Publication

Original article

 

Ta, H., Nonomura, K.I. (2025) Profiling of 24-nt phasiRNAs in Rice Anther by Massively Parallel Sequencing and Stem-Loop Reverse Transcription PCR. In "Methods Mol Biol. 2025 (Kawakatsu, T. eds.) :135-146, 10.1007/978-1-0716-4204-7_14. PMID: 39499474.

 

Somashekar, H.*, Takanami, K., Benitez-Alfonso, Y., Oishi, A., Hiratsuka, R., Nonomura, K.I.* (2024) Callose Deficiency Modulates Plasmodesmata Frequency and Extracellular Distance in Rice Pollen Mother and Tapetal cells. Annals Bot mcae137, https://doi.org/10.1093/aob/mcae137.​​

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Tonosaki, K., Susaki, D., Morinaka, H., Ono, A., Nagata, H., Furuumi, H., Nonomura, K.I., Sato, Y., Sugimoto, K., Comai, L., Hatakeyama, K., Kakutani, T., Kinoshita, T.* (2024) Multi-layered epigenetic control of persistent and stage-specific imprinted genes in rice endosperm. Nature Plants, 10.1038/s41477-024-01754-4.​

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Mimura, M., Ono, S., Somashekar, H., and Nonomura, K.I.* (2024) Impact of protein domains on the MEL2 granule, a cytoplasmic ribonucleoprotein complex maintaining faithful meiosis progression in rice. New Phytologist, https://doi.org/10.1111/nph.19968.​

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Tsuda, K.*, Maeno, A., Otake, A., Kato, K., Tanaka, W., Hibara, K., and Nonomura, K.I. (2024). YABBY and diverged KNOX1 genes shape nodes and internodes in the stem. Science 384, 1241-1247, https://www.science.org/doi/10.1126/science.adn6748.

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Somashekar, H., Mimura, M., Tsuda, K., and Nonomura, K.I.* (2023). Rice GLUCAN SYNTHASE-LIKE5 promotes anther callose deposition to maintain meiosis initiation and progression. Plant Physiol 191, 400-413, https://doi.org/10.1093/plphys/kiac488.

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Tsuda, K.*, Maeno, A., and Nonomura, K.I. (2023) Heat shock-inducible clonal analysis reveals the stepwise establishment of cell fate in the rice stem. Plant Cell 35, 4366-4382, 10.1093/plcell/koad241.　

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Tsuda, K.*, Suzuki, T., Mimura, M., and Nonomura K.I. (2022). Comparison of constitutive promoter activities and development of maize ubiquitin promoter- and Gateway-based binary vectors for rice. Plant Biotechnol (Tokyo) 39, 139-146, https://doi.org/10.5511/plantbiotechnology.22.0120a.

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Liu, H.*, Shang, H., Yang, H., Liu, W., Tsugama, D., Nonomura, K.I., Zhou, A., Wu, W., Takano, T., and Liu, S.* (2022). RNA-binding protein MAC5A is required for gibberellin-regulated stamen development. Int J Mol Sci 23, 2009, https://doi.org/10.3390/ijms23042009.

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Kawai, K., Takehara, S., Kashio, T., Morii, M., Sugihara, A., Yoshimura, H., Ito, A., Hattori, M., Toda, Y., Kojima, M., Takebayashi, Y., Furuumi, H., Nonomura, K. I., Mikami, B., Akagi, T., Sakakibara, H., Kitano, H., Matsuoka, M., and Ueguchi-Tanaka, M.* (2022). Evolutionary alterations in gene expression and enzymatic activities of gibberellin 3-oxidase 1 in Oryza. Commun Biol 5, 67, https://doi.org/10.1038/s42003-022-03008-5.

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Ishikawa, R.*, Castillo, C.C.*, Htun, T.M., Numaguchi, K., Inoue, K., Oka, Y., Ogasawara, M., Sugiyama, S., Takama, N., Orn, C., Inoue, C., Nonomura, K.I., Allaby, R., Fuller, D. Q., and Ishii, T. (2022). A stepwise route to domesticate rice by controlling seed shattering and panicle shape. Proc Natl Acad Sci USA 119, e2121692119, https://doi.org/10.1073/pnas.2121692119.

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Fukai, E.*, Yoshikawa, M., Shah, N., Sandal, N., Miyao, A., Ono, S., Hirakawa, H., Akyol, T.Y., Umehara, Y., Nonomura, K.I., Stougaard, J., Hirochika, H., Hayashi, M., Sato, S., Andersen, S. U., and Okazaki, K. (2022). Widespread and transgenerational retrotransposon activation in inter- and intraspecies recombinant inbred populations of Lotus japonicus. Plant J 111, 1397-1410, https://doi.org/10.1111/tpj.15896.

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Tonosaki, K., Ono, A., Kunisada, M., Nishino, M., Nagata, H., Sakamoto, S., Kijima, S.T., Furuumi, H., Nonomura, K.I., Sato, Y., Ohme-Takagi, M., Endo, M., Comai, L., Hatakeyama, K., Kawakatsu, T., and Kinoshita, T.* (2021). Mutation of the imprinted gene OsEMF2a induces autonomous endosperm development and delayed cellularization in rice. Plant Cell 33, 85-103, https://doi.org/10.1093/plcell/koaa006.

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Shimizu-Sato, S., Tsuda, K., Nosaka-Takahashi, M., Suzuki, T., Ono, S., Ta, K.N., Yoshida, Y., Nonomura, K.I., and Sato, Y.* (2020). Agrobacterium-mediated genetic transformation of wild Oryza species using immature embryos. Rice (N Y) 13, 33, https://doi.org/10.1186/s12284-020-00394-4.

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Shenton, M., Kobayashi, M., Terashima, S., Ohyanagi, H., Copetti, D., Hernandez-Hernandez, T., Zhang, J., Ohmido, N., Fujita, M., Toyoda, A., Ikawa, H., Fujiyama, A., Furuumi, H., Miyabayashi, T., Kubo, T., Kudrna, D., Wing, R., Yano, K., Nonomura, K.I., Sato, Y.*, and Kurata, N. (2020). Evolution and diversity of the wild rice Oryza officinalis complex, across continents, genome types, and ploidy levels. Genome Biol Evol 12, 413-428, https://doi.org/10.1093/gbe/evaa037.

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Hanamata, S., Sawada, J., Ono, S., Ogawa, K., Fukunaga, T., Nonomura K.I.., Kimura, S., Kurusu, T., and Kuchitsu, K.* (2020). Impact of autophagy on gene expression and tapetal programmed cell death during pollen development in rice. Front Plant Sci 11, 172, https://doi.org/10.3389/fpls.2020.00172.

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Araki, S., Le, N.T., Koizumi, K., Villar-Briones, A., Nonomura, K.I., Endo, M., Inoue, H., Saze, H., and Komiya, R.* (2020). miR2118-dependent U-rich phasiRNA production in rice anther wall development. Nature Commun 11, 3115, https://doi.org/10.1038/s41467-020-16637-3.

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Sera, Y., Hanamata, S., Sakamoto, S., Ono, S., Kaneko, K., Mitsui, Y., Koyano, T., Fujita, N., Sasou, A., Masumura, T., Saji, H., Nonomura, K.I., Mitsuda, N., Mitsui, T., Kurusu, T., and Kuchitsu, K. (2019). Essential roles of autophagy in metabolic regulation in endosperm development during rice seed maturation. Sci Rep 9, 18544, https://doi.org/10.1038/s41598-019-54361-1.

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Hanamata, S., Sawada, J., Toh, B., Ono, S., Ogawa, K., Fukunaga, T., Nonomura, K.I., Kurusu, T., and Kuchitsu, K.* (2019). Monitoring autophagy in rice tapetal cells during pollen maturation. Plant Biotechnol (Tokyo) 36, 99-105, https://doi.org/10.5511/plantbiotechnology.19.0417a.

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Ono, S., Liu, H., Tsuda, K., Fukai, E., Tanaka, K., Sasaki, T., and Nonomura, K.I.* (2018). EAT1 transcription factor, a non-cell-autonomous regulator of pollen production, activates meiotic small RNA biogenesis in rice anther tapetum. PLoS Genet 14, e1007238, https://doi.org/10.1371/journal.pgen.1007238.

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Tsuda, K., Abraham-Juarez, M.J., Maeno, A., Dong, Z., Aromdee, D., Meeley, R., Shiroishi, T., Nonomura, K.I., and Hake, S.* (2017). KNOTTED1 cofactors, BLH12 and BLH14, regulate internode patterning and vein anastomosis in maize. Plant Cell 29, 1105-1118, https://doi.org/10.1105/tpc.16.00967.

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Liu, H., and Nonomura, K.I.* (2016). A wide reprogramming of histone H3 modifications during male meiosis I in rice is dependent on the Argonaute protein MEL1. J Cell Sci 129, 3553-3561, https://pubmed.ncbi.nlm.nih.gov/27521428/.

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Niihama, M., Mochizuki, M., Kurata, N., and Nonomura, K.I.* (2015). PCR-based INDEL markers co-dominant between Oryza sativa, japonica cultivars and closely-related wild Oryza species. Breed Sci 65, 357-361, https://pmc.ncbi.nlm.nih.gov/articles/PMC8076200/.

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Miyazaki, S., Sato, Y., Asano, T., Nagamura, Y., and Nonomura, K.I.* (2015). Rice MEL2, the RNA recognition motif (RRM) protein, binds in vitro to meiosis-expressed genes containing U-rich RNA consensus sequences in the 3'-UTR. Plant Mol Biol 89, 293-307, https://doi.org/10.1007/s11103-015-0369-z.

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Komiya, R.*, Ohyanagi, H., Niihama, M., Watanabe, T., Nakano, M., Kurata, N., and Nonomura, K.I.* (2014). Rice germline-specific Argonaute MEL1 protein binds to phasiRNAs generated from more than 700 lincRNAs. Plant J 78, 385-397, https://doi.org/10.1111/tpj.12483.

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Komiya, R., and Nonomura, K.I.* (2014) Isolation and bioinformatic analyses of small RNAs interacting with germ cell-specific argonauts in rice. Methods in Molecular Biology 1093: 235-245, https://doi.org/10.1007/978-1-62703-694-8_19.

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Yamaki, S., Ohyanagi, H., Yamasaki, M., Eiguchi, M., Miyabayashi, T., Kubo, T., Kurata, N., and Nonomura, K.I.* (2013). Development of INDEL markers to discriminate all genome types rapidly in the genus Oryza. Breed Sci 63, 246-254, https://doi.org/10.1270/jsbbs.63.246.

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Ueda, K.*, Yoshimura, F., Miyao, A., Hirochika, H., Nonomura, K.I., and Wabiko, H. (2013). Collapsed abnormal pollen1 gene encoding the Arabinokinase-like protein is involved in pollen development in rice. Plant Physiol 162, 858-871, https://doi.org/10.1104/pp.113.216523.

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Yamaki, S., Nagato, Y., Kurata, N., and Nonomura, K.I.* (2011). Ovule is a lateral organ finally differentiated from the terminating floral meristem in rice. Dev Biol 351, 208-216, https://doi.org/10.1016/j.ydbio.2010.12.006.

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Nonomura, K.I.*, Eiguchi, M., Nakano, M., Takashima, K., Komeda, N., Fukuchi, S., Miyazaki, S., Miyao, A., Hirochika, H., and Kurata, N. (2011). A novel RNA-recognition-motif protein is required for premeiotic G1/S-phase transition in rice (Oryza sativa L.). PLoS Genet 7, e1001265, https://doi.org/10.1371/journal.pgen.1001265.

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Yamaki, S., Miyabayashi, T., Eiguchi, M., Kitano, H., Nonomura, K.I., and Kurata, N.* (2010). Diversity of panicle branching patterns in wild relatives of rice. Breed Sci 60, 586-596, https://doi.org/10.1270/jsbbs.60.586.

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Nonomura, K.I.*, Morohoshi, A., Nakano, M., Eiguchi, M., Miyao, A., Hirochika, H., and Kurata, N.* (2007). A germ cell specific gene of the ARGONAUTE family is essential for the progression of premeiotic mitosis and meiosis during sporogenesis in rice. Plant Cell 19, 2583-2594, https://doi.org/10.1105/tpc.107.053199.

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Miyabayashi, T., Nonomura, K.I., Morishima, H., and Kurata, N.* (2007). Genome size of twenty wild species of Oryza determined by flow cytometric and chromosome analyses. Breed Sci 57, 73-78, https://www.jstage.jst.go.jp/article/jsbbs/57/1/57_1_73/_article.

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Nonomura, K.I.*, Nakano, M., Eiguchi, M., Suzuki, T., and Kurata, N.* (2006). PAIR2 is essential for homologous chromosome synapsis in rice meiosis I. J Cell Sci 119, 217-225, https://doi.org/10.1242/jcs.02736.

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Nonomura, K.I.*, Nakano, M., Murata, K., Miyoshi, K., Eiguchi, M., Miyao, A., Hirochika, H., and Kurata, N. (2004). An insertional mutation in the rice PAIR2 gene, the ortholog of Arabidopsis ASY1, results in a defect in homologous chromosome pairing during meiosis. Mol Genet Genomics 271, 121-129, https://doi.org/10.1007/s00438-003-0934-z.

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Nonomura, K.I.*, Nakano, M., Fukuda, T., Eiguchi, M., Miyao, A., Hirochika, H., and Kurata, N. (2004). The novel gene HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS1 of rice encodes a putative coiled-coil protein required for homologous chromosome pairing in meiosis. Plant Cell 16, 1008-1020, https://doi.org/10.1105/tpc.020701.

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Nonomura, K.I.*, Miyoshi, K., Eiguchi, M., Suzuki, T., Miyao, A., Hirochika, H., and Kurata, N. (2003). The MSP1 gene is necessary to restrict the number of cells entering into male and female sporogenesis and to initiate anther wall formation in rice. Plant Cell 15, 1728-1739, https://doi.org/10.1105/tpc.012401.​

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Review in English

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Nonomura, K.I., Ono, S., and Ueda, K. (2018) Genetic and Epigenetic Regulation of Meiotic Fate Decision and Gametophyte Specification in Rice. In "Rice Genomics, Genetics and Breeding (Sasaki, T., Ashikari, M. eds)", Springer, Singapore, https://doi.org/10.1007/978-981-10-7461-5_5.

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Somashekar, H., and Nonomura, K.I.* (2023). Genetic regulation of mitosis-meiosis fate decision in plants: Is callose an oversighted polysaccharide in these processes? Plants 12, 1936, https://doi.org/10.3390/plants12101936.

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Sato, Y.*, Tsuda, K., Yamagata, Y., Matsusaka, H., Kajiya-Kanegae, H., Yoshida, Y., Agata, A., Ta, K.N., Shimizu-Sato, S., Suzuki, T., Nosaka-Takahashi, M., Kubo, T., Kawamoto, S., Nonomura, K.I., Yasui, H., and Kumamaru, T. (2021). Collection, preservation and distribution of Oryza genetic resources by the National Bioresource Project RICE (NBRP-RICE). Breed Sci 71, 291-298, https://doi.org/10.1270/jsbbs.21005.​

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Nonomura, K.I.*, Ono, S., and Ueda, K. (2018). Genetic and epigenetic regulation of meiotic fate decision and gametophyte specification in rice. In Rice Genomics, Genetics and Breeding, pp. 69-95, https://link.springer.com/book/10.1007/978-981-10-7461-5.

 

Nonomura, K.I.* (2018). Small RNA pathways responsible for non-cell-autonomous regulation of plant reproduction. Plant Reprod 31, 21-29, 10.1007/s00497-018-0321-x.

 

Yamazaki, Y.*, Sakaniwa, S., Tsuchiya, R., Nonomura, K.I., and Kurata, N. (2010). Oryzabase: an integrated information resource for rice science. Breed Sci 60, 544-548, https://doi.org/10.1270/jsbbs.60.459.

 

Nonomura, K.I., Morishima, H., Miyabayashi, T., Yamaki, S., Eiguchi, M., Kubo, T., and Kurata, N.* (2010). The wild Oryza collection in National BioResource Project (NBRP) of Japan: History, biodiversity and utility. Breed Sci 60, 502-508, https://doi.org/10.1270/jsbbs.60.502.

Nonomura, K.I.*, and Yamaki, S. (2008). Genetic dissection of sexual reproduction in rice (Oryza sativa L.). In Rice Biology in the Genomics Era, Hirano, H.Y., Hirai, A., Sano, Y. and Sasaki, T., eds. (Berlin Heidelberg: Springer-Verlag), pp. 191-204, 10.1007/978-3-540-74250-0_15.
 

Kurata, N.*, Miyoshi, K., Nonomura, K.I., Yamazaki, Y., Ito, Y. (2005). Rice mutants and genes related to organ development, morphogenesis and physiological traits. Plant Cell Physiol. 46: 48-62, https://doi.org/10.1093/pcp/pci506

 

Itoh, J. I., Nonomura, K.I., Ikeda, K., Yamaki, S., Inukai, Y., Yamagishi, H., Nagato, Y.* (2005). Rice plant development: from zygote to spikelet. Plant Cell Physiol. 46: 23-47, https://doi.org/10.1093/pcp/pci501

 

Kurata, N.*, Nonomura, K.I., Harushima, Y. (2002). Rice genome organization: the centromere and genome interaction. Annals of Botany 90: 427-435, https://doi.org/10.1093/aob/mcf218.

 

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Review in Japanese

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野々村賢一* (2020). 小分子RNAを介した植物の減数分裂制御機構の研究. アグリバイオ 4, 38-41.

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Ono, S., and Nonomura, K.I.* (2019). 植物において 減数分裂期に 高発現するphasiRNAの産生経路および機能. 領域融合レビュー 8, e002, http://leading.lifesciencedb.jp/8-e002.

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米田典央、野々村賢一* (2009). 減数分裂：相方を探すための植物染色体のダイナミックな挙動,　生物の科学遺伝（５月号）特集I：植物染色体の最前線　株式会社エヌ・ティー・エス：48-54.

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野々村賢一* (2007). イネ生殖細胞形成過程を制御する遺伝子群の単離と機能解析, 育種学研究9: 147-152, https://doi.org/10.1270/jsbbr.9.147.

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野々村賢一, 倉田のり* (1998). 植物人工染色体と核機構研究. 日本育種学会編、育種学最近の進歩40: 41 - 44.

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Book chapter in Japanese

 

野々村賢一 (2022). 花粉と胚のうの形成, 遺伝学の百科事典 継承と多様性の源, 丸善出版株式会社.

 

野々村賢一 (2017). 遺伝単 : 遺伝学用語集, 日本遺伝学会監修・編（遺伝 : 生物の科学, 別冊no. 22）, 株式会社エヌ・ティー・エス, pp. 26-29.

 

野々村賢一 (2009) 受粉と受精, 種子の科学とバイオテクノロジー, 学会出版センター, pp. 13-16.

 

野々村賢一, 土井一行 (2004) 生殖研究, イネゲノム配列で何ができるのか（編者：矢野昌裕, 松岡信）, 農山漁村文化協会, pp. 90-102.