Education

Ph. D. (Zoology): Kyoto University, Japan, 2006
PhD thesis: Diversity and dynamics of virus-like agents killing blue green alga　Microcystis aeruginosa.
M. Sc. (Zoology): Kyoto University, Japan, 2001
Ms thesis: The role of virus on phosphorus cycling in the north basin of Lake Biwa, Japan
B. Sc.: The University of Shiga Prefecture, Japan, 1999

2006-2012: Researcher, Research Institute for Humanity and Nature

2012-present: Researcher, Center for Ecological Research, Kyoto University

Papers (reviewed)

 

1.      Honjo MN, Emura N., Kawagoe T., Sugisaka J., Kamitani M., Nagano AJ, Kudoh H. (in press) Seasonality of interactions between a plant virus and its host during persistent infection in a natural environment. The ISME Journal

 

2.      Honjo MN, Marhold K., Kudoh H. (in press) 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

 

3.      Honjo MN, Kudoh H. (in press) Arabidopsis halleri: A perennial model system for studying population differentiation and local adaptation. AoB Plants

 

4.      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

 

5.      Kamitani M, Nagano AJ, Honjo MN, Kudoh H (2018) A Survey on Plant Viruses in Natural Brassicaceae Communities Using RNA-Seq, Microbial Ecology, https://doi.org/10.1007/s00248-018-1271-4

 

6.      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

 

7.      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

 

8.      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

 

9.      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

 

10.    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

 

11.    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

 

12.    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

 

13.    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

 

14.    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

 

15.    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

 

16.    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

 

17.    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.

 

18.    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.

 

19.    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

 

20.    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

 

21.    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

 

22.    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

 

23.    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

 

24.    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

 

25.    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

 

26.    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

 

27.    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

 

28.    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

 

29.    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

 

30.    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

 

31.    *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

 

32.    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.

 

33.    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

 

34.    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.

 

35.    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

 

36.    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

 

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

 

38.    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

 

39.    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

 

40.    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

 

41.    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

 

42.    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

 

43.    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 

 

 

Oral Presentations

9. Minamoto, T., Honjo, N. M., Kawabata, Z. Distribution and seasonal variation of cyprinid herpesvirus 3 in Lake Biwa. The 56th Annual Meeting of the Ecological Society of Japan, (Iwate prefecture) March 2009 (in Japanese)

 

8. Honjo, N. M., Minamoto, T., Matsui, K., Uchii, K., Yamanaka, H., Suzuki, A. A., Kohmatsu, Y., Kawabata, Z., Quantification of cyprinid herpesvirus 3 in environmental water.. 73th Annual Meeting of The Japanese Society of Limnology, (Hokkaido Prefecture) October 2008  (in Japanese)

 

7. Tanaka, N., Itayama, T. Minamoto, T., Honjo, M., Kawabata, Z. Development of a rapid concentration method of virus-like particles and detection of KHV in environmental water. 41th Annual Conference of Japan Society on Water Environment, (Nagoya Prefecture) March 2008 (in Japanese)

 

6. M. Honjo, T. Kakihara, M. Fujihara, K. Choi, M. Ueki, Z. Kawabata “Effect of temperature on the composition and algicidal activity of virus-like agents killingMicrocystis aeruginosa” 71th Annual Meeting of The Japanese Society of Limnology (Ehime Prefecture) September 2006

 

5. M. Honjo, T. Kakihara, T. Fukushima, M. Fujihara, K. Choi, M. Ueki, Z. Kawabata “Diversity and potential algicidal activity of viruses infectious to Microcystis aeruginosa in a hyper-eutrophic pond” 69th Annual Meeting of The Japanese Society of Limnology (Niigata Prefecture) September 2004

4. R. Nakamura, M. Ueki, M. Honjo, Z. Kawabata “Effects of attached bacteria to Microcystis spp. on the decrease of Microcystis aeruginosa by an algicidal bacterium” 69th Annual Meeting of The Japanese Society of Limnology (Niigata Prefecture) September 2004

 

3. K. Matsui, M. Honjo, Z. Kawabata “Estimation of the fate of dissolved DNA in lake water from the stability of exogenous plasmid DNA.” 17th Annual Meeting of Japanese Society of Microbial Ecology（Shizuoka Prefecture）November 2001

2. M. Honjo, K. Matsui, N. Ishii, M. Nakanishi and Z. Kawabata “Viral abundance and its related factors in the north basin of Lake Biwa.” 65th Annual Meeting of The Japanese Society of Limnology (Fukuoka Prefecture) September 2000

 

1. M. Honjo, K. Matsui, M. Nakanishi and Z. Kawabata “Existence form and Vertical distribution of phosphorus in the north basin of Lake Biwa.” 65th Annual Meeting of The Japanese Society of Limnology (Fukuoka Prefecture) September 2000

 

 

Poster Presentations

1. K. Matsui, M. Honjo, M. Ueki, Y. Koumatsu and Z. Kawabata Detection of Koi Herpesvirus (KHV) in freshwater environment. RIHN First International Symposium~Water and Better Human Life in the Future~, Kyoto, Japan, November 2006

2. M. Honjo, K. Matsui, M. Ueki, R. Nakamura, J. A. Fuhrman and Z. Kawabata Diversity of viruses infectious to bloom-forming cyanobacteria, Microcystis aeruginosa in a hyper-eutrophic pond. Symposium “Perspectives of the Biodiversity Research in the Western Pacific and Asiain the 21st Century”, Kyoto, Japan, December 2003

3. M. Honjo, K. Matsui, M. Ueki, R. Nakamura and Z. Kawabata Diversity of cyanophages infectious to Microcystis aeruginosa in a hyper-eutrophic pond. THE 3rd ALGAL VIRUS WORKSHOP, Hiroshima, Japan, May 2002