Hiroshi Kudoh Laboratory, Center for Ecological reserach, Kyoto University.

Japanese / English

Publication

Peer-reviewed Articles

  1. Nishio H, Cano-Ramirez DL, Muranaka T, de Barros Dantas LL, Honjo MN, Sugisaka J, Kudoh H, Dodd AN (2024) Circadian and environmental signal integration in a natural population of Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 121: e2402697121 (Journal)
  2. 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 (Journal)
  3. Nakayama T, Tanikawa M, Okushi Y, Itoh T, Shimmura T, Maruyama M, Yamaguchi T, Matsumiya A, Shinomiya A, Guh YJ, Chen J, Naruse K, Kudoh H, Kondo Y, Naoki H, Aoki K, Nagano AJ, Yoshimura, T (2023) A transcriptional program underlying the circannual rhythms of gonadal development in medaka. Proceedings of the National Academy of Sciences of the United States of America, 120:e2313514120. (Journal)
  4. Seki M, Kuze Y, Zhang X, Kurotani KI, Notaguchi M, Nishio H, Kudoh H, Suzaki T, Yoshida S, Sugano S, Matsushita T, Suzuki Y (2023) An improved method for the highly specific detection of transcription start sites. Nucleic Acids Research gkad1116 (Journal)
  5. Akiyama R, Goto T, Tameshige T, Sugisaka J, Kuroki K, Sun J, Akita J, Hatakeyama M, Kudoh H, Tanaka K, Tonouchi A, Shimahara Y, Sese J, Kutsuna N, Shimizu-Inatsugi R, Shimizu KK (2023) Seasonal pigment fluctuation in diploid and polyploid Arabidopsis revealed by machine learning-based phenotyping method PlantServation. Nature Communiations 14: 5792 (Journal)
  6. 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 (Journal)
  7. Nishio H, Kudoh H (2023) Distinct responses to autumn and spring temperatures by the key flowering-time regulator FLOWERING LOCUS C. Current Opinion in Genetics & Development 78: 102016 (Journal)
  8. Muranaka T, Ito S, Kudoh H, Oyama T (2022) Circadian-period variation underlies the local adaptation of photoperiodism in the short-day plant Lemna aequinoctialis. iScience 25: 104634 (Journal)
  9. Yumoto G, Sasaki-Sekimoto Y, Aryal B, Ohta H, Kudoh H (2021) Altitudinal differentiation in the leaf wax-mediated flowering bud protection against frost in a perennial Arabidopsis. Oecologia 95(3):677-687(Journal)
  10. Akiyama R, Sun J, Hatakeyama M, Lischer H E L, Briskine R V, Hay A, Gan X, Tsiantis M, Kudoh H, Kanaoka M M, Sese J, Shimizu K K, Shimizu‐Inatsugi R (2021) Fine‐scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species.New phytologist 229:3587–3601(Journal)
  11. Nishio H, Iwayama K, Kudoh H (2020) Duration of cold exposure defines the rate of reactivation of a perennial FLC orthologue via H3K27me3 accumulation. Scientific Reports 10:16056 (Journal)
  12. Nishio H, Nagano AJ, Ito T, Suzuki Y, Kudoh H (2020) Seasonal plasticity and diel stability of H3K27me3 in natural fluctuating environments. Nature Plants 6:1091–1097(Journal)
  13. Araki KS, Nagano AJ, Nakano RT, Kitazume T, Yamaguchi K, Hara-Nishimura I, Shigenobu S, Kudoh H (2020) Characterization of rhizome transcriptome and identification of a rhizomatous ER body in the clonal plant Cardamine leucantha. Scientific Reports 10:13291 (Journal)
  14. Nishio H, Buzas DM, Nagano AJ, Iwayama K, Ushio M, Kudoh H (2020) Repressive chromatin modification underpins the long-term expression trend of a perennial flowering gene in nature. Nature Communications 11, 2065. (Journal)
  15. Honjo MN, Marhold K, Kudoh H (2020) Experimental evaluation of differences in plastic phenotypes between Cardamine fallax and C. occulta: effects of seasonality on phenology and gross morphology. Acta Phytotaxonomica et Geobotanica 71: 23-32. (Journal)
  16. 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 plants12(1):plz080 (Journal)
  17. Honjo MN, Emura N, Kawagoe T, Sugisaka J, Kamitani M, Nagano AJ, Kudoh H (2020) Seasonality in interactions between a plant virus and its host in a persistent infection. The ISME Journal14 506–518 (Journal)
  18. Honjo MN, Kudoh H (2019) Arabidopsis halleri: a perennial model system for studying population differentiation and local adaptation. AoB plants11(6):plz076 (Journal)
  19. Mandáková T, Zozomová-Lihová J, Kudoh H, Zhao Y, Lysak MA, Marhold K (2019) The story of promiscuous crucifers: origin and genome evolution of an invasive species, Cardamine occult (Brassicaceae), and its relatives Annals of Botany 124(2) 209-220 (Journal)
  20. 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(7) 544 (Journal)
  21. Nagano AJ, Kawagoe T, Sugisaka J, Honjo MN, Iwayama K, Kudoh H (2019) Annual transcriptome dynamics in natural environments reveals plant seasonal adaptation, Nature Plants 5:74-83 (Journal)
  22. Kamitani M, Nagano AJ, Honjo MN, Kudoh H (2018) A Survey on Plant Viruses in Natural Brassicaceae Communities Using RNA-Seq, Microbial Ecology78:113-121 (Journal)
  23. Miryeganeh M, Yamaguchi M, Kudoh H (2018) Synchronisation of Arabidopsis flowering time and whole-plant senescence in seasonal environments. Scientific Reports 2018; 8: 10282. (Journal)
  24. 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 mcy033 (Journal)
  25. 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(5):329-332 (Journal)
  26. Sato Y, Kudoh H (2017) Herbivore-mediated interaction promotes the maintenance of trichome dimorphism through negative frequency-dependent selection. The American Naturalist
  27. Sato Y, Kudoh H (2017) Fine-scale frequency differentiation along a herbivory gradient in the trichome dirmorphism of a wild Arabidopsis. Ecology and Evolution 7(7):2133-2141. (Open Access)
  28. Sato Y, Kudoh H (2016) Presence of substitute diets alters plant resistance to specialist and generalist herbivores: a meta-analysis. Ecosphere doi:10.1002/ecs2.1446
  29. Kamitani M, Nagano AJ, Honjo MN, Kudoh H (2016), RNA-Seq reveals virus-virus and virus-plant interactions in nature. FEMS Microbiology Ecology, 92 doi: 10.1093/femsec/fiw176
  30. Shimizu‐Inatsugi, R., Terada, A., Hirose, K., Kudoh, H., Sese, J., & Shimizu, K. K. (2016). Plant adaptive radiation mediated by polyploid plasticity in transcriptomes. Molecular Ecology
  31. Nishio H., Buzas D.M., Nagano A.J., Suzuki Y., Sugano S., Ito M., Morinaga S.I., Kudoh H. (in press) From the laboratory to the field: assaying histone methylation at FLOWERING LOCUS C in naturally growing Arabidopsis halleri. Genes & Genetic Systems
  32. Kudoh H. (in press) Molecular phenology in plants: systems biology for the comprehensive understanding of seasonal responses under natural environments. New Phytologist doi:10.1111/nph.13733
  33. Sato Y., Kudoh H. (in press) Associational effects against a leaf beetle mediate a minority advantage in defense and growth between hairy and glabrous plants. Evolutionary Ecology doi:10.1007/s10682-015-9809-0
  34. Sakaguchi S., Sugino T., Tsumura Y., Ito M., Crisp M.D., Bowman M.J.S.D., Nagano A.J., Honjo M.N., Yasugi M., Kudoh H., Matsuki Y., Suyama Y., Isagi Y. (in press) High-throughput linkage mapping of Australian white cypress pine (Callitris glaucophylla) and map transferability to related species. Tree Genetics & Genomes doi:10.1007/s11295-015-0944-0
  35. Ushio M., Yamasaki E., Takasu H., Nagano A. J., Honjo M. N., Fujinaga S., Ikemoto M., Sakai S., Kudoh H. (2015) Microbial communities on flower surfaces act as signatures of pollinator visitation. Scientific Reports 5: 8695
  36. Sato Y., Kudoh H. (2015) Tests of associational defence provided by hairy plants for glabrous plants of Arabidopsis halleri subsp. gemmifera against insect herbivores. Ecological Entomology 40: 269-279
  37. Nagano A. J., Honjo M. N., Mihara M., Sato M., Kudoh H. (2015) Detection of plant viruses in natural environments by using RNA-Seq. Methods in Molecular Biology 1236: 89-98
  38. Sato Y., Kudoh H. (2014) Fine-scale genetic differentiation of a temperate herb: relevance of local environments and demographic change. AoB PLANTS 6: plu70
  39. Mochizuki K., Nagano A. J., Kudoh H., Kawakita A. (2014) Isolation and characterization of 11 microsatellite markers for Glochidion acuminatum (Phyllanthaceae). Applications in Plant Sciences 2:(9)
  40. Sato Y., Kawagoe T., Sawada Y., Hirai M. Y., Kudoh H. (2014) Frequency-dependent herbivory by a leaf beetle, Phaedon brassicae, on hairy and glabrous plants of Arabidopsis halleri subsp. gemmifera. Evolutionary Ecology 28: 545-559
  41. Nishio H., Nagano A. J., Buzas D. M., Kudoh H. (2013) Seasonal analysis of histone modifications at FLOWERING LOCUS C in a natural perennial population. GENES & GENETIC SYSTEMS 88: 336-336
  42. Kudoh H., Takayama K., Kachi N. (2013) Loss of seed buoyancy in Hibiscus glaber on the oceanic Bonin Islands. Pacific Science 67: 591-597
  43. Satake A., Kawagoe T., Saburi Y., Chiba Y., Sakurai G., Kudoh H. (2013) Forecasting flowering phenology under climate warming by modelling the regulatory dynamics of flowering-time genes. Nature Communications 4: 2303
  44. Sato Y., Kudoh H. (2013) Relative strength of phenotypic selection on the height and number of flowering-stalks in the rosette annual Cardamine hirsuta (Brassicaceae). Journal of Ecology and Environment 36: 151-158
  45. Araki K. S., Nakazawa T., Kawakita A., Kudoh H., Okuda N. (2012) Development of nine markers and characterization of the microsatellite loci in the endangered Gymnogobius isaza (Gobiidae). International Journal of Molecular Sciences 13: 5700-5705.
  46. Matsuhashi S., Sakai S., Kudoh H. (2012) Temperature-dependent fluctuation of stamen number in Cardamine hirsuta (Brassicaceae). International Journal of Plant Sciences 173: 391-398.
  47. Kawagoe T., Shimizu K. K., Kakutani T., Kudoh H. (2011) Coexistence of trichome variation in a natural plant population: a combined study using ecological and candidate gene approaches. PLoS ONE 6: e22184.
  48. Fujimoto R., Sasaki T., Kudoh H., Taylor J. M., Kakutani T., Dennis E. S. (2011) Epigenetic variation in the FWA gene within the genus Arabidopsis. The Plant Journal 66: 831-843.
  49. Araki K. S., Kaneko S., Isagi Y., Kudoh H. (2012) Isolation and characterization of miocrosatellite loci in a clonal herb, Cardamine leucantha (Brassicaceae). American Journal of Botany: e385-e387.
  50. Momokawa N., Kadono Y., Kudoh H. (2011) Effects of light quality on leaf morphogenesis of a heterophyllous amphibious plant, Rotala hippuris. Annals of Botany 108: 1299-1306.
  51. Shimizu K. K., Kudoh H., Kobayashi M. J. (2011) Plant sexual reproduction during climate change: gene function in natura studied by ecological and evolutionary systems biology. Annals of Botany 108: 777-787.
  52. Kawagoe T., Kudoh H. (2010) Escape from floral herbivory by early flowering in Arabidopsis halleri subsp. gemmifera. Oecologia 164: 713-720.
  53. Aikawa S., Kobayashi M. J., Satake A., Shimizu K. K., Kudoh, H. (2010) Robust control of seasonal expression of Arabidopsis FLC gene in a fluctuating environment. Proceedings of the National Academy of Sciences of the United States of America 107: 11632-11637.
  54. Marhold K., Kudoh H., Pak J.-H., Watanabe K., Spaniel S., Lihova J. (2010) Cytotypic diversity and genome size variation in eastern Asian polyploid Cardamine (Brassicaceae) species. Annals of Botany 105: 249-264.
  55. Shinohara W., Ushio Y., Seo A., Nakato N., Kono M., Kudoh H., Tobe H., Murakami N. (2010) Evidence for hybrid origin and segmental allopolyploidy in eutetraploid and aneutetraploid Leposorus thunbergianus (Polypodiaceae). Systematic Botany 35: 20-29.
  56. Lihova J., Kudoh H., Marhold K. (2010) Morphometric studies of polyploid Cardamine species (Brassicaceae) from Japan: solving a long-standing taxonomic and nomenclatural controversy. Australian Systematic Botany 23: 1-18.
  57. Lihova J., Kudoh H., Marhold K. (2010) Genetic structure and phylogeography of a temperate-boreal herb, Cardamine scutata (Brassicaceae), in northeastern Asia from AFLPs and cpDNA haplotypes. American Journal of Botany 97: 1-13.
  58. Shimizu-Inatsugi R., Lihova J., Iwanaga H., Kudoh H., Marhold K., Savolainen O., Watanabe K., Yakubov V. V., Shimizu K. K. (2008) The allopolyploid Arabidopsis kamchatica originated from multiple individuals of Arabidopsis lyrata and Arabidopsis halleri. Molecular Ecology 18: 4024-4048.
  59. Sugisaka J., Kudoh, H. (2008) Breeding system of the annual Cruciferae, Arabidopsis kamchatica subsp. kawasakiana. Journal of Plant Research 121: 65-68.
  60. Hosaka, N., Kachi, N., Kudoh, H., Stuefer, J. F., Whigham, D. F. (2008) Patch structures and ramet demography of the clonal tree, Asimina triloba, under gap and closed-canopy. Plant Ecology 197: 219-228.
  61. Fujimoto R., Kinoshita Y., Kawabe A., Kinoshita T., Takashima K., Nordborg M., Nasrallah M. E., Shimizu K. K., Kudoh H., Kakutani, T. (2008) Evolution and control of imprinted FWA genes in the genus Arabidopsis. PLoS Genetics 4: e1000048
  62. Kudoh H., Nakayama M., Lihova J., Marhold K. (2007) Does invasion involve alternation of germination requirements? A comparative study between native and introduced strains of an annual Brassicaceae, Cardamine hirsuta. Ecological Research 22: 869-875
  63. Marhold K., Lihova J., Al-Shehbaz I. A., Kudoh H. (2007) The correct interpretation and lectotypification of the name Cardamine fallax (Brassicaceae). Journal of Plant Research 120: 655-660
  64. Shimamura R., Kachi N. Kudoh H., Whigham D. F. (2007) Hydrochory as a determinant of genetic distribution of seeds within Hibiscus moscheutos (Malvaceae) populations. American Journal of Botany 94: 1137-1145
  65. Lihova J., Marhold K., Kudoh H., Koch M. A. (2006) Worldwide phylogeny and biogeography of Cardamine flexuosa (Brassicaceae) and its relatives. American Journal of Botany 93: 1206-1221
  66. Kudoh H., Shimamura R., Takayama K., Whigham D. F. (2006) Consequence of hydrochory in Hibiscus. Plant Species Biology 21: 127-133
  67. Shimizu K. K., Fujii S., Marhold K., Watanabe K., Kudoh H. (2005) Arabidopsis kamchatica (Fisch. ex DC.) K. Shimizu & Kudoh and A. kamchatica subsp. kawasakiana (Makino) K. Shimizu & Kudoh, New combinations. Acta Phytotaxonomica et Geobotanica 56: 163-172.
  68. Shimamura R., Kachi N., Kudoh H., Whigham D. F. (2005) Visitation of a specialist pollen feeder Althaeus hibisci Olivier (Coleoptera: Bruchidae) to flowers of Hibiscus moscheutos L. (Malvaceae). The Journal of the Torrey Botanical Society 132: 197-203. [Abstract]
  69. Takayama K., Ohi-Toma T. Kudoh H., Kato H. (2005) Origin and diversification of Hibiscus glaber, species endemic to the oceanic Bonin Islands, revealed by chroloplast DNA polymorphism. Molecular Ecology 14: 1059-1071.
  70. Kawagoe T., Suzuki N. (2005) Self-pollen on a stigma interferes with outcrossed seed production in a self-incompatible monoecious plant Akebia quinata (Lardizabalaceae). Functional Ecology 19: 49-54.
  71. Kawagoe T., Suzuki N. (2004) Cryptic dioecy in Actinidia polygama: a test of the pollinator attraction hypothesis. Canadian Journal of Botany 82: 214-218.
  72. Kawagoe T., Suzuki N. (2003) Flower-size dimorphism avoids geitonogamous pollination in a nectarless monoecious plant Akebia quinata. International Journal of Plant Sciences 164: 893-897.
  73. Yatsu Y., Kachi N., Kudoh H. (2003) Ecological distribution and phenology of an invasive species, Cardamine hirsuta L. and its native counterpart, Cardamine flexuosa With., in central Japan. Plant Species Biology 18: 35-42.
  74. Kitamura K., Morita T., Kudoh H., O'Neill J., Utech F. H., Whigham D. F., Kawano S. (2003) Demographic genetics of the American beech (Fagus grandifolia Ehrh.) III. Genetic substructuring of coastal plain population in Maryland. Plant Species Biology 18: 13-33.
  75. Tani T., Kudoh H., Kachi N. (2003) Responses of root length/leaf area ratio and specific root length of an understory herb, Pteridophyllum racemosum, to increases in irradiance. Plant & Soil 255: 227-237.
  76. Suzuki O. R., Kudoh H., Kachi, N. (2003) Spatial and temporal variations in mortality of the biennial Lysimachia rubida: effects of intraspecific competition and environmental heterogeneity. Journal of Ecology 91: 114-125.
  77. Feller I. C., Kudoh H., Tanner C. E., Whigham D. F. (2003) Sex-biased herbivory in Jack-in-the-Pulpit (Arisaema triphyllum) by a specialist Thrips (Heterothrips arisaemae). Proceedings 7th International Thysanoptera Conference. Reggio Callabrio, Italy.
  78. Kudoh H., Kachi N., Kawano S., Whigham D. F. (2002) Intrinsic cost of delayed flowering in annual plants: negative correlation between flowering time and reproductive effort. Plant Species Biology 17: 101-107.
  79. Kawagoe T., Suzuki N. (2002) Floral sexual dimorphism and flower choice by pollinators in a nectarless monoecious vine Akebia quinata (Lardizabalaceae). Ecological Research 17: 295-303.
  80. Kawagoe T., Suzuki N., Matsumoto K. (2001) Multiple mating reduces longevity of females of the windmill butterfly, Atrophaneura alcinous. Ecological Entomology 26: 258-262.
  81. Ozawa M., Kudoh H., Kachi N. (2001) Breeding system of Pteridophyllum racemosum Sieb. et Zucc. (Papaveraceae). Plant Species Biology 16: 237-239.
  82. Tani T., Kudoh H., Kachi N. (2001) Responses of photosynthesis and biomass allocation of an understorey herb, Pteridophyllum racemosum, to gradual increases in irradiance. Annals of Botany 88: 393-402.
  83. Kudoh H., Sugawara T., Wu S., Murata J. (2001) Morph specific correlations between floral traits in a distylous Ophiorrhiza napoensis Lo (Rubiaceae) population in southern China. Journal of Tropical Ecology 17: 719-728.
  84. Kudoh H., Whigham D. F. (2001) A genetic analysis of hydrologically dispersed seeds of Hibiscus moscheutos (Malvaceae). American Journal of Botany 88: 588-593.
  85. Kudoh H., Shibaike H., Takasu H., Whigham D. F., Kawano S. (1999) Genet structure and determinants of clonal structure in a temperate deciduous woodland herb, Uvularia perfoliata. Journal of Ecology 84: 244-257.
  86. Kudoh H., Whigham D. F. (1998) The effect of petal size manipulation on pollinator/seed-predator mediated female reproductive success of Hibiscus moscheutos. Oecologia 117: 70-79.
  87. Kudoh H., Whigham D. F. (1997) Microgeographic genetic structure and gene flow in Hibiscus moscheutos (Malvaceae) Populations. American Journal of Botany 84: 1285-1293.
  88. Kudoh H., Ishiguri Y., Kawano S. (1996) Phenotypic plasticity in age and size at maturity and its effects on the integrated phenotypic expressions of life history traits of Cardamine flexuosa (Cruciferae). Journal of Evolutionary Biology 9: 541-570.
  89. Kudoh H., Ishiguri Y., Kawano S. (1995) Phenotypic plasticity in Cardamine flexuosa: variation among populations in plastic response to chilling treatments and photoperiods. Oecologia 103: 148-156.
  90. Ishiguri Y., Kudoh H., Kawano S. (1994) Effects of different photoperiods and chilling treatments on growth and reproduction of Cardamine flexuosa With. and its ecological implications. Plant Species Biology 9: 75-84.
  91. Kudoh H., Ishiguri Y., Kawano S. (1993) Phenotypic variability in life history traits and phenology of field populations of Cardamine flexuosa and C. fallax (Cruciferae) in Honshu, Japan. Plant Species Biology 8: 7-20.
  92. Kudoh H., Ishiguri Y., Kawano S. (1992) December. Cardamine hirsuta L., a new ruderal species introduced into Japan. The Journal of Phytogeography and Taxonomy 40: 85-89.

Books & Reviews

  1. Kudoh H., Nagano A. J. 2013. Memory of Temperature in the Seasonal Control of Flowering Time: An Unexplored Link Between Meteorology and Molecular Biology. Evolutionary Biology: Exobiology and Evolutionary Mechanisms. pp. 195-215, Springer

Proceedings

  1. Takayama, K., Ohi, T., Kato, H. and Kudoh, H. 2002. Capsulemorphology and geographic distribution of Ogasawara Research 27: 31-55.
  2. Hirota, Y., Kudoh, H. and Kachi, N. 2000. Determinants of reproductive success in woody Hibiscus in the Bonin (Ogasawara) Islands. Ogasawara Research 25: 27-51.
  3. Kudoh, H., Wada, M., Murata, J. and Wcicki, J.J. 1999. Japonskie Towarzysto Botaniczne (The Botanical Society of Japan). Wiadomosci Botaniczne 43: 82-84 (translated into Polish).
  4. Kudoh, H., Uchiyama, M. and Kachi, N. 1998. Flower size variation in Hibiscus glaber and H. tiliaceus in Chichijima Island, theBonin (Ogasawara) Islands. Ogasawara Research 24: 25-34.

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