業績

査読付き論文

1. Yumoto G., Nishio H., Muranaka T., Sugisaka J., Honjo MN., Kudoh H (2024) Seasonal switching of integrated leaf senescence controls in an evergreen perennial Arabidopsis. Nat Commun 15, 4719 https://doi.org/10.1038/s41467-024-48814-z

2. Tsugeki, N., Hashimoto, I., Nakane, K. Honjo MN., Uchii K (2024) Establishment success of alien Daphnia in the ancient Lake Biwa: insights from sedimentary archives. Hydrobiologia. https://doi.org/10.1007/s10750-024-05519-0

3. Kohmei K, Honjo MN, Nakamura N, Kitagawa Y, Ishihara MI, Matsuoka S, Tachiki Y, Fukushima K, Sakaguchi S,  Mizuki I, Fujiki D, Sakai M,  Takayanagi A,  Yamasaki M,   Tokuchi N, Takahashi D, Nagasawa K, Masuda K (2023) eDNA metabarcoding analysis reveals the consequence of creating ecosystem‐scale refugia from deer grazing for the soil microbial communities. Environmental DNA 5: 1732-1742, DOI: 10.1002/edn3.498. 京大プレスリリース    

4. Miki T, Yamanaka H, Sogabe A, Omori K, Saito Y, Minamoto T, Uchii K, Honjo MN, Suzuki AA, Kohmatsu Y, Kawabata Z (2023) Spatial epidemiology model can explain the seasonal dynamics of infectious disease Cyprinid herpesvirus 3 (CyHV-3) by thermoregulation behavior of the host, common carp (Cyprinus carpio). Theoretical Ecology 16: 195–208, link.springer.com/article/10.1007/s12080-023-00563-3 

5. Emura N, Muranaka T, Iwasaki T, Honjo MN, Nagano A, Isagi Y, Kudoh H (2022) Effects of fruit dimorphism on genetic structure and gene flow in the coastal shrub Scaevola taccada. Annals of Botany mcac138

6. Tsugeki NK*, Honjo MN*, Kuwae M (2021) (*equal contribution) Interspecific variation in ephippial size between Daphnia galeata and D. pulicaria in Lake Biwa, Japan. Limnology　22: 197–207, https://doi.org/10.1007/s10201-020-00646-8

7. Honjo MN, Marhold K., Kudoh H. (2020) Experimental evaluation of plastic phenotypes as diagnostic characters between Cardamine fallax and C. occulta: Effects of seasonal environments on phenology and gross morphology. Acta Phytotaxonomica et Geobotanica　 71: 23-32. https://www.jstage.jst.go.jp/article/apg/71/1/71_201912/_pdf

8. Simon NML, Sugisaka J, Honjo MN, Tunstad SA, Tunna G, Kudoh H, Dodd AN. (2020) Altered stomatal patterning accompanies a trichome dimorphism in a natural population of Arabidopsis. Plant Direct 4: e00262

9. Tsujimoto M, Araki KS, Honjo MN, Yasugi M, Nagano AJ, Akama S, Hatakeyama M, Shimizu-Inatsugi R, Sese J, Shimizu KK, Kudoh H. (2020) Genet assignment and population structure analysis in a clonal forest-floor herb, Cardamine leucantha, using RAD-seq. AoB PLANTS 12(1) plz080

10. Honjo MN, Emura N, Kawagoe T, Sugisaka J, Kamitani M, Nagano AJ, Kudoh H (2020) Seasonality of interactions between a plant virus and its host during persistent infection in a natural environment. The ISME Journal 14: 506 – 518.  https://doi.org/10.1038/s41396-019-0519-4,　京大プレスリリース

11.  Honjo MN, Kudoh H (2019) Arabidopsis halleri: A perennial model system for studying population differentiation and local adaptation. AoB PLANTS 11(6): Plz076. https://doi.org/10.1093/aobpla/plz076 

12. Ito T, Nishio H, Tarutani Y, Emura N, Honjo MN, Toyoda A, Fujiyama A, Kakutani T, Kudoh H (2019) Seasonal stability and dynamics of DNA methylation in plants in a natural environment. Genes 10: 544. DOI: 10.3390/genes10070544

13. Nagano AJ, Kawagoe T, Sugisaka J, Honjo MN, Iwayama K, Kudoh H (2019) Annual transcriptome dynamics in natural environments reveals plant seasonal adaptation. 5: 74–83, Nature plants, https://doi.org/10.1038/s41477-018-0338-z

14.  Kamitani M, Nagano AJ, Honjo MN, Kudoh H (2019) A survey on plant viruses in natural Brassicaceae communities using RNA-Seq. Microbial Ecology 78(1): 113-121 https://doi.org/10.1007/s00248-018-1271-4

15. Tanigaki Y, Higashi T, Takayama K, Nagano AJ, Honjo MN, Tezuka A (2019) Simplification of circadian rhythm measurement using species-independent time-indicated genes. Current Plant Biology 19: 100118

16. Kudoh H, Honjo MN, Nishio H, Sugisaka J (2018) The Long-Term "In Natura" Study Sites of Arabidopsis halleri for Plant Transcription and Epigenetic Modification Analyses in Natural Environments. Methods in Molecular Biology, 1830:41-57, https://doi.org/10.1007/978-1-4939-8657-6_3

17. Aryal B, Shinohara W, Honjo MN, Kudoh H (2018) Genetic differentiation in cauline-leaf-specific wettability of a rosette-forming perennial Arabidopsis from two contrasting montane habitats. Annals of Botany, 121(7):1351–1360, https://doi.org/10.1093/aob/mcy033

18. Sakaguchi S, Kimura T, Kyan R, Maki M, Nishino T, Ishikawa N, Nagano AJ, Honjo MN, Yasugi M, Kudoh H, Li P, Choi HJ, Chernyagina OA, Ito M (2018) Phylogeographic analysis of the East Asian goldenrod (Solidago virgaurea complex, Asteraceae) reveals hidden ecological diversification with recurrent formation of ecotypes. Annals of botany, 121: 489–500, https://doi.org/10.1093/aob/mcx182

19. Takeoka M, Higashi T, Honjo MN, Tezuka A, Nagano AJ, Tanigaki Y, Fukuda H (2018) Estimation of the Circadian Phase by Oscillatory Analysis of the Transcriptome in Plants, Environmental Control in Biology, 56(2): 67-72, https://doi.org/10.2525/ecb.56.67

20. Tanigaki Y, Higashi T, Nagano AJ, Honjo MN, Fukuda H (2018) Growth and Environmental Change-Independent Genes Associated with Clock Gene TOC1 in Green Perilla, Environmental Control in Biology, 56(4):137-142, https://doi.org/10.2525/ecb.56.137

21. Nagano Y, Mimura T, Kotoda N, Matsumoto R, Nagano AJ, Honjo MN,  Kudoh H, Yamamoto M (2018) Phylogenetic relationships of Aurantioideae (Rutaceae) based on RAD-Seq. Tree Genetics & Genomes,14:6, https://doi.org/10.1007/s11295-017-1223-z

22. Kamitani M, Nagano AJ, Honjo MN, Kudoh H (2017) First report of Pelargonium zonate spot virus from wild Brassicaceae plants in Japan. Journal of General Plant Pathology, 83; 329–332

23. Izuno A, Kitayama K, Onoda Y, Tsujii Y, Hatakeyama M, Nagano AJ, Honjo MN, Shimizu-Inatsugi R, Kudoh H, Shimizu KK, Isagi Y  (2017) The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha (Myrtaceae). Molecular Ecology 26: 1515-1532

24. Tanigaki Y, Higashi T, Nagano AJ, Honjo MN, Fukuda H. Transcriptome Analysis of a Cultivar of Green Perilla (Perilla frutescens) Using Genetic Similarity with Other Plants via Public Databases. (2017). Environmental Control in Biology 55 (2): 77-83

25. Penjor T, Mimura T, Kotoda N, Matsumoto R, Nagano AJ, Honjo MN, Kudoh H, Yamamoto M, Nagano Y. (2016) RAD-Seq analysis of typical and minor Citrus accessions, including Bhutanese varieties. Breeding Science 66: 797–807

26. Hoshino A, Jayakumar V, Nitasaka E, Toyoda A, Noguchi H, Itoh T, Shin-I T, Minakuchi Y, Koda Y, Nagano AJ, Yasugi M, Honjo MN, Kudoh H, Seki M, Kamiya A, Shiraki T, Carninci P, Asamizu E, Nishide H, Tanaka S, Park Kl, Morita Y, Yokoyama K, Uchiyama I, Tanaka Y, Tabata S, Shinozaki K, Hayashizaki Y, Kohara Y, Suzuki Y, Sugano S, Fujiyama A, Iida S, Sakakibara Y (2016) Genome sequence and analysis of the Japanese morning glory, Ipomoea nil. Nature Communications 7:13295

27. Kamitani M, Nagano AJ, Honjo MN, Kudoh H. (2016) RNA-Seq reveals virus-virus and virus-pant interactions in nature. FEMS Microbiology Ecology, 92(11): fiw176.

28. Higashi T, Aoki K, Nagano AJ, Honjo MN, Fukuda H. (2016) Circadian Oscillation of the Lettuce Transcriptome under Constant Light and Light-dark Conditions. Frontiers in Plant Science. 7: Article 1114.

29. Hagiwara-Komoda Y, Hee CS, Sato M, Atsumi G, Abe J, Fukuda J, Honjo MN, Nagano AJ, Komoda K, Nakahara K, Uyeda I, Naito S. (2016) Truncated yet functional viral protein produced via RNA polymerase slippage implies underestimated coding capacity of RNA viruses. Scientific Reports. 6: 21411

30. Higashi T, Tanigaki Y, Takayama K, Nagano A J, Honjo MN, Fukuda H. (2016) Detection of diurnal variation of tomato transcriptome through the molecular timetable method in a sunlight-type plant factory. Frontiers in Plant Science. 7 Article 87

31. Tanigaki Y, Higashi T, Takayama K, Nagano AJ, Honjo MN, Fukuda H. (2015) Transcriptome Analysis of Plant Hormone-Related Tomato (Solanum lycopersicum) Genes in a Sunlight-Type Plant Factory. PloS one. 10 (12), e0143412

32. Sakaguchi S, Sugino T, Tsumura Y, Ito M, Crisp MD, Bowman DMJS, Nagano AJ, Honjo MN, Yasugi M, Kudoh H, Matsuki Y, Suyama Y, Isagi Y., (2015) High-throughput linkage mapping of Australian white cypress pine (Callitris glaucophylla) and map transferability to related species. Tree Genetics & Genomes. 11: 1-12

33. Ushio M, Yamasaki E, Takasu H, Nagano AJ, Honjo MN, Fujinaga S, Ikemoto M, Sakai S, Kudoh H. (2015) Microbial communities on flower surfaces act as signatures of pollinator visitation. Scientific Reports. 5 Article number:8695

34. Nagano AJ*, Honjo MN*, Mihara M, Sato M, Kudoh H (*equal contribution) (2015) Detection of plant viruses in natural environments by using RNA-seq Methods in Molecular Biology. 1236: 89-98

35. Minamoto T, Pu X, Xie J, Dong Y, Wu D, Kong H, Yang X, Takahara T, Honjo MN, Yamanaka H, Kawabata Z. (2015) Monitoring fish pathogenic viruses in natural lakes in Yunnan, China. Limnology. 16: 69-77

36. Takahara T, Honjo MN, Uchii K, Minamoto T, Doi H, Ito T, Kawabata Z. (2014) Effects of daily temperature fluctuation on the survival of carp infected with Cyprinid herpesvirus 3. Aquaculture. 433: 208–213

37. Uchii K, Minamoto T, Honjo MN, Kawabata Z. (2014) Seasonal reactivation enables Cyprinid herpesvirus 3 to persist in a wild host population. FEMS Microbiology Ecology. 87:536-542

38. Xie J, Wu D, Chen X, Kong H, Pu X, Yang X, Minamoto T, Yamanaka H, Honjo MN, Kawabata Z. (2013) Relationship between aquatic vegetation and water quality in the littoral zones of Lake Dian-chi and Lake Er-hai. Environmental Science & Technology [Wuhan] (in Chinese with English abstract)   36: 61-65

39. Honjo MN, Minamoto T, Kawabata Z. (2012) Reservoirs of Cyprinid herpesvirus 3 (CyHV-3) DNA in sediments of natural lakes and ponds. Veterinary Microbiology. 155: 183–190, https://doi.org/10.1016/j.vetmic.2011.09.005

40. Minamoto T, Honjo MN, Yamanaka H, Uchii K, Kawabata Z. (2012) Nationwide Cyprinid herpesvirus 3 contamination in natural rivers of Japan. Research in Veterinary Science. 93: 508-514

41.  *Minamoto T, *Yamanaka H, Takahara T, Honjo MN, Kawabata Z. (*equal contribution) (2012) Surveillance of fish species composition using environmental DNA. Limnology. 13: 193-197. https://doi.org/10.1007/s10201-011-0362-4 

42. Takahara T, Yamanaka H, Suzuki AA, Honjo MN, Minamoto T, Yonekura R, Itayama T, Kohmatsu Y, Ito T, Kawabata Z. (2011) Stress response to daily temperature fluctuation in common carp Cyprinus carpio L.. Hydrobiologia. 675: 65-73.

43. Kawabata Z., Minamoto T, Honjo MN, Uchii K, Yamanaka H, Suzuki AA, Kohmatsu Y, Asano K, Itayama T, Ichijo T, Omori K, Okuda N, Kakehashi M, Nasu M, Matsui K, Matsuoka M, Kong H, Takahara T, Wu D, Yonekura R. (2011) Environment-KHV-carp-human linkage as a model for environmental diseases. Ecological Research. 26 :1011-1016

44.  Minamoto T, Honjo MN, Yamanaka H, Tanaka N, Itayama T, Kawabata Z. (2011) Detection of cyprinid herpesvirus-3 DNA in lake plankton. Research in Veterinary Science 90 :530-532.

45. Uchii K, Telschow A, Minamoto T, Yamanaka H, Honjo MN, Matsui K, Kawabata Z. (2011) Transmission dynamics of an emerging infectious disease in wildlife through host reproductive cycles The ISME Journal. 5: 244-251

46. Honjo MN, Minamoto T, Matsui K, Uchii K, Yamanaka H, Suzuki AA, Kohmatsu Y, Iida T, Kawabata Z. (2010) Quantification of cyprinid herpesvirus-3 (CyHV-3) in environmental water using an external standard virus. Applied and Environmental Microbiology. 76: 161-168, https://doi.org/10.1128/AEM.02011-09

47. Minamoto T, Honjo MN, Kawabata Z. (2009) Seasonal Distribution of Cyprinid Herpesvirus 3 in Lake Biwa, Japan. Applied and Environmental Microbiology. 75 6900-6904

48. Minamoto T, Honjo MN, Uchii K, Yamanaka H, Suzuki AA, Kohmatsu Y, Iida T, Kawabata Z. (2009) Detection of cyprinid herpesvirus 3 DNA in river water during and after an outbreak. Veterinary Microbiology. 135: 261-266

49. Matsui K, Honjo M, Kohmatsu Y, Uchii K, Yonekura R, Kawabata Z. (2008) Detection and significance of koi herpesvirus (KHV) in freshwater environments. Freshwater Biology. 53: 1262-1272

50. Honjo M, Matsui K, Ishii N, Nakanishi M, Kawabata Z. (2007) Viral abundance and its related factors in a stratified lake. Fundamental and Applied Limnology/　Archiv für Hydrobiologie. 168: 105-112, https://doi.org/10.1127/1863-9135/2007/0168-0105

51. Honjo M, Matsui K, Ueki M, Nakamura R, Fuhrman JA, Kawabata Z. (2006) Diversity of virus-like agents killing Microcystis aeruginosa in a hyper-eutrophic pond. Journal of Plankton Research. 28: 407-412, https://doi.org/10.1093/plankt/fbi128

52. Matsui K, Ishii N, Honjo M, Kawabata Z. (2004) Use of the SYBR Green I fluorescent dye and a centrifugal filter device for rapid determination of dissolved DNA concentration in fresh water. Aquatic Microbial Ecology. 36: 99-105

53. Matsui K, Honjo M, Kawabata Z. (2001) Estimation of the fate of dissolved DNA in thermally stratified lake water from the stability of exogenous plasmid DNA. Aquatic Microbial Ecology. 26: 95-102