1. Fukuda A, Hirose T, Aoki N, Kondo S, Yonekura M, Kataoka T, Ohto C, Nagano AJ (2018) Selection of Transcripts Affecting Initial Growth Rate of Rice Backcrossed Inbred Lines Using RNA Sequencing Data, Frontiers in Plant Science, 9:1880. doi: 10.3389/fpls.2018.01880
  2. 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
  3. Kubo N, Mimura Y, Matsuda T, Nagano AJ, Hirai N, Higashimoto S, Yoshida H, Uemura N, Fujii T (2018) Classification of tea (Camellia sinensis) landraces and cultivars in Kyoto, Japan and other regions, based on SSR markers and RAD-seq analysis, Genetic Resources and Crop Evolution, doi: 10.1007/s10722-018-0722-6
  4. Ono T, Ohara K, Takenouchi A, Ishikawa A, Kouguchi T, Nagano AJ, Igawa T, Tsudzuki M (2018) Mapping quantitative trait loci for the growth and carcass-related traits of chickens using a restriction-site associated DNA sequence technique, Journal of Poultry Sciencein press
  5. Ono T, Kouguchi T, Ishikawa A, Nagano AJ, Takenouchi A, Igawa T, Tsudzuki M (2018) Quantitative trait loci mapping for the shear force value in breast muscle of F2 chickens, Poultry Science, doi: 10.3382/ps/pey493.
  6. Kamitani M, Nagano AJ, Honjo MN, Kudoh H (2018) A Survey on Plant Viruses in Natural Brassicaceae Communities Using RNA-Seq, Microbial Ecology, doi: 10.1007/s00248-018-1271-4.
  7. Koeda S, Sato K, Saito H, Nagano AJ, Yasugi M, Kudoh H, Tanaka Y (2018) Mutation in the putative ketoacyl-ACP reductase CaKR1 induces loss of pungency in Capsicum, Theoretical and Applied Genetics, doi: 10.1007/s00122-018-3195-2
  8. Hosoya S, Kikychi K, Nagashima H, Onodera J, Sugimoto K, Satoh K, Matsuzaki K, Yasugi M, Tezuka A, Nagano AJ, Kumagayi A, Ueda K, Kurokawa T (2018) Assessment of genetic diversity in Coho salmon (Oncorhynchus kisutch) populations with no family records using ddRAD-seq, BMC Research Note, 11:548
  9. Yasugi M, Tezuka A, Nagano AJ (2018) Stacksbinder: online tool for visualizing and summarizing Stacks output to aid filtering of SNPs identified using RAD sequencing, Conservation Genetics Resources, doi: 10.1007/s12686-018-1050-z
  10. Chen YY, Nishii K, Barber S, Hackett C, Kidner CA, Gharbi K, Nagano AJ, Iwamoto A, Moller M (2018) A first genetic map in the genus Streptocarpus generated with RAD sequencing based SNP markers, South African Journal of Botany, 117: 158-168
  11. Kim S, Mochizuki N, Deguchi A, Nagano AJ, Suzuki T, Nagatani A (2018) Auxin Contributes to the Intraorgan Regulation of Gene Expression in Response to Shade, Plant physiology, 177(2): 847-862
  12. Awazu A, Tanabe T, Kamitani M, Tezuka A, Nagano AJ (2018) Broad distribution spectrum from Gaussian to power law appears in stochastic variations in RNA-seq data, Scientific reports, 8(1): 8339
  13. Kobayashi H, Haino Y, Iwasaki T, Tezuka A, Nagano AJ, Shimada S (2018) ddRAD-seq based phylogeographic study of Sargassum thunbergii (Phaeophyceae, Heterokonta) around Japanese coast, Marine environmental research, doi: 10.1016/j.marenvres.2018.05.021
  14. 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(1): 6
  15. Kagiya S, Yasugi M, Kudoh H, Nagano AJ, Utsumi S (2018) Does genomic variation in a foundation species predict arthropod community structure in a riparian forest?, Molecular Ecology, 27(5):1284-1295
  16. Hanada K, Tezuka A, Nozawa M, Suzuki Y, Sugano S, Nagano AJ, Ito M, Morinaga S-I (2018) Functional divergence of duplicate genes several million years after gene duplication in Arabidopsis, DNA Research, dsy005.
  17. 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
  18. Sakaguchi S, Horie K, Kimura T, Nagano AJ, Isagi Y, Ito M (2017) Phylogeographic testing of alternative histories of single-origin versus parallel evolution of early flowering serpentine populations of Picris hieracioides L. (Asteraceae) in Japan, Ecological Research, doi: 10.1007/s11284-017-1536-2.
  19. Murata J, Ono E, Yoroizuka S, Toyonaga H, Shiraishi A, Mori S, Tera M, Azuma T, Nagano AJ, Nakayasu M, Mizutani M, Wakasugi T, Yamamoto MP, Horikawa M (2017) Oxidative rearrangement of (+)-sesamin by CYP92B14 co-generates twin dietary lignans in sesame, Nature Communications, 7, 13295
  20. Sakaguchi S, Kimura T, Kyan R, Maki M, Nishino T, Ishikawa N, Nagano AJ, Honjo M, Yasugi M, Kudoh H, Li P, Choi H-J, Chernyagina O, Ito M (2017) Phylogeographic analysis of the East Asian goldenrod (Solidago virgaurea complex, Asteraceae) reveals hidden ecological diversification with recurrent formation of ecotypes, Annals of Botany, doi: 10.1093/aob/mcx182.
  21. Ishikawa T, Kashima M, Nagano AJ, Ishikawa-Fujiwara T, Kamei Y, Todo T, Mori K (2017) Unfolded Protein Response Transducer IRE1-mediated Signaling Independent of XBP1 mRNA Splicing Is Not Required for Growth and Development of Medaka Fish. eLife, 6: e26845
  22. Goto S, Kajiya-Kanegae H, Ishizuka W, Kitamura K, Ueno S, Hisamoto Y, Kudoh H, Yasugi M, Nagano AJ, Iwata H (2017) Genetic mapping of local adaptation along the altitudinal gradient in Abies sachalinensisTree Genetics & Genomes, 13: 104.
  23. Sakaguchi S, Horie K, Ishikawa N, Nagano AJ,  Yasugi M, Kudoh H and Ito M (2017) Simultaneous evaluation of the effects of geographic, environmental and temporal isolation in ecotypic populations of Solidago virgaureaNew Phytologist, doi:10.1111/nph.14744
  24. 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
  25. Kobayashi M, Ohyanagi H, Takanashi H, Asano S, Kudo T, Kanegae H, Nagano AJ, Tainaka H, Tokunaga T, Sazuka T, Iwata H, Tsutsumi N, Yano K (2017) Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data. DNA Research, dsx012
  26. Iwayama K, Aisaka Y, Kutsuna N, Nagano AJ (2017) FIT: Statistical modeling tool for transcriptome dynamics under fluctuating field conditions., Bioinformatics, btx049
  27. Tanigaki Y, Higashi T, Nagano AJ, Honjo MN, Fukuda H (2017) Transcriptome Analysis of a Cultivar of Green Perilla (Perilla frutescens) Using Genetic Similarity with Other Plants via Public Databases., Environmental Control in Biology, 55(2): 77-83
  28. Izuno A, Kitayama K, Onoda Y, Tsujii Y, Hatakeyama M, Nagano AJ, Honjo MN, Shimizu-Inatsugi R, Kudoh K, 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(6):1515-1532
  29. Kawakatsu Y, Nakayama H, Kaminoyama K, Igarashi K, Yasugi M, Kudoh H, Nagano AJ, Yano K, Kuboh N, Kimura S (2017) A GLABRA1 ortholog on LG A9 controls trichome number in the Japanese leafy vegetables Mizuna and Mibuna (Brassica rapa L. supsp. nipposinica L. H. Bailey): evidence from QTL analysis., Journal of Plant Research, 130(3): 539-550
  30. 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(5): 797-807
  31. Hoshino A, Jayakumar V, Nitasaka E, Toyoda A, Noguchi H, Itoh T, Shin-I T, Minakuchi Y, Koda Y, Nagano AJ, Yasugi M, Honjo M, Kudoh H, Seki M, Kamiya A, Shiraki T, Carninci P, Asamizu E, Nishide H, Tanaka S, Park KI, 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
  32. Kamitani M, Nagano AJ, Honjo MN, Kudoh H (2016) RNA-Seq reveals virus-virus and virus-plant interactions in nature., FEMS Microbiology Ecology, 92(11). pii: fiw176
  33. 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: 1114
  34. Kolar F, Fuxova G, Zaveska E, Nagano AJ, Hyklova L, Lucanova M, Kudoh H, Marhold K (2016) Northern glacial refugia and altitudinal niche divergence shape genome-wide differentiation in the emerging plant model Arabidopsis arenosa., Molecular Ecology, 25(16):3929-49
  35. Tamaki H, Mitsuhashi S, Kudoh H, Nagano AJ and Yasugi M (2016) Genome wide Molecular Polymorphisms among Maize (Zea mays L.) Inbred Lines Found from Restriction-Associated DNA Tag Sequencing (RAD-Seq) Analysis as a Preliminary Study on “Genomewide Selection” for Breeding by Japanese Public Sectors., Bulletin of NARO Institute of Livestock and Grassland Science, 16: 1-9.
  36. Hagiwara-Komoda Y, Choi SH, Sato M, Atsumi G, Abe J, Fukuda J, Honjo MN, Nagano AJ, Komoda K, Nakahara KS, 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.
  37. Higashi T,  Tanigaki Y, Takayama K, Nagano AJ,  Honjo MN and  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: 87.
  38. Nishio H, Buzas DM, Nagano AJ, Suzuki Y, Sugano S, Ito M, Morinaga S-I and Kudoh H (2016) From the laboratory to the field: assaying histone methylation at FLOWERING LOCUS C in naturally growing Arabidopsis halleri, Genes & Genetic Systems, 91(1):15-26
  39. Kawamura K, Kawanabe T, Shimizu M, Nagano AJ, Saeki N, Okazaki K, Kaji M, Dennis ES, Osabe K and Fujimoto R (2016) Genetic distance of inbred lines of Chinese cabbage and its relationship to heterosis., Plant Gene, 5: 1-7.
  40. Tanigaki Y, Higashi T, Takayama K, Nagano AJ and Fukuda H (2015) Transcriptome analysis of plant hormone-related tomato (Solanum lycopersicum) genes in a sunlight-type plant factory., PLoS ONE, 10(12): e0143412.
  41. Sakaguchi S, Sugino T, Tsumura Y, Ito M, Crisp MD, Bowman DMJS, Nagano AJ, Honjo MN, Yasugi M, Kudoh H, Matsuki Y, Suyama Y and Isagi Y (2015) High-throughput linkage mapping of Australian white cypress pine (Callitris glaucophylla) and map transferability to related species., Tree Genetics & Genomes, 11: 121.
  42. Hirao K, Nagano AJ, and Awazu A (2015) Noise-plasticity correlations of gene expression in the multicellular organism Arabidopsis thaliana., Journal of Theoretical Biology, 387:13-22
  43. Kubota S, Iwasaki T, Hanada K, Nagano AJ, Fujiyama A, Toyoda A, Sugano S, Suzuki Y, Hikosaka K, Ito M and Morinaga S (2015) A Genome Scan for Genes Underlying Microgeographic-Scale Local Adaptation in a Wild Arabidopsis Species., PLoS Genetics, 14;11(7):e1005361.
  44. Ushio M, Yamasaki E, Takasu H, Nagano AJ, Fujinaga S, Honjo NM, Ikemoto M, Sakai S and Kudoh H, (2015) Microbial Communities on Flower Surfaces Act as Signatures of Pollinator Visitation., Scientific Reports, 5: 8695.
  45. Nagano AJ, Honjo NM, Mihara M, Sato M and Kudoh H, (2015) Detection of Plant Viruses in Natural Environments by Using RNA-Seq., Methods in  Molecular Biology, 1236: 89-98.
  46. Shirakawa M, Ueda H, Nagano AJ, Shimada T, Kohchi T and Hara-Nishimura I, (2014) FAMA Is an Essential Component for the Differentiation of Two Distinct Cell Types, Myrosin Cells and Guard Cells, in Arabidopsis., Plant Cell, 26(10):4039-52.
  47. Mochizuki K, Nagano AJ, Kudoh H and Kawakita A, (2014) Isolation and Characterization of 11 Microsatellite Markers for Glochidion acuminatum (Phyllanthaceae)., Applications in Plant Sciences, 2 (9):1400045.
  48. Satoh M, Tokaji Y, Nagano AJ, Hara-Nishimura I, Hayashi M, Nishimura M, Ohta H and Masuda S, (2014) Arabidopsis mutants affecting oxylipin signaling in photo-oxidative stress responses., Plant Physiology and Biochemistry, 80: 90-95.
  49. Yamada K, Nagano AJ, Nishina M, Hara-Nishimura I and Nishimura M, (2013) Identification of Two Novel Endoplasmic Reticulum Body-Specific Integral Membrane Proteins., Plant Physiology, 161(1): 108-20.
  50. Nagano AJ, Sato Y, Mihara M, Antonio BA, Motoyama R, Itoh H, Nagamura Y and Izawa T, (2012) Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions., Cell, 51(6):1358-69.
    • Preview article: Jaeger PA, Doherty C and Ideker T, (2012) Modeling Transcriptome Dynamics in a Complex World., Cell, 51(6):1161-2.
    • Selected paper in Research Highlights of Nature Biotechnology., Nature Biotechnology, 31: 37 (2013)
  51. Nakano RT, Matsushima R, Nagano AJ, Fukao Y, Fujiwara M, Kondo M, Nishimura M and Hara-Nishimura I, (2012) ERMO3/MVP1/GOLD36 Is Involved in a Cell Type-Specific Mechanism for Maintaining ER Morphology in Arabidopsis thalianaPLoS ONE, 7(11): e49103.
  52. Nagano AJ, Tsuchimatsu T, Okuyama Y and  Hara-Nishimura I, (2012), Bimodal Expression Level Polymorphisms in Arabidopsis thalianaPlant Signaling & Behavior, 7(7): 864-73.
  53. Izawa T, Mihara M, Suzuki Y, Gupta M, Itoh H, Nagano AJ, Motoyama R, Sawada Y, Yano M, Hirai MY, Makino A, and Nagamura Y, (2011), Os-GIGANTEA Confers Robust Diurnal Rhythms on the Global Transcriptome of Rice in the Field, Plant Cell, 23(5): 1741-55.
  54. Yamada K, Nagano AJ, Ogasawara K, Hara-Nishimura I, and Nishimura M, (2009), The ER body, a new organelle in Arabidopsis thaliana, requires NAI2 for its formation and accumulates specific beta-glucosidases, Plant Signaling & Behavior, 4(9): 1-4.
  55. Nagano AJ, Maekawa A, Nakano RT, Miyahara M, Higaki T, Kutsuna N, Hasezawa S and Hara-Nishimura I, (2009), Quantitative Analysis of ER body Morphology  in an Arabidopsis  Mutants., Plant & Cell Physiology., 50(12): 2000-2014.
  56. Yamada K,* Nagano AJ*, Nishina M, Hara-Nishimura I, and Nishimura M, (* these authors contributed equally), (2008) NAI2 Is an Endoplasmic Reticulum (ER) Body Component That Enables ER Body Formation in Arabidopsis thaliana., Plant Cell, 20(9):2529-40.
  57. Nagano AJ, Fukazawa Y, Hayashi M, Ikeuchi M, Tsukaya H, Nishimura M and Hara-Nishimura I, (2008) AtMap1: a DNA Microarray for Genomic Deletion Mapping in Arabidopsis thaliana., The Plant Journal, 56(6): 1058-65.
  58. Nagano AJ, Fukao Y, Fujiwara M, Nishimura M and Hara-Nishimura I, (2008), Antagonistic Jacalin-Related Lectins Regulate the Size of ER-Body-Type beta-Glucosidase Complexes in Arabidopsis thaliana., Plant & Cell Physiology., 49(6): 969-980.
  59. Morinaga S-I, Nagano AJ, Miyazaki S, Kubo M, Demura T, Fukuda H, Sakai S and Hasebe M, (2008), Ecogenomics of cleistogamous and chasmogamous flowering: genome-wide gene expression patterns from cross-species microarray analysis in Cardamine kokaiensis (Brassicaceae)., Journal of Ecology., 96: 1086-1097.
  60. Nagano AJ, Matsushima R and  Hara-Nishimura I, (2005), Activation of an ER-body-localized beta-Glucosidase via a Cytosolic Binding Partner in Damaged Tissues of Arabidopsis thaliana., Plant & Cell Physiology., 46(7): 1140-8.


  1. 永野 惇「稲妻」In 「広辞苑を3倍楽しむ その2 (岩波科学ライブラリー)」(2018)
  2. 神谷 麻梨, 永野 惇, 本庄 三恵,  工藤 洋,「野生植物とウイルスの見えない相互作用をRNA-Seqで観る」, (2017), BSJ-Review, 8A:12-21
  3. 宅見 薫雄, 吉田 健太郎, 水野 信之, 小林 史典, 永野 惇, 半田 裕一, 「高速シークエンサーを活用したコムギゲノム研究の新展開」, (2016), 育種学研究, 18(2), 78-84
  4. 工藤 洋, 永野 惇, 「開花季節の調節における気温の記憶:気象と分子生物学から見た生物機能の頑健性」, (2015), In 新田 梢, 陶山 佳久 (編), 生物時計の生態学, 151-169
  5. 岩田 洋佳, 平藤 雅之, 永野 惇, 澤田 有司, Scott Chapman, 「作物環境応答の網羅的計測とモデリング~その育種への活用~」, (2015), 育種学研究, 17(2), 57-63
  6. 永野 惇, 「野外でのトランスクリプトーム解析から見えること」, (2014), 植物の生長調節, 49(2), 137-42
  7. 永野 惇, 工藤 洋, 「野外の環境における生物の環境応答の理解にむけて:トランスクリプトームデータと気象データの統合」, (2014), ライフサイエンス領域融合レビュー, 3, e009
  8. 永野 惇, 「広辞苑を3倍楽しむ<68> 稲妻」, (2014), 科学, 84(3), 岩波書店
  9. 永野 惇, 「フィールド・トランスクリプトミクスから30年後の生物学を考える」, (2013), 光合成研究, 23(3): 129-35.
  10. Kudoh H and Nagano AJ, (2013) Memory of temperature in the seasonal control of flowering time: an unexplored link between meteorology and molecular biology. In Pontarotti P. ed. Evolutionary Biology: Exobiology and Evolutionary Mechanisms, Springer:195-215.
  11. 永野 惇, 森長 真一 (責任編集), 「ゲノムが拓く生態学 -遺伝子の網羅的解析で迫る植物の生きざま-」, (2011), 文一総合出版,<amazon>
  12. 永野 惇, 「実験室と野外のすきまとその組織化」, In 鳥海 光弘 (編), 「すきまの組織化」, (2011), 国際高等研究所学術出版
  13. 永野 惇, 桧垣 匠 (文), 西村 幹夫, 三村 徹郎, 西村 いくこ, 真野 昌二 (監修), 「Photobook 植物細胞の知られざる世界」, (2010), 化学同人, <amazon>
  14. 永野 惇, 「生物学の中の隙間、生物学と外の隙間」, In 鳥海 光弘 (編), 「隙間~自然・人間・社会の現象学~」, (2008), 国際高等研究所学術出版


  1. 第80回日本植物学会年会シンポジウム「植物-微生物の見えない相互作用を観る:現在と未来」, 沖縄, 2016年9月
  2. 第57回日本植物生理学会年会シンポジウム「Challenge to the outdoor environment by the experimental plant physiology」, 岩手, 2016年3月
  3. 「データ科学の発展と植物科学との融合」ワークショップ, 東京, 2014年11月
  4. 京都大学生態学研究センター共同利用研究集会 「RAD-Seqデータ解析ワークショップ2014」, 京都, 2014年11月
  5. 日本植物学会第77回大会シンポジウム 「RAD-Seqが切り拓く植物研究―栽培種から野生種まで」,  北海道,  2013年9月
  6. BGI special seminar. ゲノミクス・バイオインフォマティクスの最前線, 京都, 2012年9月
  7. Theory of Bio-Mathematics and Its Applications VII シンポジウム 「生物の実データに基づく数理・統計モデル解析」,  京都,  2010年11月
  8. 日本植物学会第74回大会シンポジウム「画像情報から植物を定量的に捉える」,  愛知,  2010年9月
  9. 第40回種生物学シンポジウム「ポストゲノム時代の生態学」, 茨城,  2008年12月