Accomplishments
2020
Original Paper
Sobhy S H Abdelsalam, Yusuke Kouzai, Megumi Watanabe, Komaki Inoue, Hidenori Matsui, Mikihiro Yamamoto, Yuki Ichinose, Kazuhiro Toyoda, Seiji Tsuge, Keiichi Mochida, Yoshiteru Noutoshi.(2020)Identification of effector candidate genes of Rhizoctonia solani AG-1 IA expressed during infection in Brachypodium distachyon. Sci. Rep. 10(1)
https://pubmed.ncbi.nlm.nih.gov/32913311/
Yusuke Kouzai, Minami Shimizu, Komaki Inoue, Yukiko Uehara-Yamaguchi, Kotaro Takahagi, Risa Nakayama, Takakazu Matsuura, Izumi C Mori, Takashi Hirayama, Sobhy S H Abdelsalam, Yoshiteru Noutoshi, Keiichi Mochida.(2020)BdWRKY38 is required for the incompatible interaction of Brachypodium distachyon with the necrotrophic fungus Rhizoctonia solani. Plant J.
https://pubmed.ncbi.nlm.nih.gov/32891065/
Keiichi Mochida, Ryuei Nishii, Takashi Hirayama .(2020)Decoding Plant-Environment Interactions That Influence Crop Agronomic Traits. Plant Cell Physiol. 61(8)
https://pubmed.ncbi.nlm.nih.gov/32392328/
Keiichi Mochida, Alexander E Lipka, Takashi Hirayama.(2020)Exploration of Life-Course Factors Influencing Phenotypic Outcomes in Crops. Plant Cell Physiol. 61(8)
https://pubmed.ncbi.nlm.nih.gov/32603418/
Takashi Hirayama, Daisuke Saisho, Takakazu Matsuura, Satoshi Okada, Kotaro Takahagi, Asaka Kanatani, Jun Ito, Hiroyuki Tsuji, Yoko Ikeda, Keiichi Mochida.(2020)Life-Course Monitoring of Endogenous Phytohormone Levels under Field Conditions Reveals Diversity of Physiological States among Barley Accessions. Plant Cell Physiol. 61(8)
https://pubmed.ncbi.nlm.nih.gov/32294217/
Yuko Ukai, Komaki Inoue, Manaka Kamada, Hiroshi Teramura, Shunsuke Yanagisawa, Kazuyoshi Kitazaki, Kazuhiro Shoji, Fumiyuki Goto, Keiichi Mochida, Toshihiro Yoshihara, Hiroaki Shimada.(2020)De novo transcriptome analysis reveals an unperturbed transcriptome under high cadmium conditions in the Cd-hypertolerant fern Athyrium yokoscense. Genes Genet. Syst. 95(2)
https://pubmed.ncbi.nlm.nih.gov/32389921/
Kazuhiro Sato, Makoto Ishii, Kotaro Takahagi, Komaki Inoue, Minami Shimizu, Yukiko Uehara-Yamaguchi, Ryuei Nishii, Keiichi Mochida.(2020)Genetic Factors Associated with Heading Responses Revealed by Field Evaluation of 274 Barley Accessions for 20 Seasons. iScience. 23(6)
https://pubmed.ncbi.nlm.nih.gov/32454448/
Review Paper
Ryo Harada, Toshihisa Nomura, Koji Yamada, Keiichi Mochida, Kengo Suzuki .(2020)Genetic Engineering Strategies for Euglena gracilis and Its Industrial Contribution to Sustainable Development Goals: A Review. Front. Bioeng. Biotechnol. 8
https://pubmed.ncbi.nlm.nih.gov/32760709/
2019
Original Paper
Toshihisa Nomura, Komaki Inoue, Yukiko Uehara-Yamaguchi, Koji Yamada, Osamu Iwata, Kengo Suzuki, Keiichi Mochida.(2019)Highly efficient transgene-free targeted mutagenesis and single-stranded oligodeoxynucleotide-mediated precise knock-in in the industrial microalga Euglena gracilis using Cas9 ribonucleoproteins. Plant Biotechnol. J. 17(11)
https://pubmed.ncbi.nlm.nih.gov/31131534/
Onda Y, Inoue K, Sawada Y, Shimizu M, Takahagi K, Uehara-Yamaguchi Y, Hirai MY, Garvin DF, Mochida K.(2019)Genetic Variation for Seed Metabolite Levels in Brachypodium distachyon. Int. J. Mol. Sci. 20(9)
https://pubmed.ncbi.nlm.nih.gov/31083584/
Koji Yamada, Tomoaki Nitta, Kohei Atsuji, Maeka Shiroyama, Komaki Inoue, Chieko Higuchi, Nobuko Nitta, Satoshi Oshiro, Keiichi Mochida, Osamu Iwata, Iwao Ohtsu, Kengo Suzuki.(2019)Characterization of sulfur-compound metabolism underlying wax-ester fermentation in Euglena gracilis. Sci. Rep. 9(1)
https://pubmed.ncbi.nlm.nih.gov/30696857/
Mochida K, Koda S, Inoue K, Hirayama T, Tanaka S, Nishii R, Melgani F. (2019) Computer vision-based phenotyping for improvement of plant productivity: a machine learning perspective. Gigascience. 8(1)
https://www.ncbi.nlm.nih.gov/pubmed/30520975
2018
Original Paper
Chu HD, Nguyen KH, Watanabe Y, Le DT, Pham, Mochida K, Tran LP. (2018) Identification, Structural Characterization and Gene Expression Analysis of Members of the Nuclear Factor-Y Family in Chickpea (Cicer arietinum L.) under Dehydration and Abscisic Acid Treatments. Int J Mol Sci. 19(11)
https://www.ncbi.nlm.nih.gov/pubmed/30360493
Takahagi K, Inoue K, Mochida K. (2018) Gene Co-expression Network Analysis Suggests the Existence of Transcriptional Modules Containing a High Proportion of Transcriptionally Differentiated Homoeologs in Hexaploid Wheat. Front Plant Sci. 9(9):1163
https://www.ncbi.nlm.nih.gov/pubmed/30135697
Ogita S, Nomura T, Kato Y, Uehara-Yamaguchi Y, Inoue K, Yoshida T, Sakurai T, Shinozaki K, Mochida K. (2018) Transcriptional alterations during proliferation and lignification in Phyllostachys nigra cells. Sci Rep. 8(1):11347
https://www.ncbi.nlm.nih.gov/pubmed/30054534
Kouzai Y, Noutoshi Y, Inoue K, Shimizu M, Onda Y, Mochida K. (2018) Benzothiadiazole, a plant defense inducer, negatively regulates sheath blight resistance in Brachypodium distachyon. Sci Rep. 8(1):17358
https://www.ncbi.nlm.nih.gov/pubmed/30478396
Tamura K, Yoshida K, Hiraoka Y, Sakaguchi D, Chikugo A, Mochida K, Kojoma M, Mitsuda N, Saito K, Muranaka T, Seki H. (2018) The Basic Helix-Loop-Helix Transcription Factor GubHLH3 Positively Regulates Soyasaponin Biosynthetic Genes in Glycyrrhiza uralensis. Plant Cell Physiol. 59(4):783-796
https://www.ncbi.nlm.nih.gov/pubmed/29648666
Onda Y, Takahagi K, Shimizu M, Inoue K, Mochida K. (2018) Multiplex PCR Targeted Amplicon Sequencing (MTA-Seq): Simple, Flexible, and Versatile SNP Genotyping by Highly Multiplexed PCR Amplicon Sequencing. Front Plant Sci. 9(201):201
https://www.ncbi.nlm.nih.gov/pubmed/29628929
Takahagi K, Inoue K, Shimizu M, Uehara-Yamaguchi Y, Onda Y, Mochida K. (2018) Homoeolog-specific activation of genes for heat acclimation in the allopolyploid grass Brachypodium hybridum. Gigascience. 7(4)
https://www.ncbi.nlm.nih.gov/pubmed/29697823
Review Paper
Mochida K, Koda S, Inoue K, Nishii R. (2018) Statistical and Machine Learning Approaches to Predict Gene Regulatory Networks From Transcriptome Datasets. Front Plant Sci. 9(9):1770
https://www.ncbi.nlm.nih.gov/pubmed/30555503
2017
Original Paper
Koda S, Onda Y, Matsui H, Takahagi K, Yamaguchi-Uehara Y, Shimizu M, Inoue K, Yoshida T, Sakurai T, Honda H, Eguchi S, Nishii R, Mochida K. (2017) Diurnal Transcriptome and Gene Network Represented through Sparse Modeling in Brachypodium distachyon. Front Plant Sci. 8(8):2055
https://www.ncbi.nlm.nih.gov/pubmed/29234348
Ren Y, Sekine-Kondo E, Shibata R, Kato-Itoh M, Umino A, Yanagida A, Satoh M, Inoue K, Yamaguchi T, Mochida K, Nakae S, Van Kaer L, Iwabuchi K, Nakauchi H, Watarai H. (2017) A Novel Mouse Model of iNKT Cell-deficiency Generated by CRISPR/Cas9 Reveals a Pathogenic Role of iNKT Cells in Metabolic Disease. Sci Rep. 7(12765)
https://www.ncbi.nlm.nih.gov/pubmed/28986544
Mochida K, Shinozaki K. (2017) Information Resources for Functional Genomics Studies in Brachypodium distachyon. Methods Mol Biol. 1667:87-99
https://www.ncbi.nlm.nih.gov/pubmed/29039006
Kouzai Y, Kimura M, Watanabe M, Kusunoki K, Osaka D, Suzuki T, Matsui H, Yamamoto M, Ichinose Y, Toyoda K, Matsuura T, Mori IC, Hirayama T, Minami E, Nishizawa Y, Inoue K, Onda Y, Mochida K, Noutoshi Y. (2017) Salicylic acidādependent immunity contributes to resistance against Rhizoctonia solani, a necrotrophic fungal agent of sheath blight, in rice and Brachypodium distachyon. New Phytol. 217(2):771-783
https://www.ncbi.nlm.nih.gov/pubmed/29048113
Sano N, Kim JS, Onda Y, Nomura T, Mochida K, Okamoto M, Seo M. (2017) RNA-Seq using bulked recombinant inbred line populations uncovers the importance of brassinosteroid for seed longevity after priming treatments. Sci Rep. 7(8095)
https://www.ncbi.nlm.nih.gov/pubmed/28808238
Nasr Esfahani M, Inoue K, Chu HD, Nguyen KH, Van Ha C, Watanabe Y, Burritt DJ, Herrera-Estrella L, Mochida K, Tran LP. (2017) Comparative transcriptome analysis of nodules of two Mesorhizobium-chickpea associations with differential symbiotic efficiency under phosphate deficiency. Plant J.91(5):911-926
https://www.ncbi.nlm.nih.gov/pubmed/28628240
2016
Original Paper
Mochida K, Sakurai T, Seki H, Yoshida T, Takahagi K, Sawai S, Uchiyama H, Muranaka T, Saito K. (2016) Draft genome assembly and annotation of Glycyrrhiza uralensis, a medicinal legume. Plant J. 89(2):181-194
https://www.ncbi.nlm.nih.gov/pubmed/27775193
Takahagi K, Uehara-Yamaguchi Y, Yoshida T, Sakurai T, Shinozaki K, Mochida K, Saisho D. (2016) Analysis of single nucleotide polymorphisms based on RNA sequencing data of diverse bio-geographical accessions in barley. Sci Rep. 6(6):33199
https://www.ncbi.nlm.nih.gov/pubmed/27616653
Utsumi Y, Tanaka M, Kurotani A, Yoshida T, Mochida K, Matsui A, Ishitani M, Sraphet S, Whankaew S, Asvarak T, Narangajavana J, Triwitayakorn K, Sakurai T, Seki M. (2016) Cassava (Manihot esculenta) transcriptome analysis in response to infection by the fungus Colletotrichum gloeosporioides using an oligonucleotide-DNA microarray. J Plant Res. 129(4):771-726
https://www.ncbi.nlm.nih.gov/pubmed/27138000
Kouzai Y, Kimura M, Yamanaka Y, Watanabe M, Matsui H, Yamamoto M, Ichinose Y, Toyoda K, Onda Y, Mochida K, Noutoshi Y. (2016) Expression profiling of marker genes responsive to the defence-associated phytohormones salicylic acid, jasmonic acid and ethylene in Brachypodium distachyon. BMC Plant Biol. 16(16):59
https://www.ncbi.nlm.nih.gov/pubmed/6935959
Review Paper
Onda Y, Mochida K. (2016) Exploring Genetic Diversity in Plants Using High-Throughput Sequencing Techniques. Curr Genomics. 17(4):358-367
https://www.ncbi.nlm.nih.gov/pubmed/27499684
2015
Original Paper
Onda, Y., Hashimoto, K., Yoshida, T., Sakurai, T., Sawada, Y., Hirai, M. Y., Toyooka, K., Mochida, K. and Shinozaki, K. (2015a) Determination of growth stages and metabolic profiles in Brachypodium distachyon for comparison of developmental context with Triticeae crops. Proc Biol Sci, 282, 1811.
http://www.ncbi.nlm.nih.gov/pubmed/26156770
Onda Y, Mochida K, Yoshida T, Sakurai T, Seymour RS, Umekawa Y, Pirintsos SA, Shinozaki K and Ito K (2015) Transcriptome analysis of thermogenic Arum concinnatum reveals the molecular components of floral scent production. Sci Rep., 5, 8753.
http://www.ncbi.nlm.nih.gov/pubmed/25736477
Kakei, Y., Mochida, K., Sakurai, T., Yoshida, T., Shinozaki, K. and Shimada, Y. (2015) Transcriptome analysis of hormone-induced gene expression in Brachypodium distachyon. Sci Rep, 5, 14476.
http://www.ncbi.nlm.nih.gov/pubmed/26419335
Review Paper
Mochida K, Saisho D, Hirayama T. (2015) Crop improvement using life cycle datasets acquired
under field conditions. Front Plant Sci. 22, 740.
http://www.ncbi.nlm.nih.gov/pubmed/26442053
Book
Mochida K. and Tran L-S. P. (2015) The Jatropha Genome. Transcription factors in Jatropha in press.
2014
Original Paper
Miyazaki Y, Maruyama Y, Chiba Y, Kobayashi MJ, Joseph B, Shimizu KK, Mochida K, Hiura T, Kon H, Satake A. (2014) Nitrogen as a key regulator of flowering in Fagus crenata: understanding the physiological mechanism of masting by gene expression analysis. Ecol Lett, 17, 1299-1309.
http://www.ncbi.nlm.nih.gov/pubmed/25103959
Chien Van Ha, Maryam Nasr Esfahani, Watanabe Y, Uyen Thi Tran, Sulieman S, Mochida K, Dong Van Nguyen, Tran L-S P (2014) Genome-Wide Identification and Expression Analysis of the CaNAC Family Members in Chickpea during Development, Dehydration and ABA Treatments. Plos One, 9, e114107.
http://www.ncbi.nlm.nih.gov/pubmed/25479253