HOLOBIONT & RESILIENCE Research Team

Geoderma Volume 463, November 2025, 117578

  High-resolution monitoring and modeling of subsurface CO2 dynamics in soybean field [Journal]

Hamamoto S, Saito H, Matsunami H, Nihei N, Ichihashi Y, Tatsuno T, Moldrup M, Nishimura T

Frontiers in Education Volume 10 - 2025

  Making a difference through presentations: Let’s speak, communicate, and connect! [Journal]

Furumizu C, Ichiashi Y

Nature Plants volume 11, pages483-504 (2025)

  Co-option and neofunctionalization of stomatal executors for defence against herbivores in Brassicales [PubMed] [Journal]

Shirakawa M, Oguro T, Sugano S, Yamaoka S, Sagara M, Tanida M, Sunuma K, Iwami T, Nakanishi T, Horiuchi K, Kumaishi K, Yoshida S, Watanabe M, Tohge T, Suzuki T, Ichihashi Y, Takemiya A, Yamaguchi N, Kohchi T, Ito T

Scientific Reports volume 15, Article number: 1928 (2025)

  A quantitative prediction method utilizing whole omics data for biosensing [PubMed] [Journal]

Koizumi T, Suzuki K, Mizuki I, Kumaishi K, Ichihashi Y.

Plant J. doi: 10.1111/tpj.17178. 2024

  Establishing a comprehensive web-based analysis platform for Nicotiana benthamiana genome and transcriptome. [PubMed] [Journal]

Kurotani K, Hirakawa H, Shirasawa K, Tagiri K, Mori M, Ramadan A, Ichihashi Y, Suzuki T, Tanizawa Y, An J, Winefield C, Waterhouse PM, Miura K, Nakamura Y, Isobe S, Notaguchi M.

iScience. 27[11]: 111074. 2024

  Time course transcriptomic profiling suggests Crp/Fnr transcriptional regulation of nosZ gene in a N2O-reducing thermophile. [PubMed] [Journal]

Tsuchiya J, Mino S, Fujiwara F, Okuma N, Ichihashi Y, Morris RM, Nunn BL, Emma TS, Sawabe T.

Sci. Rep. 14: 20541. 2024

  Soil volatilomics uncovers tight linkage between soybean presence and soil omics profiles in agricultural fields. [PubMed] [Journal]

Kuchikata H, Sano M, Fujiwara F, Murashima K, Kumaishi K, Narukawa M, Nose Y, Kobayashi M, Hamamoto S, Kobayashi NI, Sugiyama A, Nihei N, Ichihashi Y, Kusano M.

PLOS ONE. 19[4]: e0301981. 2024

  Global changes in gene expression during compatible and incompatible interactions of faba bean (Vicia faba L.) during Orobanche foetida parasitism [PubMed] [Journal]

Boukteb A, Sato K, Gan P, Kharrat M, Sakouhi H, Shibata A, Shirasu K, Ichihashi Y, Bouhadida M.

Nature Communications. 15: 1098. 2024

  Petal abscission is promoted by jasmonic acid-induced autophagy at Arabidopsis petal bases. [PubMed] [Journal]

Furuta Y, Yamamoto H, Hirakawa T, Uemura A, Pelayo MA, Iimura H, Katagiri N, Takeda-Kamiya N, Kumaishi K, Shirakawa M, Ishiguro S, Ichihashi Y, Suzuki T, Goh T, Toyooka K, Ito T, Yamaguchi N.

Current Biology. 33: 1-15. 2023

  Genetic and phosphoproteomic basis of LysM-mediated immune signaling in Marchantia polymorpha highlights conserved elements and new aspect of pattern-triggered immunity in land plants. [PubMed] [Journal]

Yotsui I, Matsui H, Miyauchi S, Iwakawa H, Melkonian K, Schlüter T, Gimenez-Ibanez S, Kanazawa T, Nomura Y, Stolze SC, Jeon HW, Sugano S, Shirakawa M, Nishihama M, Ichihashi Y, Shirasu K, Ueda T, Kohchi T, Nakagami H.

ISME Commun. 3[1]: 28. 2023

  An agroecological structure model of compost—soil—plant interactions for sustainable organic farming. [PubMed] [Journal]

Miyamoto H, Shigeta K, Suda W, Ichihashi Y, Nihei N, Matsuura M, Tsuboi A, Tominaga N, Aono M, Sato M, Taguchi S, Nakaguma T, Tsuji N, Ishii C, Matsushita T, Shindo C, Ito T, Kato T, Kurotani A, Shima H, Moriya S, Wada S, Horiuchi S, Satoh T, Mori K, Nishiuchi T, Miyamoto H, Kodama H, Hattori M, Ohno H, Kikuchi J, Hirai M.

Front Plant Sci. 13: 1047563. 2022

  Effects of irrigation on root growth and development of soybean: a 3-year sandy field experiment. [PubMed] [Journal]

Bui KT, Naruse T, Yoshida H, Toda Y, Ohmori Y, Tsuda M, Kaga A, Yamasaki Y, Tsujimoto H, Ichihashi Y, Hirai YM, Fujiwara T, Iwata H, Matsuoka M, Takahashi H, Nakazono M.

Front Plant Sci. 13: 1077996. 2022

  Phenolic signals for prehaustorium formation in Striga hermonthica. [PubMed] [Journal]

Aoki N, Cui S, Ito S, Kumaishi K, Kobori S, Ichihashi Y, Yoshida S.

Microbiome. 10[1]: 236. 2022

 Stochastic variational variable selection for high-dimensional microbiome data. [PubMed] [Journal]

Dang T, Kumaishi K, Usui E, Kobori S, Sato T, Toda Y, Yamasaki Y, Tsujimoto H, Ichihashi Y, Iwata H.

Sci. Rep. 12: 19289. 2022

  High throughput method of 16S rRNA gene sequencing library preparation for plant root microbial community profiling. [PubMed] [Journal]

Kumaishi K, Usui E, Suzuki K, Kobori S, Sato T, Toda Y, Takanashi H, Shinozaki S, Noda M, Takakura A, Matsumoto K, Yamasaki Y, Tsujimoto H, Iwata H, Ichihashi Y.

bio Rxiv. 2022

 A novel genomic DNA library preparation method with low GC bias. [Journal]

Kelly S. T, Hakoyama T, Kumaishi K, Okuda-Yabukami H, Kato S, Hayashi M, Minoda A, Ichihashi Y.

Acta virologica. 66: 206-215. 2022

  A novel RNA virus, Thesium chinense closterovirus 1, identified by high-throughput RNA-sequencing of the parasitic plant Thesium chinense. [PubMed] [Journal]

Shin C, Choi D, Shirasu K, Ichihashi Y, Hahn Y.

Plant Biotechnology. 39[3]: 323-327. 2022

  Oxicam-type nonsteroidal anti-inflammatory drugs enhance Agrobacterium-mediated transient transformation in plants. [Journal]

Choi SW, Kumaishi K, Motohashi R, Enoki H, Chacuttayapong W, Takamizo T, Saika H, Endo E, Yamada T, Hirose A, Koizuka N, Kimura S, Kawakatsu Y, Koga H, Ito E, Shirasu K, Ichihashi Y.

Acta virologica. 66[2]: 149-156. 2022

  Artemisia capillaris nucleorhabdovirus 1, a novel member of the genus Alphanucleorhabdovirus, identified in the Artemisia capillaris transcriptome. [PubMed] [Journal]

hoi D, Shin C, Shirasu K, Ichihashi Y, Hahn Y.

New Phytol. 234[3]: 867-883. 2022

  Ranjan A, Spatial control of cell division by GA-OsGRF7/8 module in a leaf explains the leaf length variation between cultivated and wild rice. [PubMed] [Journal]

Jathar V, Saini K, Chauhan A, Rani R, Ichihashi Y.

Int. J. Environ. Res. Public Health. 19[3]: 1228. 2022

 Chemical-Mediated Microbial Interactions Can Reduce the Effectiveness of Time-Series-Based Inference of Ecological Interaction Networks. [PubMed] [Journal]

Suzuki K, Abe M. S, Kumakura D, Nakaoka S, Fujiwara F, Miyamoto H, Nakaguma T, Okada M, Sakurai K, Shimizu S, Iwata H, Masuya H, Nihei N, Ichihashi Y.

Hortic. Res. 9: uhab056. 2022

 Discovery of the interfamily grafting capacity of Petunia, a floricultural species. [Journal]

Notaguchi M, Kurotani K, Huang C, Okayasu K, Suzuki T, Ichihashi Y, Shirasu K, Higashiyamam T, Niwa M.

bio Rxiv. 2021

  Phosphorus is a critical factor of the in vitro monoxenic culture method for a wide range of arbuscular mycorrhizal fungi culture collections. [Journal]

Sato T, Suzuki K, Usui E, Ichihashi Y.

Commn. Biol. 4: 707. 2021

  A pair of effectors encoded on a conditionally dispensable chromosome of Fusarium oxysporum suppress host-specific immunity. [PubMed] [Journal]

Ayukawa Y, Asai S, Gan P, Tsushima A, Ichihashi Y, Shibata A, Komatsu K, Houterman PM., Rep M, Shirasu K, Arie T.

Front Plant Sci. 12: 680151. 2021

  Transcriptomic analysis of resistant and susceptible responses in a new model root-knot nematode infection system using Solanum torvum and Meloidogyne arenaria. [PubMed] [Journal]

Sato K, Uehara T, Holbein J, Sasaki-Sekimoto Y, Gan P, Bino T, Yamaguchi K, Ichihashi Y, Maki N, Shigenobu S, Ohta H, Franke RB., Siddique S, Grundler FM.W., Suzuki T, Kadota Y, Shirasu K.

Plant Physiol. 186: 2093–2110. 2021

  LATERAL ORGAN BOUNDARIES DOMAIN 25 functions as a key regulator of haustorium development in dodders. [PubMed] [Journal]

Jhu MY, Ichihashi Y, Farhi M, Wong C, Sinha N.

J. Nat .Med. 75: 1067–1079. 2021

  Characterization of inter-annual changes in soil microbial lora of Panax ginseng cultivation ields in Shimane Prefecture of Western Japan by DNA metabarcoding using next-generation sequencing. [PubMed] [Journal]

Fujii T, Minami M, Watanabe T, Sato Takumi Kumaishi K, Ichihashi Y.

Front Plant Sci.12: 618245. 2021

  Analysis of genetic diversity and population structure of Orobanche foetida populations from Tunisia using RADseq. [PubMed] [Journal]

Boukteb A, Sakaguchi S, Ichihashi Y, Kharrat M, Nagano AJ, Shirasu K, Bouhadida M.

Plant Physiol. 185: 1429-1442. 2021

  Three-dimensional reconstructions of the internal structures of haustoria in parasitic Orobanchaceae. [PubMed] [Journal]

Masumoto N, Suzuki Y, Cui S, Wakazaki M, Sato M, Kumaishi K, Shibata A, Furuta M. K, Ichihashi Y, Shirasu K, Toyooka K, Sato Y, Yoshida S.

Plant Physiol. 185[4]: 1381-1394. 2020

  Subtilase activity in the intrusive cells mediates haustorium maturation in parasitic plants. [PubMed] [Journal]

Ogawa S, Wakatake T, Spallek T, Ishida JK, Sano R, Kurata T, Demura T, Yoshida S, Ichihashi Y, Schaller A, Shirasu K.

Front. Plant Sci. 11: 600726. 2020

  Morphological and physiological framework underlying plant longevity in Arabidopsis thaliana. [PubMed] [Journal]

Wang Y, Kumaishi K, Suzuki T, Ichihashi Y, Yamaguchi N, Shirakawa M, Ito T.

Pest Management Science, 76[12]: 3945-3953. 2020

  Solanum palinacanthum : broad‐spectrum resistance to root‐knot nematodes [Meloidogyne spp]. [PubMed] [Journal]

Murata G, Uesugi K, Uehara T, Kumaishi K, Ichihashi Y, Saito T, Shinmura Y.

Science 369[6504]: 698-702. 2020

  Cell–cell adhesion in plant grafting is facilitated by β-1,4-glucanases. [PubMed] [Journal]

Notaguchi M, Kurotani K, Sato Y, Tabata R, Kawakatsu Y, Okayasu K, Sawai Y, Okada R, Asahina M, Ichihashi Y, Shirasu K, Suzuki T, Niwa M, Higashiyama T.

Commn. Biol. 3: 407. 2020

  Host-parasite tissue adhesion by a secreted type of β-1,4-glucanase in the parasitic plant Phtheirospermum japonicum. [PubMed] [Journal]

Kurotani K, Wakatake T, Ichihashi Y, Okayasu K, Sawai Y, Ogawa S, Cui S, Suzuki T, Shirasu K, Notaguchi M.

PNAS 117[25]: 14552-14560. 2020

 Multi-omics analysis on an agroecosystem reveals the significant role of organic nitrogen to increase agricultural crop yield. [PubMed] [Journal]

Ichihashi Y, Date Y, Shino A, Shimizu T, Shibata A, Kumaishi K, Funahashi F, Wakayama K, Yamazaki K, Umezawa A, Sato T, Kobayashi M, Kamimura M, Kusano M, Che F-S, O`Brien M, Tanoi K, Hayashi M, Nakamura R, Shirasu K, Kikuchi J, Nihei N.

Front. Plant Sci. 11: 563. 2020

 Short-Term Magnesium Deficiency Triggers Nutrient Retranslocation in Arabidopsis thaliana. [PubMed] [Journal]

Ogura T, Kobayashi NI, Hermans C, Ohmae Y, Ichihashi Y, Shibata A, Shirasu K, Aoki N, Sugita R, Ogawa T, Suzuki H, Iwata R, Nakanishi TM, Tanoi K.

Plant Microbe Interact. 33: 474-487. 2020

  Exogenous treatment with glutamate induces immune responses in Arabidopsis. Mol. [PubMed] [Journal]

Goto Y, Maki N, Ichihashi Y, Kitazawa D, Igarashi D, Kadota Y, Shirasu K.

Plant Cell Physiol. 61[4]: 712-721. 2019

  AtNOT1 is a novel regulator of gene expression during pollen development. [PubMed] [Journal]

Motomura K, Arae T, Uramoto HA, Suzuki Y, Takeuchi H, Suzuki T, Ichihashi Y, Shibata A, Shirasu K, Takeda A, Higashiyama T, Chiba Y.

Front. Ecol. Evol. 7: 437. 2019

  CRABS CLAW and SUPERMAN Coordinate Hormone-, Stress-, and Metabolic-Related Gene Expression During Arabidopsis Stamen Development. [Journal]

Lee ZH, Tatsumi Y, Ichihashi Y, Suzuki T, Shibata A, Shirasu K, Yamaguchi N, Ito T.

Plant Cell Environ. 42: 2198-2214. 2019

  Abscisic acid-dependent histone demethylation during postgermination growth arrest in Arabidopsis. [PubMed] [Journal]

Wu J, Ichihashi Y, Suzuki T, Shibata A, Shirasu K, Yamaguchi N, Ito T.

Current Biology 29: 3041-3052. 2019

  Genome Sequence of Striga asiatica Provides Insight into the Evolution of Plant Parasitism. [PubMed] [Journal]

Yoshida S, Kim S, Wafula EK, Tanskanen J, Kim YM, Honaas L, Yang Z, Spallek T, Conn CE, Ichihashi Y, Cheong K, Cui S, Der JP, Gundlach H, Jiao Y, Hori C, Ishida JK, Kasahara H, Kiba T, Kim MS, Koo N, Laohavisit A, Lee YH, Lumba S, McCourt P, Mortimer JC, Mutuku JM, Nomura T, Sasaki-Sekimoto Y, Seto Y, Wang Y, Wakatake T, Sakakibara H, Demura T, Yamaguchi S, Yoneyama K, Manabe RI, Nelson DC, Schulman AH, Timko MP, dePamphilis CW, Choi D, Shirasu K.

Nature Plants 4: 247-257. 2018

  Core microbiomes for sustainable agroecosystems. [PubMed] [Journal]

Toju H, Peay KG, Yamamichi M, Narisawa K, Hiruma K, Naito K, Fukuda S, Ushio M, Nakaoka S, Onoda Y, Yoshida K, Schlaeppi K, Bai Y, Sugiura R, Ichihashi Y, Minamisawa K, Kiers ET.

New Phytologist 220[1]: 278-287. 2018

  Decoding the gene co-expression network underlying the ability of Gevuina avellana to live in diverse light conditions. [PubMed] [Journal]

Ostria-Gallardo E, Ranjan A, Ichihashi Y, Corcuera L, Sinha N.

Genome Announc. 6[26]: e00519-18. 2018

  High-Quality Genome Sequence of the Root-Knot Nematode Meloidogyne arenaria Genotype A2-O. [PubMed] [Journal]

Sato K, Kadota Y, Gan P, Bino T, Uehara T, Yamaguchi K, Ichihashi Y, Maki N, Iwahori H, Suzuki T, Shigenobu S, Shirasu K.

Scientific Reports 8: 3302. 2018

  Comparative transcriptomics with self-organizing map reveals cryptic photosynthetic differences between two accessions of North American Lake cress. [PubMed] [Journal]

Nakayama H, Sakamoto T, Okegawa Y, Kaminoyama K, Fujie M, Ichihashi Y, Kurata T, Motohashi K, Al-Shehbaz I, Sinha N, Kimura S.

Methods in Molecular Biology 1830: 163-189. 2018

  High Impact Gene Discovery: Simple Strand Specific mRNA Library Construction and Differential Regulatory Analysis Based on Gene Co-expression Network. [PubMed] [Journal]

Ichihashi Y, Fukushima A, Shibata A, Shirasu K.

Plant Cell Physiol. 59[4]: 729-738. 2018

  Transcriptomic and Metabolomic Reprogramming from Roots to Haustoria in the Parasitic Plant, Thesium chinense. [PubMed] [Journal]

Ichihashi Y, Kusano M, Kobayashi M, Suetsugu K, Yoshida S, Wakatake T, Kumaishi K, Shibata A, Saito K, Shirasu K.

Plant Reproduction 31[1]: 89-105. 2018

  Regulation of floral meristem activity through the interaction of AGAMOUS, SUPERMAN, and CLAVATA3 in Arabidopsis. [PubMed] [Journal]

Uemura A, Yamaguchi N, Xu Y, Wee W, Ichihashi Y, Suzuki T, Shibata A, Shirasu K, Ito T.

>PLOS ONE 11[11]: e0166574. 2016 †equal contribution.

 T ranscriptome Dynamics and Potential Roles of Sox6 in the Postnatal Heart. [PubMed] [Journal]

An CI†, Ichihashi Y†, Peng J, Sinha NR, and Hagiwara N.

G3 6[10]: 3169-3184. 2016

  A New Advanced Backcross Tomato Population Enables High Resolution Leaf QTL Mapping and Gene Identification. [PubMed] [Journal]

Fulop D, Ranjan A, Ofner I, Covington MF, Chitwood DH, West D, Ichihashi Y, Headland L, Zamir D, Maloof JN, and Sinha N.

Plant Physiol. 172[1]: 328-340. 2016

  eQTL regulating Transcript Levels Associated with Diverse Biological Processes in Tomato. [PubMed] [Journal]

Ranjan A, Budke J, Rowland SD, Chitwood DH, Kumar R, Carriedo LG, Ichihashi Y, Zumstein K, Maloof JN, and Sinha N.

Plant Cell 28[6]: 1250-1262. 2016

  Vascular Cell Induction Culture System Using Arabidopsis Leaves (VISUAL) Reveals the Sequential Differentiation of Sieve Element-like Cells. [PubMed] [Journal]

Kondo Y, Nurani AM, Saito C, Ichihashi Y, Saito M, Yamazaki K, Mitsuda N, Ohme-Takagi M, and Fukuda H.

New Phytologist. 210[2]: 694-708. 2016

  Transcriptomic analysis suggests a key role for SQUAMOSA PROMOTER BINDING PROTEIN LIKE, NAC and YUCCA genes in the heteroblastic development of the temperate rainforest tree Gevuina avellana (Proteaceae). [PubMed] [Journal]

Ostria-Gallardo E, Ranjan A, Chitwood DH, Kumar R, Townsley BT, Ichihashi Y, Corcuera LJ, and Sinha NR.

Plant Physiol. 169[3]: 2030-2047. 2015

  Light-induced indeterminacy alters shade avoiding tomato leaf morphology. [PubMed] [Journal]

Chitwood DH, Kumar R,Ranjan A, Pelletier JM, Townsley B, Ichihashi Y, Martinez CC, Zumstein K, Harada JJ, Maloof JN, and Sinha N.

Front. Plant Sci. 6: 366. 2015

  BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction. [PubMed] [Journal]

Townsley BT, Covington MF, Ichihashi Y, Zumstein K, Sinha NR.

Plant Physiol. 168[3]: 1152-1163. 2015

  The WRKY45-dependent signaling pathway is required for resistance against Striga parasitism. [PubMed] [Journal]

Mutuku JM, Yoshida S, Shimizu T, Ichihashi Y, Wakatake T, Seo M, Takahashi A, Shirasu K.

PLOS Genet. 11[4]: e1004953. 2015

  Shade avoidance components and pathways in adult plants revealed by phenotypic profiling. [PubMed] [Journal]

Nozue K, Tat A, Devisetty UK, Robinson M, Ichihashi Y, Lekkala S, Maloof J.

PLOS Genet. 11[1]: e1004900. 2015

  An Intracellular Transcriptomic Atlas of the Giant Coenocyte Caulerpa taxifolia. [PubMed] [Journal]

Ranjan A, Townsley, BT, Ichihashi Y, Sinha NR and Chitwood DH.

PNAS 111[25]: E2616-E2621. 2014

  Evolutionary developmental transcriptomics reveals a gene network module regulating interspecific diversity in plant leaf shape. [PubMed] [Journal]

Ichihashi Y, Aguilar-Martínez JA, Farhi M, Chitwood DH, Kumar R, Millon LV, Peng J, Maloof JN, and Sinha NR.

Plant Physiol. 166[3]: 1186-1199. 2014

  De novo assembly and characterization of the transcriptome of the parasitic weed Cuscuta pentagona identifies genes associated with plant parasitism. [PubMed] [Journal]

Ranjan A, Ichihashi Y, Farhi M, Zumstein K, Townsley B, David-Schwartz R, Sinha NR.

Plant Cell 26[9]: 3616-3629. 2014

  Resolving distinct genetic regulators of tomato leaf shape within a heteroblastic and ontogenetic context. [PubMed] [Journal]

Chitwood DH, Ranjan A, Kumar R, Ichihashi Y, Zumstein K, Headland L, Gallardo E, Aguilar-Martinez JA, Bush S, Carriedo L, Fulop D, Martinez C, Peng J, Maloof J, and Sinha NR.

Plant Cell 25[7]: 2465-248. 2013

  A quantitative genetic basis for leaf morphology in a set of precisely defined tomato introgression lines. [PubMed] [Journal]

Chitwood DH, Kumar R, Headland LR, Ranjan A, Covington MF, Ichihashi Y, Fulop D, Jiménez-Gómez JM, Peng J, Maloof JN, Sinha NR.

Front. Plant Sci. 3: 202. 2012.

  A High-Throughput Method for Illumina RNA-Seq Library Preparation. [PubMed] [Journal]

Kumar R†, Ichihashi Y†, Kimura S, Chitwood DH, Headland LR, Peng J, Maloof JN, Sinha NR.

Plant Physiol. 157[3]: 1151-1162. 2011

  Key proliferative activity in the junction between the leaf blade and leaf petiole of Arabidopsis. [PubMed] [Journal]

Ichihashi Y, Kawade K, Usami T, Horiguchi G, Takahashi T, Tsukaya H.

Plant Cell Physiol. 51: 252-261. 2010

  The bHLH transcription factor SPATULA controls final leaf size in Arabidopsis thaliana. [PubMed] [Journal]

Ichihashi Y, Horiguchi G, Gleissberg S, Tsukaya H.

Plant Cell Physiol. 51: 1046-1054. 2010

  The mechanism of cell cycle arrest front progression explained by a KLUH/CYP78A5-dependent mobile growth factor in developing leaves of Arabidopsis thaliana. [PubMed] [Journal]

Kazama T, Ichihashi Y, Murata S, Tsukaya H.

J Phytogeo Tax. 57: 7-16. 2009

  Phylogenetic positions of Tokai hilly land element, Drosera tokaiensis (Droseraceae) and its parental species, D. rotundifolia and D. [Journal]

Ichihashi Y, Minami M.