Plant Genomic Network Research Team

Laboratories

Publications

2024

Original Papers

Todaka, D., Quynh, D.T.N., Tanaka, M., Utsumi, Y., Utsumi, C., Ezoe, A., Takahashi, S., Ishida, J., Kusano, M., Kobayashi, M., Saito, K., Nagano, A.J., Nakano, Y., Mitsuda, N., Fujiwara, S. and Seki, M. (2024) Application of ethanol alleviates heat damage to leaf growth and yield in tomato. Front. Plant Sci. 15:1325365.

Sulieman, S., Ha, C.V., Le, D.T., Abdelrahman, M., Tran, C.D., Watanabe, Y., Tanaka, M., Ulhassan, Z., Sheteiwy, M.S., Gangurde, S.S., Mochida, K., Seki, M. and Tran, L.S. (2024) Comparative transcriptome analysis of respiration-related genes in nodules of phosphate-deficient soybean (Glycine max cv. Williams 82). Plant Stress 11: 100368.

Tachibana, R., Abe, S., Marugami, M., Yamagami, A., Akema, R., Ohashi, T., Nishida, K., Nosaki, S., Miyakawa, T., Tanokura, M., Kim, J.M., Seki, M., Inaba, T., Matsui, M., Ifuku, K., Kushiro, T., Asami, T. and Nakano, T. (2024) BPG4 regulates chloroplast development and homeostasis by suppressing GLK transcription factors and involving light and brassinosteroid signaling. Nature Communications 15: 370.

2023

Original Papers

Adachi, H., Sakai, T., Kourelis, J., Pai, H., Gonzalez Hernandez, J.L., Utsumi, Y., Seki, M., Maqbool, A. and Kamoun, S. (2023) Jurassic NLR: conserved and dynamic evolutionary features of the atypically ancient immune receptor ZAR1. Plant Cell 35: 3662-3685.

Takano, S.I., Utsumi, Y., Nagano, A., Takahashi, S., Ezoe, A., Seki, M., Le. T.X. and Takasu, K. (2023) Induction of leaf curling in cassava plants by the cassava mealybug Phenacoccus manihoti (Hemiptera: Pseudococcidae). Appl. Entomol. & Zool. 58: 279-290.

Ezoe, A., Iuchi, S., Sakurai, T., Aso, Y., Ishida, J., Tokunaga, H., Vu, A.T., Utsumi, Y., Takahashi, S., Tanaka, M., Ishitani, M. and Seki, M. (2023) Fully sequencing the cassava full-length cDNA library reveals unannotated transcript structures and alternative splicing events in regions with a high density of single nucleotide variations, insertions–deletions, and heterozygous sequences. Plant Mol. Biol. 112:33-45.

Takatsuka, H., Sasaki, A., Takahashi, N., Shibata, M., Sugimoto, K., Tanaka, M., Seki, M. and Umeda, M. (2023) Cytokinin signaling promotes root hair growth by directly regulating RSL4 expression. J. Exp. Bot. 74:3579-3594.

Hayashi, K., Kato, N., Bashir, K., Nomoto, H., Nakayama, M., Chini, A., Takahashi, S., Saito, H., Watanabe, R., Takaoka, Y., Tanaka, M., Nagano, A.J., Seki, M., Solano, R. and Ueda, M. (2023) Subtype-selective agonists of plant hormone co-receptor COI1-JAZs identified from the stereoisomers of coronatine. Commun. Biol. 6:320.

Temman, H., Sakamoto, T., Ueda, M, Sugimoto, K., Migihashi, M., Yamamoto, K., Tsujimoto-Inui, Y., Sato, H., Shibuta, M. K., Nishino, N., Nakamura, T., Shimada, H., Taniguchi, Y. Y., Takeda, S., Aida, M., Suzuki, T., Seki, M. and Matsunaga, S. (2023) Histone deacetylation regulates de novo shoot regeneration. PNAS Nexus 2:pgad002.

Feng Z, Liang X, Tian H, Watanabe Y, Nguyen KH, Tran CD, Abdelrahman M, Xu K, Mostofa MG, Ha CV, Mochida K, Tian C, Tanaka M, Seki M, Liang Z, Miao Y, Tran LP, Li W. (2023) SUPPRESSOR of MAX2 1 (SMAX1) and SMAX1-LIKE2 (SMXL2) Negatively Regulate Drought Resistance in Arabidopsis thaliana. Plant Cell Physiol. 63:1900-1913.

Abdelrahman, M., Mostofa, M.G., Tran, C.D., El-Sayed, M., Li, W., Sulieman, S., Tanaka, M., Seki, M. and Tran, L.P. (2023) The Karrikin Receptor Karrikin Insensitive2 Positively Regulates Heat Stress Tolerance in Arabidopsis thaliana. Plant Cell Physiol. 63:1914-1926.

Review Papers

Ueda, M., Higashiyama, T., Sugimoto, K., Mochida, K., Nakajima, K., Hayashi, M., Okamoto, M., Nakamura, Y. and Seki, M. (2023) MEETING REPORT: The 33rd International Conference on Arabidopsis Research (ICAR2023). Genes to Cells 28:825-830.

Manavella, P., Herz, M.G., Kornblihtt, A., Sorenson, R., Sieburth, L., Nakaminami, K., Seki, M., Ding, Y., Sun, Q., Kang, H., Ariel, F., Crespi, M., Giudicatti , A., Cai, Q., Jin, H., Feng, X., Qi, Y., and Pikaard, C. (2023) Beyond transcription: compelling open questions in plant RNA biology. Plant Cell 35:1626-1653.

2022

Original Papers

Bashir, K., Todaka, D., Rasheed, S., Matsui, A., Ahmad, Z., Sako, K., Utsumi, Y., Vu, A.T., Tanaka, M., Takahashi, S., Ishida, J., Tsuboi, Y., Watanabe, S., Kanno, Y., Ando, E., Shin, K.C., Seito, M., Motegi, H., Sato, M., Li, R., Kikuchi, S., Fujita, M., Kusano, M., Kobayashi, M., Habu, Y., Nagano, A.J., Kawaura, K., Kikuchi, J., Saito, K., Hirai, M.Y., Seo, M., Shinozaki, K., Kinoshita, T. and Seki, M. (2022) Ethanol-mediated novel survival strategy against drought stress in plants. Plant Cell Physiol (Rapid Paper) 63:1181-1192.

Vu, A.T., Utsumi, Y., Utsumi, C., Tanaka, M., Takahashi, S., Todaka, D., Kanno, Y., Seo, M., Ando, E., Sako, K., Bashir, K., Kinoshita, T., Pham, X.H. and Seki, M. (2022) Ethanol treatment enhances drought stress avoidance in cassava (Manihot esculenta Crantz). Plant Mol. Biol. 110:269-285.

Ha, C.V, Mostofa, M.G., Nguyen, K.H., Tran, C.D., Watanabe, Y, Li, W., Osakabe, Y., Sato, M., Toyooka, K., Tanaka, M., Seki, M., Burritt, D.J., Anderson, C., Zhang, R., Nguyen, H.M., Le, V.P., Bui, H.T., Mochida, K. and Tran, L.S.P. (2022) The histidine phosphotransfer AHP4 plays a negative role in Arabidopsis plant response to drought. Plant J. 111:1732-1752.

Tian, H., Watanabe, Y., Nguyen, K.H., Tran, C.D., Abdelrahman, M., Liang, X., Xu, K., Sepulveda, C., Mostofa, M.G., Ha, C.V., Nelson, D.C., Mochida, K., Tian, C., Tanaka, M., Seki, M., Miao, Y., Tran, L.S.P. and Li, W. (2022) KARRIKIN UPREGULATED F-BOX 1 negatively regulates drought resistance in 1 Arabidopsis thaliana. Plant Physiol. 190:2671-2687.

Sakamoto, T., SakamotSakamoto, T., Sakamoto, Y., Grob, S., Slane, D., Yamashita, T., Ito, N., Oko, Y., Sugiyama, T., Higaki, T., Hasezawa, S., Tanaka, M., Matsui, A., Seki, M., Suzuki, T., Grossniklaus, U. and Matsunaga, S. (2022). Two-step regulation of centromere distribution by condensin II and the nuclear envelope proteins. Nature Plants. 8: 940-953.

Zhang, R., Kuo, R., Coulter, M., Calixto, C.P.G., Entizne, J.C., Guo, W., Marquez, Y., Milne, L., Riegler, S., Matsui, A., Tanaka, M., Harvey, S., Gao, Y., Wießner-Kroh, T., Paniagua, A., Crespi, M., Denby, K., Hur, A.B., Huq, E., Jantsch, M.F., Jarmolowski, A., Koester, T., Laubinger, S., Li, Q.Q., Gu, L., Seki, M., Staiger, D., Sunkar, R., Szweykowska-Kulinska, Z., Tu, S.L., Wachter, A., Waugh, R., Xiong, L., Zhang, X.N., Conesa, A., Reddy, A.S.N., Barta, A., Kalyna, M., Brown, J.W.S. (2022) A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. Genome Biol. 23:149. doi: 10.1186/s13059-022-02711-0.

Matsui, A., Todaka, D., Tanaka, M., Mizunashi, K., Takahashi, S., Sunaoshi, Y., Tsuboi, Y., Ishida, J., Bashir, K., Kikuchi, J., Kusano, M., Kobayashi, M., Kawaura, K. and Seki, M. (2022) Ethanol induces heat tolerance in plants by stimulating unfolded protein response. Plant Mol. Biol. 110:131-145.

Vincent, S., Kim, J.M., Pérez-Salamó, I., To, T.K., Torii, C., Ishida, J., Tanaka, M., Endo, T.A., Bhat, P., Devlin, P., *Seki, M., and *Devoto, A. (2022) Jasmonates and histone deacetylase 6 activate Arabidopsis genome-wide histone acetylation and methylation during the early acute response. BMC Biol. 20: 83.

Onosato, H., Fujimoto, G., Higami, T., Sakamoto, T., Yamada, A., Suzuki, T., Ozawa, R., Matsunaga, S., Seki, M., Ueda, M., Sako, K., Galis, I. and Arimura, G. (2022) Sustained defense response via volatile signaling and its epigenetic transcriptional regulation. Plant Physiol. 189:922-933.

Akter, M.A., Mehraj, H., Miyaji, N., Takahashi, S., Takasaki-Yasuda, T., Seki, M., Dennis, E.S., Fujimoto, R. and Osabe, K. (2022) Transcriptional association between mRNAs and their paired natural antisense transcripts following Fusarium oxysporum inoculation in Brassica rapa L. Horticulturae 8, 17.

Review Papers

Matsui, A. and Seki, M. (2022) Plant Non-coding Transcriptomics. In “Plant Omics: Advances in Big Data Biology” (Edited by Drs. Hajime Ohyanagi, Eiji Yamamoto, Kentaro Yano)". CABI, Nosworthy Way, Wallingford OX10 8DE, UK. 79-96.

Press Releases

Ethanol pretreated soil protects plants from drought (Aug. 25, 2022)

Ethanol increases high temperature tolerance in plants (Jun. 22, 2022)

Unwinding the secrets of stress in plants could help feed the world during climate crisis (Apr. 11, 2022)

2021

Original Papers

Baba, T., Nomura, H., Utsumi, Y., Sokheang, U.Y., Song, P., Kameda, A., Ishitani, M., Seki, M., Srean, P. and Ito, K. (2021) Plant density optimisation to improve sustainable cassava (Manihot esculenta Crantz) stem and tuberous root yield in Cambodia. Asian Journal of Agricultural and Environmental Safety 2: 51-58.

Utsumi, Y., Utsumi, C., Tanaka, M., Okamoto, Y., Takahashi, S., Huong, T.T., Nguyen, A.V., Nguyen, V.D., Tokunaga, H., Nigel T. and Seki, M. (2021) Agrobacterium-mediated cassava transformation for the Asian-elite variety KU50. Plant Mol. Biol. doi: 10.1007/s11103-021-01212-1.

Utsumi, Y., Utsumi, C., Tanaka, M., Takahashi, S., Okamoto, Y., Ono, M., Nakamura, Y. and Seki, M. (2021) Suppressed expression of starch branching enzyme 1 and 2 increases resistant starch and amylose content and modifies amylopectin structure in cassava. Plant Mol. Biol. doi: 10.1007/s11103-021-01209-w.

Ahmad Z., Bashir, K., Matsui, A., Tanaka, M., Sasaki, R., Oikawa, A., Hirai, M.Y., Chaomurilege, Zu, Y., Kawai-Yamada M., Rashid, B., Husnain, T. and Seki, M. (2021) Overexpression of nicotinamidase 3 (NIC3) gene and the exogenous application of nicotinic acid (NA) enhance drought tolerance and increase biomass in Arabidopsis. Plant Mol. Biol. 107:63-84.
Cover page of the journal PMB

Sako, K., Ha, C.V., Matsui, A., Tanaka, M., Sato, A. and Seki, M. (2021) Transcriptome analysis of Arabidopsis thaliana plants treated with a new compound Natolen128, enhancing salt stress tolerance. Plants 10: 978.

Sako, K., Nagashima, R., Tamoi, M. and Seki, M. (2021) Exogenous ethanol treatment alleviates oxidative damage of Arabidopsis thaliana under conditions of high light stress. Plant Biotechnol. 38:339-344.

Mehraj, H., Shea, D.J., Takahashi, S., Miyaji, N., Akter, A., Seki, M., Dennis, E.S., Fujimoto R. and Osabe, K. (2021) Genome-wide analysis of long noncoding RNAs, 24-nt siRNAs, DNA methylation and H3K27me3 marks in Brassica rapa. PLOS ONE 16: e0242530.

Mehraj, H., Takahashi, S., Miyaji, N., Akter, A., Suzuki, Y., Seki, M., Dennis, E. and Fujimoto, R. (2021) Characterization of histone H3 lysine 4 and 36 tri-methylation in Brassica rapa L. Front. Plant Sci. 12:659634.

Babak, B., Higo, A., Yamaguchi, K., Tokunaga, H., Utsumi, Y., Selvaraj, M.G., Seki, M., Ishitani, M., Lopez-Lavalle, L.A,B and Tsuji, H. (2021) Field-transcriptome analyses reveal developmental transitions during flowering in cassava (Manihot esculenta Crantz). Plant Mol. Biol. doi: 10.1007/s11103-021-01149-5.

Ogawa, D., Suzuki, Y., Yokoo, T.,Katoh, E., Teruya, M., Muramatsu, M.,Ma, J.F., Yoshida, Y., Isaji, S., Ogo, Y., Miyao, M., Kim, J.M., Kojima, M., Takebayashi, Y., Sakakibara, H., Takeda, S., Okada, K., Mori, N., Seki, M. and Habu, Y. (2021) Acetic-acid-induced jasmonate signaling in root enhances drought avoidance in rice. Scientific Rep. 11: 6280.

Review Papers

Uke, A., Tokunaga, H.*, Utsumi, Y., Vu, N.A., Nhan, P.T., Srean, P., Hy, N.H., Ham, L.H., Lopez-Lavalle, L.A. B., Ishitani, M., Hung, N., Tuan, L.N., Hong, N.V., Huy, N.Q., Hoat, T.X., Takasu, K., Seki, M.* and Ugaki, M.* (2021) Cassava mosaic disease and its management in South-East Asia. Plant Mol. Biol. doi: 10.1007/s11103-021-01168-2.

Bashir, K., Ahmad, Z., Kobayashi, T., Seki, M. and Nishizawa, N.K. (2021) Roles of subcellular metal homeostasis in crop improvement. J. Exp. Bot. 72: 2083–2098.

Sako, K., Nguyen, H.M. and Seki, M. (2021) Advances in chemical priming to enhance abiotic stress tolerance in plants. Plant Cell Physiol. 61:1995-2003.