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Affiliation |
Faculty of Agriculture Region of Forest Environment and Sustainability Sciences |
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Associate Professor |
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External Link |
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Related SDGs |
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TOKUMOTO Yuji
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Research Areas 【 display / non-display 】
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Environmental Science/Agriculture Science / Conservation of biological resources
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Life Science / Ecology and environment
Papers 【 display / non-display 】
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Tokumoto Yuji, Okuyama Souta, Sueyoshi Koki, Tanigawa Harunobu, Ren Rui, Azuma Wakana A.
Landscape and Ecological Engineering 2026.1
Language：English Publishing type：Research paper (scientific journal)
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Tokumoto Yuji, Katayama Ayumi
Ecological Research 41 ( 1 ) e70031 2026.1
Language：English Publishing type：Research paper (scientific journal)
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徳本 雄史, 雉子谷 佳男
Journal of Forest Research 1 - 8 2025.5
Language：English Publishing type：Research paper (scientific journal) Publisher：Taylor & Francis
Castanopsis sieboldii is a dominant tree species in the warm-temperate forests of western Japan, playing crucial roles in forest ecosystems and human cultures. This species and Castanopsis cuspidata often hybridize in overlapping distribution regions, leading to long-standing debates over their classifications. Although several morphological and genetic markers have been proposed to differentiate the species and their hybrids, the genes underlying phenotypic differences remain unknown. In this study, we estimated the genome size and assembled the genome of Castanopsis sieboldii subsp. sieboldii. Using short reads (98.68 Gb generated using DNBSEQ-G400 and DNBSEQ-T7 sequencers), the genome size was estimated at 812.91 Mbp, with a heterozygosity level of 2.13%. Genome assembly was conducted using long reads generated via MinION (20.54 Gb; 25.30× genome coverage) and Revio (21.59 Gb; 26.59× genome coverage). The assembled genome consisted of 267 contigs with a total length of 959.00 Mb and an N50 length of 22.26 Mb. The draft genome achieved over 90% read mapping rates for both DNA and RNA sequencing reads as well as 98.7% gene completeness, as estimated using the Benchmarking Universal Single-Copy Orthologue tool. The genome sequence of C. sieboldii will be valuable for species identifications, ecological research, wood science, and applications such as tree breeding.
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Hayato Abe, Dongchuan Fu, Tadamichi Sato, Yuji Tokumoto, Fujio Hyodo, Ayumi Katayama
Journal of Environmental Management 371 123146 - 123146 2024.11
Language：English Publishing type：Research paper (scientific journal)
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Tokumoto Yuji, Sakurai Yuki, Abe Hayato, Katayama Ayumi
Forest Ecology and Management 564 121993 - 121993 2024.7
Language：English Publishing type：Research paper (scientific journal) Publisher：Elsevier BV
The increasing deer population has significantly altered the forest ecosystems. Deer browsing affects not only plant species diversity and composition but also other organisms indirectly, along with soil properties. However, the effects of deer grazing on the soil microbial community and the underlying mechanisms have not been well understood. To assess these effects, we compared the understory environment and soil microbial community inside and outside fences at Mt. Shiraga, where severe soil environmental degradation has occurred due to sika deer grazing. We selected 20 Fagus trees inhabiting areas within and outside the fences with similar topological features. Eleven environmental variables and both soil prokaryotic and fungal communities were compared between samples inside and outside the fences. The area inside the fence had significantly higher dwarf bamboo density and soil carbon (C) and nitrogen (N) content, whereas soils outside the fences had higher pH and bulk density. The diversity index of the fungal community, in terms of the number of amplicon sequence variants, inside the fence was higher than that outside, whereas that of the prokaryotic community did not differ between fences. Both prokaryotic and fungal communities differed between inside and outside fences. The prokaryotic community changed with the soil C/N ratio, and the relative abundance of oligotrophic bacteria increased with decreasing soil C/N ratio. The fungal community also changed with soil pH and dwarf bamboo density, with the relative abundances of symbiotrophic fungi and ectomycorrhizae increasing with increasing soil pH. Comparative analyses between inside and outside fence samples might provide information on soil microbial community changes with the changes in soil properties after deer grazing.
Awards 【 display / non-display 】
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Top 10% of most-viewed paper published in Ecological Research between January 1, 2023 - December 31, 2023
2025.4 Wiley Utility of commercial high‐resolution satellite imagery for monitoring general flowering in Sarawak, Borneo
Tomoaki Miura, Yuji Tokumoto, Nagai Shin, Kentaro K. Shimizu, Runi Anak Sylvester Pungga, Tomoaki Ichie
Award type：International academic award (Japan or overseas)
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Top 10 most-cited paper published in Ecological Research between January 1, 2023 and December 31, 2023
2025.3 Wiley Utility of commercial high-resolution satellite imagery for monitoring general flowering in Sarawak, Borneo
Tomoaki Miura, Yuji Tokumoto, Nagai Shin, Kentaro K. Shimizu, Runi Anak Sylvester Pungga, Tomoaki Ichie
Award type：International academic award (Japan or overseas)
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Top 10 most-cited paper published in Ecological Research between 1st January 2022 – 31st December 2023
2024.4 Wiley Utility of commercial high-resolution satellite imagery for monitoring general flowering in Sarawak, Borneo
Tomoaki Miura, Yuji Tokumoto, Nagai Shin, Kentaro K. Shimizu, Runi Anak Sylvester Pungga, Tomoaki Ichie
Award type：International academic award (Japan or overseas)
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Best paper awards, Journal of Plant Research
2021.5 Assessment of Polygala paniculata (Polygalaceae) characteristics for evolutionary studies of legume–rhizobia symbiosis
Yuji Tokumoto, Kayo Hashimoto, Takashi Soyano, Seishiro Aoki, Wataru Iwasaki, Mai Fukuhara, Tomomi Nakagawa, Kazuhiko Saeki, Jun Yokoyama, Hironori Fujita, Masayoshi Kawaguchi
Award type：International academic award (Japan or overseas)
Grant-in-Aid for Scientific Research 【 display / non-display 】
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下層植生消失によるブナの水・養分ストレスが土壌生物多様性と生態系機能に与える影響
Grant number：23K25047 2024.04 - 2026.03
独立行政法人日本学術振興会 科学研究費基金 基盤研究(B)
Authorship：Coinvestigator(s)
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Impact of beech water and nutrient stress induced by understory degradation on soil biodiversity and ecosystem function
Grant number：22H03793 2022.04 - 2026.03
Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B) Grant-in-Aid for Scientific Research (B)
Authorship：Coinvestigator(s)
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Elucidation of ecological function of pioneer tree species and interspecific interaction with late succession tree species for vegetation restoration in Southeast Asia
Grant number：22K05692 2022.04 - 2026.03
Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C) Grant-in-Aid for Scientific Research (C)
Authorship：Principal investigator
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Discrimination and broad-scale mapping of evergreen broad-leaved trees in Japan and Borneo by satellite remote-sensing with high frequency and high spatial resolution
Grant number：22K12352 2022.04 - 2026.03
Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C) Grant-in-Aid for Scientific Research (C)
Authorship：Coinvestigator(s)
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Community-wide phenological study by transcriptome analysis in Southeast Asian tropical plant
Grant number：19K15875 2019.04 - 2022.03
Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research Grant-in-Aid for Early-Career Scientists Grant-in-Aid for Early-Career Scientists
Tokumoto Yuji
Authorship：Principal investigator
This study aimed to clarifying the species-level and community-level phenology phenomena from the relationship among phenology, meteorological data, and expressed genes in the trees of Dipterocarpaceae, Leguminosae, and Ebenaceae families in Southeast Asian tropical forest. During the study period, precipitation decreased, community-wide synchronous flowering occurred, and many of the targeted individuals flowered. The expressed genes analysis revealed that the expression levels of either drought response genes and cold response genes or both were changed before flowering. This suggests that the two flowering factors, drought, and low temperature, which have been discussed as the triggers for synchronized flowering, have been confirmed from the level of expressed genes in multiple canopy tree species. This study suggested that many of the canopy trees might respond to the subtle changes in weather conditions followed by causing the phenological phenomena.
Available Technology 【 display / non-display 】
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Home Page： 研究者紹介
Related fields where technical consultation is available：・森林における樹木更新や下層植生変化の要因分析
・シカ食害などの撹乱が森林生態系に与える影響評価
・不嗜好性植物の増加が森林管理に及ぼす影響整理
・野外調査に基づく森林環境・植生モニタリング手法の検討
・森林管理・生態系保全に関する科学的助言Message：森林や里山の管理に関して、現場で感じている疑問や気づきについて、一緒に考えていく意見交換ができればと考えています。現場の課題を共有しながら、中長期的な視点で共に考えていける研究的なテーマがあれば、お声がけください。
