution of botanical carnivory, we compared the draft genome of the Venus flytrap (Dionaea muscipula) with that of its aquatic sister, the waterwheel plant Aldrovanda vesiculosa, and the sundew Drosera spatulata. We identified an early whole-genome duplication in the family as source for carnivory-associated genes. Recruitment of genes to the trap from the root especially was a major mechanism in the evolution of carnivory, supported by family-specific duplications. Still, these genomes belong to the gene poorest land plants sequenced thus far, suggesting reduction of selective pressure on different processes, including non-carnivorous nutrient acquisition. Our results show how non-carnivorous plants evolved into the most skillful green hunters on the planet.
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Affiliation(s)
- Gergo Palfalvi
- National Institute for Basic Biology, Okazaki 444-8585, Japan; Department of Basic Biology, The Graduate School for Advanced Studies, SOKENDAI, Okazaki 444-8585, Japan
| | - Thomas Hackl
- Department for Bioinformatics, Biocenter, University Würzburg, Am Hubland, 97074 Würzburg, Germany; Institute for Molecular Plant Physiology and Biophysics, University Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany
| | - Niklas Terhoeven
- Institute for Molecular Plant Physiology and Biophysics, University Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany; Center for Computational and Theoretical Biology, Faculty for Biology, University Würzburg, Klara-Oppenheimer-Weg 32, Campus Hubland Nord, 97074 Würzburg, Germany
| | | | - Tomoaki Nishiyama
- Advanced Science Research Center, Kanazawa University, Kanazawa 920-0934, Japan
| | - Markus Ankenbrand
- Department for Bioinformatics, Biocenter, University Würzburg, Am Hubland, 97074 Würzburg, Germany; Center for Computational and Theoretical Biology, Faculty for Biology, University Würzburg, Klara-Oppenheimer-Weg 32, Campus Hubland Nord, 97074 Würzburg, Germany
| | - Dirk Becker
- Institute for Molecular Plant Physiology and Biophysics, University Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany
| | - Frank Förster
- Department for Bioinformatics, Biocenter, University Würzburg, Am Hubland, 97074 Würzburg, Germany; Center for Computational and Theoretical Biology, Faculty for Biology, University Würzburg, Klara-Oppenheimer-Weg 32, Campus Hubland Nord, 97074 Würzburg, Germany
| | - Matthias Freund
- Institute for Molecular Plant Physiology and Biophysics, University Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany; Center for Computational and Theoretical Biology, Faculty for Biology, University Würzburg, Klara-Oppenheimer-Weg 32, Campus Hubland Nord, 97074 Würzburg, Germany
| | - Anda Iosip
- Institute for Molecular Plant Physiology and Biophysics, University Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany; Center for Computational and Theoretical Biology, Faculty for Biology, University Würzburg, Klara-Oppenheimer-Weg 32, Campus Hubland Nord, 97074 Würzburg, Germany
| | - Ines Kreuzer
- Institute for Molecular Plant Physiology and Biophysics, University Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany
| | - Franziska Saul
- Institute for Molecular Plant Physiology and Biophysics, University Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany; Center for Computational and Theoretical Biology, Faculty for Biology, University Würzburg, Klara-Oppenheimer-Weg 32, Campus Hubland Nord, 97074 Würzburg, Germany
| | - Chiharu Kamida
- National Institute for Basic Biology, Okazaki 444-8585, Japan; Department of Basic Biology, The Graduate School for Advanced Studies, SOKENDAI, Okazaki 444-8585, Japan
| | - Kenji Fukushima
- National Institute for Basic Biology, Okazaki 444-8585, Japan; Department of Basic Biology, The Graduate School for Advanced Studies, SOKENDAI, Okazaki 444-8585, Japan; Institute for Molecular Plant Physiology and Biophysics, University Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany
| | - Shuji Shigenobu
- National Institute for Basic Biology, Okazaki 444-8585, Japan; Department of Basic Biology, The Graduate School for Advanced Studies, SOKENDAI, Okazaki 444-8585, Japan
| | - Yosuke Tamada
- National Institute for Basic Biology, Okazaki 444-8585, Japan; Department of Basic Biology, The Graduate School for Advanced Studies, SOKENDAI, Okazaki 444-8585, Japan; School of Engineering, Utsunomiya University, Utsunomiya 321-8585, Japan
| | - Lubomir Adamec
- Department of Functional Ecology, Institute of Botany CAS, 379 01 Třeboň, Czech Republic
| | - Yoshikazu Hoshi
- Department of Plant Science, School of Agriculture, Tokai University, Kumamoto 862-8652, Japan
| | - Kunihiko Ueda
- Faculty of Education, Gifu University, Gifu 501-1193, Japan
| | - Traud Winkelmann
- Institute of Horticultural Production Systems, Woody Plant and Propagation Physiology, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Rainer Schwacke
- Institute of Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Corrensstraße 3, 06466 Gatersleben, Germany
| | - Khaled Al-Rasheid
- Institute for Molecular Plant Physiology and Biophysics, University Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany; Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Jörg Schultz
- Department for Bioinformatics, Biocenter, University Würzburg, Am Hubland, 97074 Würzburg, Germany; Center for Computational and Theoretical Biology, Faculty for Biology, University Würzburg, Klara-Oppenheimer-Weg 32, Campus Hubland Nord, 97074 Würzburg, Germany.
| | - Mitsuyasu Hasebe
- National Institute for Basic Biology, Okazaki 444-8585, Japan; Department of Basic Biology, The Graduate School for Advanced Studies, SOKENDAI, Okazaki 444-8585, Japan.
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, University Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany.
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11
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Nagasaki M, Kuroki Y, Shibata TF, Katsuoka F, Mimori T, Kawai Y, Minegishi N, Hozawa A, Kuriyama S, Suzuki Y, Kawame H, Nagami F, Takai-Igarashi T, Ogishima S, Kojima K, Misawa K, Tanabe O, Fuse N, Tanaka H, Yaegashi N, Kinoshita K, Kure S, Yasuda J, Yamamoto M. Construction of JRG (Japanese reference genome) with single-molecule real-time sequencing. Hum Genome Var 2019; 6:27. [PMID: 31231536 PMCID: PMC6555796 DOI: 10.1038/s41439-019-0057-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 01/28/2019] [Accepted: 03/15/2019] [Indexed: 12/14/2022] Open
Abstract
In recent genome analyses, population-specific reference panels have indicated important. However, reference panels based on short-read sequencing data do not sufficiently cover long insertions. Therefore, the nature of long insertions has not been well documented. Here, we assembled a Japanese genome using single-molecule real-time sequencing data and characterized insertions found in the assembled genome. We identified 3691 insertions ranging from 100 bps to ~10,000 bps in the assembled genome relative to the international reference sequence (GRCh38). To validate and characterize these insertions, we mapped short-reads from 1070 Japanese individuals and 728 individuals from eight other populations to insertions integrated into GRCh38. With this result, we constructed JRGv1 (Japanese Reference Genome version 1) by integrating the 903 verified insertions, totaling 1,086,173 bases, shared by at least two Japanese individuals into GRCh38. We also constructed decoyJRGv1 by concatenating 3559 verified insertions, totaling 2,536,870 bases, shared by at least two Japanese individuals or by six other assemblies. This assembly improved the alignment ratio by 0.4% on average. These results demonstrate the importance of refining the reference assembly and creating a population-specific reference genome. JRGv1 and decoyJRGv1 are available at the JRG website. Researchers in Japan have assembled a Japanese reference genome, which includes sequences missing from the international reference genome, as well as others specific to East Asian populations. A team led by Masao Nagasaki and Masayuki Yamamoto sequenced a Japanese individual using a method, which produces longer sequences than previous technologies. Using this approach, they identified thousands of sequences spanning 2.5 million bases, which were absent in the international reference genome. Many of these were sequences able to move within the genome. They showed that the majority of these sequences are also present in early humans and chimpanzees, demonstrating that their absence from the current reference is due to deletions or limitations of earlier sequencing methodologies. In addition to providing a population-specific reference, these findings demonstrate the importance of continually improving the international reference genome.
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Affiliation(s)
- Masao Nagasaki
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan.,3Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Yoko Kuroki
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan.,4Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Tomoko F Shibata
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Fumiki Katsuoka
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Takahiro Mimori
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Yosuke Kawai
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan.,3Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Naoko Minegishi
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Atsushi Hozawa
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shinichi Kuriyama
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan.,5International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Yoichi Suzuki
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Hiroshi Kawame
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Fuji Nagami
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | | | - Soichi Ogishima
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kaname Kojima
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan.,3Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Kazuharu Misawa
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Osamu Tanabe
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Nobuo Fuse
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,6Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Hiroshi Tanaka
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Nobuo Yaegashi
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan.,6Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Kengo Kinoshita
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,3Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Shiego Kure
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan.,6Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Jun Yasuda
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan
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12
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Kudo A, Shigenobu S, Kadota K, Nozawa M, Shibata TF, Ishikawa Y, Matsuo T. Comparative analysis of the brain transcriptome in a hyper-aggressive fruit fly, Drosophila prolongata. Insect Biochem Mol Biol 2017; 82:11-20. [PMID: 28115271 DOI: 10.1016/j.ibmb.2017.01.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 01/16/2017] [Accepted: 01/17/2017] [Indexed: 06/06/2023]
Abstract
Aggressive behavior is observed in many animals, but its intensity differs between species. In a model animal of genetics, Drosophila melanogaster, genetic basis of aggressive behavior has been studied intensively, including transcriptome analyses to identify genes whose expression level was associated with intra-species variation in aggressiveness. However, whether these genes are also involved in the evolution of aggressiveness among different species has not been examined. In this study, we performed de novo transcriptome analysis in the brain of Drosophila prolongata to identify genes associated with the evolution of aggressiveness. Males of D. prolongata were hyper-aggressive compared with closely related species. Comparison of the brain transcriptomes identified 21 differentially expressed genes in males of D. prolongata. They did not overlap with the list of aggression-related genes identified in D. melanogaster, suggesting that genes involved in the evolution of aggressiveness were independent of those associated with the intra-species variation in aggressiveness in Drosophila. Although females of D. prolongata were not aggressive as the males, expression levels of the 21 genes identified in this study were more similar between sexes than between species.
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Affiliation(s)
- Ayumi Kudo
- Department of Agricultural and Environmental Biology, The University of Tokyo, Tokyo, Japan
| | - Shuji Shigenobu
- National Institute for Basic Biology, Okazaki, Japan; Department of Basic Biology, Faculty of Life Science, The Graduate University for Advanced Studies, Okazaki, Japan
| | - Koji Kadota
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | | | | | - Yukio Ishikawa
- Department of Agricultural and Environmental Biology, The University of Tokyo, Tokyo, Japan
| | - Takashi Matsuo
- Department of Agricultural and Environmental Biology, The University of Tokyo, Tokyo, Japan.
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13
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Fukushima K, Fang X, Alvarez-Ponce D, Cai H, Carretero-Paulet L, Chen C, Chang TH, Farr KM, Fujita T, Hiwatashi Y, Hoshi Y, Imai T, Kasahara M, Librado P, Mao L, Mori H, Nishiyama T, Nozawa M, Pálfalvi G, Pollard ST, Rozas J, Sánchez-Gracia A, Sankoff D, Shibata TF, Shigenobu S, Sumikawa N, Uzawa T, Xie M, Zheng C, Pollock DD, Albert VA, Li S, Hasebe M. Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory. Nat Ecol Evol 2017; 1:59. [DOI: 10.1038/s41559-016-0059] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 12/16/2016] [Indexed: 11/09/2022]
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14
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Koga H, Fujitani H, Morino Y, Miyamoto N, Tsuchimoto J, Shibata TF, Nozawa M, Shigenobu S, Ogura A, Tachibana K, Kiyomoto M, Amemiya S, Wada H. Experimental Approach Reveals the Role of alx1 in the Evolution of the Echinoderm Larval Skeleton. PLoS One 2016; 11:e0149067. [PMID: 26866800 PMCID: PMC4750990 DOI: 10.1371/journal.pone.0149067] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 01/27/2016] [Indexed: 11/19/2022] Open
Abstract
Over the course of evolution, the acquisition of novel structures has ultimately led to wide variation in morphology among extant multicellular organisms. Thus, the origins of genetic systems for new morphological structures are a subject of great interest in evolutionary biology. The larval skeleton is a novel structure acquired in some echinoderm lineages via the activation of the adult skeletogenic machinery. Previously, VEGF signaling was suggested to have played an important role in the acquisition of the larval skeleton. In the present study, we compared expression patterns of Alx genes among echinoderm classes to further explore the factors involved in the acquisition of a larval skeleton. We found that the alx1 gene, originally described as crucial for sea urchin skeletogenesis, may have also played an essential role in the evolution of the larval skeleton. Unlike those echinoderms that have a larval skeleton, we found that alx1 of starfish was barely expressed in early larvae that have no skeleton. When alx1 overexpression was induced via injection of alx1 mRNA into starfish eggs, the expression patterns of certain genes, including those possibly involved in skeletogenesis, were altered. This suggested that a portion of the skeletogenic program was induced solely by alx1. However, we observed no obvious external phenotype or skeleton. We concluded that alx1 was necessary but not sufficient for the acquisition of the larval skeleton, which, in fact, requires several genetic events. Based on these results, we discuss how the larval expression of alx1 contributed to the acquisition of the larval skeleton in the putative ancestral lineage of echinoderms.
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Affiliation(s)
- Hiroyuki Koga
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Haruka Fujitani
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yoshiaki Morino
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Norio Miyamoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Jun Tsuchimoto
- Division of Life Science, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan
- Institute for Molecular Science of Medicine, Aichi Medical University, Nagakute, Japan
| | | | - Masafumi Nozawa
- Center for Information Biology, National Institute of Genetics, Mishima, Japan
- Department of Genetics, The Graduate University for Advanced Studies, Mishima, Japan
| | - Shuji Shigenobu
- National Institute for Basic Biology, Okazaki, Japan
- School of Life Science, The Graduate University for Advanced Studies, Okazaki, Japan
| | - Atsushi Ogura
- Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
| | - Kazunori Tachibana
- Graduate School of Bioscience, Tokyo Institute of Technology, Yokohama, Japan
| | - Masato Kiyomoto
- Marine and Coastal Research Center, Ochanomizu University, Tateyama, Japan
| | - Shonan Amemiya
- Marine and Coastal Research Center, Ochanomizu University, Tateyama, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- Research and Education Center of Natural Sciences, Keio University, Yokohama, Japan
| | - Hiroshi Wada
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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15
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Furuta Y, Namba-Fukuyo H, Shibata TF, Nishiyama T, Shigenobu S, Suzuki Y, Sugano S, Hasebe M, Kobayashi I. Methylome diversification through changes in DNA methyltransferase sequence specificity. PLoS Genet 2014; 10:e1004272. [PMID: 24722038 PMCID: PMC3983042 DOI: 10.1371/journal.pgen.1004272] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Accepted: 02/13/2014] [Indexed: 12/20/2022] Open
Abstract
Epigenetic modifications such as DNA methylation have large effects on gene expression and genome maintenance. Helicobacter pylori, a human gastric pathogen, has a large number of DNA methyltransferase genes, with different strains having unique repertoires. Previous genome comparisons suggested that these methyltransferases often change DNA sequence specificity through domain movement--the movement between and within genes of coding sequences of target recognition domains. Using single-molecule real-time sequencing technology, which detects N6-methyladenines and N4-methylcytosines with single-base resolution, we studied methylated DNA sites throughout the H. pylori genome for several closely related strains. Overall, the methylome was highly variable among closely related strains. Hypermethylated regions were found, for example, in rpoB gene for RNA polymerase. We identified DNA sequence motifs for methylation and then assigned each of them to a specific homology group of the target recognition domains in the specificity-determining genes for Type I and other restriction-modification systems. These results supported proposed mechanisms for sequence-specificity changes in DNA methyltransferases. Knocking out one of the Type I specificity genes led to transcriptome changes, which suggested its role in gene expression. These results are consistent with the concept of evolution driven by DNA methylation, in which changes in the methylome lead to changes in the transcriptome and potentially to changes in phenotype, providing targets for natural or artificial selection.
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Affiliation(s)
- Yoshikazu Furuta
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan
| | - Hiroe Namba-Fukuyo
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan
| | | | - Tomoaki Nishiyama
- Advanced Science Research Center, Kanazawa University, Kanazawa, Japan
| | - Shuji Shigenobu
- National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Okazaki, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan
| | - Mitsuyasu Hasebe
- National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Okazaki, Japan
| | - Ichizo Kobayashi
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan
- * E-mail:
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16
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Matsumoto R, Shibata TF, Kohtsuka H, Sekifuji M, Sugii N, Nakajima H, Kojima N, Fujii Y, Kawsar SMA, Yasumitsu H, Hamako J, Matsui T, Ozeki Y. Glycomics of a novel type-2 N-acetyllactosamine-specific lectin purified from the feather star, Oxycomanthus japonicus (Pelmatozoa: Crinoidea). Comp Biochem Physiol B Biochem Mol Biol 2010; 158:266-73. [PMID: 21176791 DOI: 10.1016/j.cbpb.2010.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 12/14/2010] [Accepted: 12/15/2010] [Indexed: 11/28/2022]
Abstract
A lectin - designated OXYL for the purposes of this study that strongly recognizes complex-type oligosaccharides of serum glycoproteins - was purified from a crinoid, the feather star Oxycomanthus japonicus, the most basal group among extant echinoderms. OXYL was purified through a combination of anion-exchange and affinity chromatography using Q-sepharose and fetuin-sepharose gel, respectively. Lectin was determined to be a 14-kDa polypeptide by sodium dodecyl sulphate-polyacrylamide gel electrophoresis under reducing conditions. However, 14-kDa and 28-kDa bands appeared in the same proportion under non-reducing conditions. Gel permeation chromatography showed a 54-kDa peak, suggesting that lectin consists of four 14-kDa subunits. Divalent cations were not indicated, and stable haemagglutination activity was demonstrated at pH 4-12 and temperatures below 60°C. Surface plasmon resonance analysis of OXYL against fetuin showed k(ass) and k(diss) values of 1.4×10(-6)M(-1)s(-1) and 3.1×10(-3)s(-1), respectively, indicating that it has a strong binding affinity to the glycoprotein as lectin. Frontal affinity chromatography using 25 types of prydylamine-conjugated glycans indicated that OXYL specifically recognizes multi-antennary complex-type oligosaccharides containing type-2 N-acetyllactosamines (Galβ1-4GlcNAc) if α2-3-linked sialic acid is linked at the non-reducing terminal. However, type-1 N-acetyllactosamine (Galβ1-3GlcNAc) chains and α2-6-linked sialic acids were never recognized by OXYL. This profiling study showed that OXYL essentially recognizes β1-4-linkage at C-1 position and free OH group at C-6 position of Gal in addition to the conservation of N-acetyl groups at C-2 position and free OH groups at C-3 position of GlcNAc in N-acetyllactosamine. This is the first report on glycomics on a lectin purified from an echinoderm belonging to the subphylum Pelmatozoa.
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Affiliation(s)
- Ryo Matsumoto
- Laboratory of Glycobiology and Marine Biochemistry, Department of Genome System Sciences, Graduate School of NanoBiosciences, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan
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Shibata TF, Oji T, Akasaka K, Agata K. Staging of regeneration process of an arm of the feather star Oxycomanthus japonicus focusing on the oral-aboral boundary. Dev Dyn 2010; 239:2947-61. [DOI: 10.1002/dvdy.22429] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Shibata TF, Sato A, Oji T, Akasaka K. Development and Growth of the Feather Star Oxycomanthus japonicus to Sexual Maturity. Zoolog Sci 2008; 25:1075-83. [DOI: 10.2108/zsj.25.1075] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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