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Publications｜Tsuchimatsu Group

Manuscripts deposited at BioRxiv

  1. Maenosono, T., Isono, K., Kuronuma, T., Hatai, M., Chimura, K., Kubo, K., Kokubun, H., Greppi, J.A., Watanabe, H., Uehara, K, and Tsuchimatsu, T. (2024) Long-read sequencing reveals the allelic diversity of the self-incompatibility gene across natural populations in Petunia (Solanaceae). BioRxiv doi: 10.1101/2024.06.18.599649.
  2. Suda, R.A., Kubota, S., Kumar, V., Castric, V., Kraemer, U., Morinaga, S.I. and Tsuchimatsu, T. (2024) Population genomics reveals demographic history and climate adaptation in Japanese Arabidopsis halleri. BioRxiv doi:10.1101/2024.04.08.588504.

Peer-reviewed papers

  1. Tsuchikane, Y., Watanabe, M., Kawaguchi, Y.W., Uehara, K., Nishiyama, T., Sekimoto, H., and Tsuchimatsu, T. (in press) Diversity of genome size and chromosome number in homothallic and heterothallic strains of the Closterium peracerosum-strigosum-littorale complex (Desmidiales, Zygnematophyceae, Streptophyta) Journal of Phycology.
  2. Yew, C.L., Tsuchimatsu, T., Shimizu-Inatsugi, R., Yasuda, S., Hatakeyama, M., Kakui, H., Ohta, T., Suwabe, K., Watanabe, M., Takayama, S., and Shimizu, K.K. (2023) Dominance in self-compatibility between subgenomes of allopolyploid Arabidopsis kamchatica shown by transgenic restoration of self-incompatibility. Nature Communications. 14: 7618.
  3. Isono, K., Nakamura, K., Hanada, K., Shirai, K., Ueki, M., Tanaka, K., Tsuchimatsu, T., Iuchi, S., Kobayashi, M., Yotsui, I., Sakata, Y., and Taji, T. (2023) LHT1/MAC7 contributes to proper alternative splicing under long-term heat stress and mediates variation in the heat tolerance of Arabidopsis. PNAS Nexus. 2: pgad348.
  4. Kawaguchi, Y.W., Tsuchikane, Y., Tanaka, K., Taji, T., Suzuki, Y., Toyoda, A., Ito, M., Watano, Y., Nishiyama, T., Sekimoto, H., and Tsuchimatsu, T. (2023) Extensive copy number variation explains genome size variation in the unicellular Zygnematophycean alga, Closterium peracerosum-strigosum-littorale complex. Genome Biology and Evolution. 15: evad115. doi: 10.1093/gbe/evad115
  5. Brachi, B., Filiault, D., Darme, P., Le Mentec, M., Kerdaffrec, E., Rabanal, F., Anastasio, A., Box, M., Duncan, S., Morton, T., Novikova, P., Perisin, M., Tsuchimatsu, T., Woolley, R., Yu, M., Dean, C., Nordborg, M., Holm, S., Bergelson, J. (2022) Plant genetic effects on microbial hubs impact host fitness in repeated field trials. Proceedings of the National Academy of Sciences of the U.S.A. 119: e2201285119.
  6. Tsuchimatsu, T., and Fujii, S. (2022) The selfing syndrome and beyond: Diverse evolutionary consequences of mating system transitions in plants. Philosophical Transactions of the Royal Society B. 377: 20200510.
  7. Kakui, H., Tsuchimatsu, T., Yamazaki, M., Hatakeyama, M., and Shimizu, K.K. (2022) Pollen number and ribosome gene expression altered in a genome-editing mutant of REDUCED POLLEN NUMBER1 gene. Frontiers in Plant Science. 12: 768584. doi: 10.3389/fpls.2021.768584
  8. Tateyama, H., Chimura, K., and Tsuchimatsu, T. (2021) Evolution of seed mass associated with mating systems in multiple plant families. Journal of Evolutionary Biology 43: 1981-1987.
  9. Kurata, S., Sakaguchi, S., Mishima, H., Tsuchimatsu, T., and Ito M. (2021) Development and characterization of nuclear microsatellite markers to reveal the neutral demographic background of flower color polymorphism in Geranium thunbergii (Geraniaceae). Genes & Genetic Systems. 96: 99-104.
  10. Bamba, M., Aoki, S., Kajita, T., Setoguchi H., Watano, Y., Sato, S., and Tsuchimatsu, T. (2020) Massive rhizobial genomic variation associated with partner quality in Lotus–Mesorhizobium symbiosis. FEMS Microbiology Ecology 96: fiaa202.
  11. Suwabe, K., Nagasaka, K., Windari, E.A., Hoshiai, C., Ota, T., Takada, M., Kitazumi, A., Masuko-Suzuki, H., Kagaya, Y., Yano, K., Tsuchimatsu, T., Shimizu, K.K., Takayama, S., Suzuki, G., and Watanabe, M. (2020) Double-locking mechanism of self-compatibility in Arabidopsis thaliana: the synergistic effect of transcriptional depression and disruption of coding region in the male specificity gene. Frontiers in Plant Science 11: 576140.
  12. Tsuchimatsu, T.*, Kakui, H.*, Yamazaki, M., Marona, C., Tsutsui, H., Hedhly, A., Meng, D., Sato, Y., Städler, T., Grossniklaus, U., Kanaoka, M.M., Lenhard, M., Nordborg, M., Shimizu, K.K. (2020) Adaptive reduction of male gamete number in the selfing plant Arabidopsis thaliana. Nature Communications 11: 2885. *equally contributed.
  13. Gutiérrez‐Ortega, J.S., Salinas‐Rodríguez, M.M., Ito, T., Pérez‐Farrera, M.A. Vovides, A.P., Martínez, J.F., Molina‐Freaner, F., Hernández‐López, A., Kawaguchi, L., Nagano, A.J., Kajita, T., Watano, Y., Tsuchimatsu, T., Takahashi, Y., Murakami, M. (2020) Niche conservatism promotes speciation in cycads: the case of Dioon merolae (Zamiaceae) in Mexico. New Phytologist 227:1872-1884.
  14. Fujii, S., Tsuchimatsu, T., Kimura, Y., Ishida, S., Tangpranomkorn, S., Shimosato-Asano, H., Iwano, M., Furukawa, S., Itoyama, W., Wada, Y., Shimizu, K.K., and Takayama, S. (2019) Identification of a stigmatic gene functions in inter-species incompatibility in the Brassicaceae. Nature Plants 5: 731-741
  15. Bamba, M., Aoki, S., Kajita, T., Setoguchi H., Watano, Y., Sato, S., and Tsuchimatsu, T. (2019) Exploring genetic diversity and signatures of horizontal gene transfer in nodule bacteria associated with Lotus japonicus in natural environments. Molecular Plant-Microbe Interactions 32: 1110-1120
  16. Bamba, M., Kawaguchi, Y.W., and Tsuchimatsu, T. (2019) Plant adaptation and speciation studied by population genomic approarches. Development, Growth & Differentiaion 61: 12-24.
  17. Ariga, H., Katori, T., Tsuchimatsu, T., Hirase, T., Tajima, Y., Parker, J., Alcazar, R., Koornneef, M., Hoekenga, O., lipka, A., Gore, M., Sakakibara, H., Kojima, M., Kobayashi, Y., Iuchi, S., Kobayashi, M., Shinozaki, K., Sakata, Y., Hayashi, T., Saijo, Y. and Taji, T. (2017) NLR locus-mediated trade-off between abiotic and biotic stress adaptation in Arabidopsis. Nature Plants 3, 17072 doi:10.1038/nplants.2017.72
  18. Durvasula, A., Fulgione, A., Gutakerd, R.M., Alacakaptan, S.I., Flood, P.J., Netoa, C., Tsuchimatsu, T., Burbano, H.A., Picó, F.X., Alonso-Blanco, C., and Hancock, A.M. (2017) African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the U.S.A. 114: 5213-5218.
  19. Tsuchimatsu, T*., Goubet, P.M.*, Gallina, S., Holl, A.C., Fobis-Loisy, I., Bergès, H., Marande, W., Prat, E., Meng, D., Long, Q., Platzer, A., Nordborg, M., Vekemans, X., and Castric, V. (2017) Patterns of polymorphism at the self-incompatibility locus in 1,083 Arabidopsis thaliana genomes. Molecular Biology and Evolution, 34: 1878-1889. *equally contributed
  20. Novikova, P.Y., Tsuchimatsu, T., Simon, S., Nizhynska, V., Voronin, V., Burns, R., Fedorenko, O.M., Holm, S., Säll, T., Prat, E., Marande, W., Castric, V. and Nordborg, M. (2017) Genome sequencing reveals the origin of the allotetraploid Arabidopsis suecica. Molecular Biology and Evolution 34: 957–968.
  21. Novikova, P.Y., Hohmann, N., Nizhynska, V., Tsuchimatsu, T., Ali, J., Muir, G., Guggisberg, A., Paape, T., Schmid, K., Fedorenko, O.M., Holm, S., Säll, T., Schlötterer, C., Marhold, K., Widmer, A., Sese, J., Shimizu, K.K., Weigel, D., Krämer, U., Koch M.A., and Nordborg, M. (2016) Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism. Nature Genetics 48: 1077–1082.
  22. Shimizu, K.K.* and Tsuchimatsu, T.* (2015) Evolution of selfing: recurrent patterns in molecular adaptation. Annual Review of Ecology, Evolution and Systematics 46: 593–622. *equally contributed
  23. Meijón, M., Satbhai, S.B., Tsuchimatsu, T. and Busch, W. (2014) Genome-wide association study using cellular traits identifies a new regulator of root development in Arabidopsis. Nature Genetics 46: 77-81.
  24. Tsuchimatsu, T., Yoshitake, H. and Ito, M. (2014) Herbivore pressure by weevils associated with flower color polymorphism in Geranium thunbergii (Geraniaceae). Journal of Plant Research 127: 265-273.
  25. Tsuchimatsu, T. and Shimizu, K.K. (2013) Effects of pollen availability and the mutation bias on the fixation of mutations disabling the male specificity of self-incompatibility. Journal of Evolutionary Biology 26: 2221-2232.
  26. Ngo, Q. A., Huguette, A., Tsuchimatsu, T. and Grossniklaus, U. (2013) The differentially regulated genes TvQR1 and TvPirin of the parasitic plant Triphysaria exhibit distinctive natural allelic diversity. BMC Plant Biology 13: 28.
  27. Tsuchimatsu, T*., Kaiser, P.*, Yew, C.-L., Bachelier, J.B. and Shimizu, K.K. (2012) Recent loss of self-incompatibility by degradation of the male component in allotetraploid Arabidopsis kamchatica. PLoS Genetics 8: e1002838. *equally contributed
  28. Nagano, A. J., Tsuchimatsu, T., Okuyama Y., and Hara-Nishimura, I. (2012) Bimodal expression level polymorphism in Arabidopsis thaliana. Plant Signaling & Behavior 7: 864-873.
  29. de la Chaux, N., Tsuchimatsu, T., Shimizu, K. K., and Wagner, A. (2012) The predominantly selfing plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata. Mobile DNA 3:2.
  30. Tsuchimatsu, T., Suwabe, K., Shimizu-Inatsugi, R., Isokawa, S., Pavlidis, P., Städler, T., Suzuki, G., Takayama, S., Watanabe, M. and Shimizu, K.K. (2010) Evolution of self-compatibility in Arabidopsis by a mutation in the male specificity gene. Nature 464: 1342-1346. *equally contributed
  31. Seeholzer, S., Tsuchimatsu, T., Jordan, T., Bieri, S., Pajonk, S., Yang, W., Jahoor, A., Shimizu, K.K., Keller, B., and Schulze-Lefert, P. (2010) Diversity at the Mla powdery mildew resistance locus from cultivated barley reveals sites of positive selection. Molecular Plant-Microbe Interactions 23: 497-509.
  32. Shimizu, K. K., Shimizu-Inatsugi, R., Tsuchimatsu, T., and Purugganan, M. D. (2008) Independent origins of self-compatibility in Arabidopsis thaliana. Molecular Ecology 17: 704-714.
  33. Tsuchimatsu, T., Sakai, S., and Ito, M. (2006) Sex allocation bias in hermaphroditic plants: effects of local competition and seed dormancy. Evolutionary Ecology Research 8: 829-842.

Publications in Japanese

  1. 番場大、佐藤修正、土松隆志（2022） 「マメ科植物の生育を促す根粒菌の多様性解明」『バイオスティミュラントハンドブック　～植物の生理活性プロセスから資材開発、適用事例まで～』エヌ・ティー・エス
  2. 田村隆明、ほか17名（2018）「分子生物学：ゲノミクスとプロテオミクス」（翻訳） 東京化学同人
  3. 土松隆志 (2017)「植物はなぜ自家受精をするのか（シリーズ・遺伝子から探る生物進化 5）」慶應義塾大学出版会
  4. 土松隆志 (2017)「植物はなぜ自家受精をするのかー花の性と進化」『知のフィールドガイド 科学の最前線を歩く』（東京大学教養学部　編）白水社
  5. 土松隆志 (2012)「DNA配列から探る自然選択の痕跡：分子集団遺伝学的手法を用いて」『現代の生態学 エコゲノミクス -遺伝子からみた適応-』 （森長真一・工藤洋　編）共立出版
  6. 土松隆志 (2011)「ゲノムワイドな多型情報を利用した分子集団遺伝学：特に自然選択の検出について」『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 種生物学シリーズ』（永野惇・森長真一　編）文一総合出版
  7. 土松隆志 (2011)「シロイヌナズナにおける自家和合性の起源 : 進化生態学と分子集団遺伝学の出会い」『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 種生物学シリーズ』（永野惇・森長真一　編）文一総合出版

総説・解説記事など

  1. 土松隆志 (2019) 「この人・この研究：ゲノムデータで解き明かす植物の生殖様式の進化」『あいみっく』国際医学情報センター 40: 77-79
  2. 土松隆志, 安田晋輔, 高田美信, 北柴大泰, 新倉聡, 藤本龍, 柿崎智博（2019）「アブラナ科植物における自家不和合性研究の最前線と育種現場での利用」『育種学研究』 doi:10.1270/jsbbr.21.W03
  3. 土松隆志 (2018)「集団ゲノミクスが解き明かす植物進化のダイナミクス：適応をゲノムから探る」『化学と生物』社団法人　日本農芸化学会 56: 317-323.
  4. 土松隆志 (2017)「集団ゲノミクスからさぐる植物の進化」『ライフサイエンス 領域融合レビュー』6: e006.
  5. 土松隆志 (2013)「海外研究室だより　楽都ウィーンで進化を学ぶ：グレゴール・メンデル研究所・Magnus Nordborg研究室」『日本進化学会ニュース』14 (2): 10-16
  6. 土松隆志・清水健太郎 (2013)「自家不和合性の進化生態学：植物の自己認識機構に働く自然選択を探る」『生物の科学　遺伝』67(2): 244-251
  7. 荒木仁志・土松隆志 (2011)「海外学会参加記 Biology2011 & PACE11 in チューリヒ、スイス」『日本進化学会ニュース』 12(2): 21-23
  8. 土松隆志・清水健太郎 (2011)「モデル植物シロイヌナズナはどのように自家受精を行なうようになったのか」『化学と生物』社団法人　日本農芸化学会 49(6): 366-367
  9. 土松隆志・清水健太郎 (2010)「他殖から自殖へ ─ シロイヌナズナにおける繁殖システムの進化をDNAから探る」『生物の科学　遺伝』64 (5): 7-12
  10. 土松隆志・清水健太郎 (2010)「シロイヌナズナ属における自家和合性進化の遺伝的背景を探る」『植物科学の最前線』 （社）日本植物学会 1: 90-95