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Loudya N, Mishra P, Takahagi K, Uehara-Yamaguchi Y, Inoue K, Bogre L, Mochida K, López-Juez E. Cellular and transcriptomic analyses reveal two-staged chloroplast biogenesis underpinning photosynthesis build-up in the wheat leaf. Genome Biol 2021; 22:151. [PMID: 33975629 PMCID: PMC8111775 DOI: 10.1186/s13059-021-02366-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 04/26/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The developmental gradient in monocot leaves has been exploited to uncover leaf developmental gene expression programs and chloroplast biogenesis processes. However, the relationship between the two is barely understood, which limits the value of transcriptome data to understand the process of chloroplast development. RESULTS Taking advantage of the developmental gradient in the bread wheat leaf, we provide a simultaneous quantitative analysis for the development of mesophyll cells and of chloroplasts as a cellular compartment. This allows us to generate the first biologically-informed gene expression map of this leaf, with the entire developmental gradient from meristematic to fully differentiated cells captured. We show that the first phase of plastid development begins with organelle proliferation, which extends well beyond cell proliferation, and continues with the establishment and then the build-up of the plastid genetic machinery. The second phase is marked by the development of photosynthetic chloroplasts which occupy the available cellular space. Using a network reconstruction algorithm, we predict that known chloroplast gene expression regulators are differentially involved across those developmental stages. CONCLUSIONS Our analysis generates both the first wheat leaf transcriptional map and one of the most comprehensive descriptions to date of the developmental history of chloroplasts in higher plants. It reveals functionally distinct plastid and chloroplast development stages, identifies processes occurring in each of them, and highlights our very limited knowledge of the earliest drivers of plastid biogenesis, while providing a basis for their future identification.
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Affiliation(s)
- Naresh Loudya
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Priyanka Mishra
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Kotaro Takahagi
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Japan
| | | | - Komaki Inoue
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Japan
| | - Laszlo Bogre
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Keiichi Mochida
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Japan.
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, Japan.
- RIKEN Baton Zone Program, Tsurumi-ku, Yokohama, Japan.
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan.
| | - Enrique López-Juez
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK.
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Hori K, Saisho D, Nagata K, Nonoue Y, Uehara-Yamaguchi Y, Kanatani A, Shu K, Hirayama T, Yonemaru JI, Fukuoka S, Mochida K. Genetic Elucidation for Response of Flowering Time to Ambient Temperatures in Asian Rice Cultivars. Int J Mol Sci 2021; 22:1024. [PMID: 33498523 PMCID: PMC7864171 DOI: 10.3390/ijms22031024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/16/2021] [Accepted: 01/17/2021] [Indexed: 11/27/2022] Open
Abstract
Climate resilience of crops is critical for global food security. Understanding the genetic basis of plant responses to ambient environmental changes is key to developing resilient crops. To detect genetic factors that set flowering time according to seasonal temperature conditions, we evaluated differences of flowering time over years by using chromosome segment substitution lines (CSSLs) derived from japonica rice cultivars "Koshihikari" × "Khao Nam Jen", each with different robustness of flowering time to environmental fluctuations. The difference of flowering times in 9 years' field tests was large in "Khao Nam Jen" (36.7 days) but small in "Koshihikari" (9.9 days). Part of this difference was explained by two QTLs. A CSSL with a "Khao Nam Jen" segment on chromosome 11 showed 28.0 days' difference; this QTL would encode a novel flowering-time gene. Another CSSL with a segment from "Khao Nam Jen" in the region around Hd16 on chromosome 3 showed 23.4 days" difference. A near-isogenic line (NIL) for Hd16 showed 21.6 days' difference, suggesting Hd16 as a candidate for this QTL. RNA-seq analysis showed differential expression of several flowering-time genes between early and late flowering seasons. Low-temperature treatment at panicle initiation stage significantly delayed flowering in the CSSL and NIL compared with "Koshihikari". Our results unravel the molecular control of flowering time under ambient temperature fluctuations.
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Affiliation(s)
- Kiyosumi Hori
- National Agriculture and Food Research Organization, Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan; (K.N.); (Y.N.); (K.S.); (J.-i.Y.); (S.F.)
| | - Daisuke Saisho
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan; (D.S.); (T.H.)
| | - Kazufumi Nagata
- National Agriculture and Food Research Organization, Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan; (K.N.); (Y.N.); (K.S.); (J.-i.Y.); (S.F.)
| | - Yasunori Nonoue
- National Agriculture and Food Research Organization, Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan; (K.N.); (Y.N.); (K.S.); (J.-i.Y.); (S.F.)
| | | | - Asaka Kanatani
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan; (Y.U.-Y.); (A.K.)
| | - Koka Shu
- National Agriculture and Food Research Organization, Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan; (K.N.); (Y.N.); (K.S.); (J.-i.Y.); (S.F.)
| | - Takashi Hirayama
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan; (D.S.); (T.H.)
| | - Jun-ichi Yonemaru
- National Agriculture and Food Research Organization, Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan; (K.N.); (Y.N.); (K.S.); (J.-i.Y.); (S.F.)
| | - Shuichi Fukuoka
- National Agriculture and Food Research Organization, Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan; (K.N.); (Y.N.); (K.S.); (J.-i.Y.); (S.F.)
| | - Keiichi Mochida
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan; (D.S.); (T.H.)
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan; (Y.U.-Y.); (A.K.)
- Kihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan
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3
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Inoue K, Takahagi K, Kouzai Y, Koda S, Shimizu M, Uehara-Yamaguchi Y, Nakayama R, Kita T, Onda Y, Nomura T, Matsui H, Nagaki K, Nishii R, Mochida K. Parental legacy and regulatory novelty in Brachypodium diurnal transcriptomes accompanying their polyploidy. NAR Genom Bioinform 2020; 2:lqaa067. [PMID: 33575616 PMCID: PMC7671347 DOI: 10.1093/nargab/lqaa067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 08/15/2020] [Accepted: 08/31/2020] [Indexed: 11/22/2022] Open
Abstract
Polyploidy is a widespread phenomenon in eukaryotes that can lead to phenotypic novelty and has important implications for evolution and diversification. The modification of phenotypes in polyploids relative to their diploid progenitors may be associated with altered gene expression. However, it is largely unknown how interactions between duplicated genes affect their diurnal expression in allopolyploid species. In this study, we explored parental legacy and hybrid novelty in the transcriptomes of an allopolyploid species and its diploid progenitors. We compared the diurnal transcriptomes of representative Brachypodium cytotypes, including the allotetraploid Brachypodium hybridum and its diploid progenitors Brachypodium distachyon and Brachypodium stacei. We also artificially induced an autotetraploid B. distachyon. We identified patterns of homoeolog expression bias (HEB) across Brachypodium cytotypes and time-dependent gain and loss of HEB in B. hybridum. Furthermore, we established that many genes with diurnal expression experienced HEB, while their expression patterns and peak times were correlated between homoeologs in B. hybridum relative to B. distachyon and B. stacei, suggesting diurnal synchronization of homoeolog expression in B. hybridum. Our findings provide insight into the parental legacy and hybrid novelty associated with polyploidy in Brachypodium, and highlight the evolutionary consequences of diurnal transcriptional regulation that accompanied allopolyploidy.
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Affiliation(s)
- Komaki Inoue
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Kotaro Takahagi
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, 244-0813, Japan
- Graduate School of Nanobioscience, Yokohama City University, Kanazawa-ku, Yokohama, 236-0027, Japan
| | - Yusuke Kouzai
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Satoru Koda
- Graduate School of Mathematics, Kyushu University, Fukuoka, 819-0395, Japan
| | - Minami Shimizu
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | | | - Risa Nakayama
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Toshie Kita
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Yoshihiko Onda
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Toshihisa Nomura
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN Baton Zone Program, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Hidetoshi Matsui
- Faculty of Data Science, Shiga University, Hikone, 522-8522, Japan
| | - Kiyotaka Nagaki
- Institute of Plant Science and Resources, Okayama University,710-0046, Kurashiki, Japan
| | - Ryuei Nishii
- School of Information and Data Science, Nagasaki University, Nagasaki, 852-8131, Japan
| | - Keiichi Mochida
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, 230-0045, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, 244-0813, Japan
- Graduate School of Nanobioscience, Yokohama City University, Kanazawa-ku, Yokohama, 236-0027, Japan
- RIKEN Baton Zone Program, Tsurumi-ku, Yokohama, 230-0045, Japan
- Institute of Plant Science and Resources, Okayama University,710-0046, Kurashiki, Japan
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4
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Sato K, Ishii M, Takahagi K, Inoue K, Shimizu M, Uehara-Yamaguchi Y, Nishii R, Mochida K. Genetic Factors Associated with Heading Responses Revealed by Field Evaluation of 274 Barley Accessions for 20 Seasons. iScience 2020; 23:101146. [PMID: 32454448 PMCID: PMC7251784 DOI: 10.1016/j.isci.2020.101146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 03/18/2020] [Accepted: 05/06/2020] [Indexed: 12/04/2022] Open
Abstract
Heading time is a key trait in cereals affecting the maturation period for optimal grain filling before harvest. Here, we aimed to understand the factors controlling heading time in barley (Hordeum vulgare). We characterized a set of 274 barley accessions collected worldwide by planting them for 20 seasons under different environmental conditions at the same location in Kurashiki, Japan. We examined interactions among accessions, known genetic factors, and an environmental factor to determine the factors controlling heading response. Locally adapted accessions have been selected for genetic factors that stabilize heading responses appropriate for barley cultivation, and these accessions show stable heading responses even under varying environmental conditions. We identified vernalization requirement and PPD-H1 haplotype as major stabilizing mechanisms of the heading response for regional adaptation in Kurashiki. Heading of 274 barley worldwide accessions were evaluated for 20 seasons Locally adapted accessions show stable heading responses Vernalization requirement and PPD-H1 haplotype stabilize the heading response
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Affiliation(s)
- Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan.
| | - Makoto Ishii
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - Kotaro Takahagi
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan; Kihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan
| | - Komaki Inoue
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Minami Shimizu
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | | | - Ryuei Nishii
- School of Information and Data Sciences, Nagasaki University, Nagasaki 852-8131, Japan
| | - Keiichi Mochida
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan; RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan; Kihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan; RIKEN Baton Zone Program, Yokohama 244-0813, Japan
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5
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Onda Y, Inoue K, Sawada Y, Shimizu M, Takahagi K, Uehara-Yamaguchi Y, Hirai MY, Garvin DF, Mochida K. Genetic Variation for Seed Metabolite Levels in Brachypodium distachyon. Int J Mol Sci 2019; 20:ijms20092348. [PMID: 31083584 PMCID: PMC6540107 DOI: 10.3390/ijms20092348] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/26/2019] [Accepted: 04/27/2019] [Indexed: 12/27/2022] Open
Abstract
Metabolite composition and concentrations in seed grains are important traits of cereals. To identify the variation in the seed metabolotypes of a model grass, namely Brachypodium distachyon, we applied a widely targeted metabolome analysis to forty inbred lines of B. distachyon and examined the accumulation patterns of 183 compounds in the seeds. By comparing the metabolotypes with the population structure of these lines, we found signature metabolites that represent different accumulation patterns for each of the three B. distachyon subpopulations. Moreover, we found that thirty-seven metabolites exhibited significant differences in their accumulation between the lines Bd21 and Bd3-1. Using a recombinant inbred line (RIL) population from a cross between Bd3-1 and Bd21, we identified the quantitative trait loci (QTLs) linked with this variation in the accumulation of thirteen metabolites. Our metabolite QTL analysis illustrated that different genetic factors may presumably regulate the accumulation of 4-pyridoxate and pyridoxamine in vitamin B6 metabolism. Moreover, we found two QTLs on chromosomes 1 and 4 that affect the accumulation of an anthocyanin, chrysanthemin. These QTLs genetically interacted to regulate the accumulation of this compound. This study demonstrates the potential for metabolite QTL mapping in B. distachyon and provides new insights into the genetic dissection of metabolomic traits in temperate grasses.
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Affiliation(s)
- Yoshihiko Onda
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
| | - Komaki Inoue
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Yuji Sawada
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Minami Shimizu
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Kotaro Takahagi
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Yukiko Uehara-Yamaguchi
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Masami Y Hirai
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - David F Garvin
- Plant Science Research Unit, United States Department of Agriculture, Agricultural Research Service, 1991 Upper Buford Circle, St. Paul, MN 55108, USA.
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Institute of Plant Science and Resource, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan.
- Microalgae Production Control Technology Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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6
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Takahagi K, Inoue K, Shimizu M, Uehara-Yamaguchi Y, Onda Y, Mochida K. Homoeolog-specific activation of genes for heat acclimation in the allopolyploid grass Brachypodium hybridum. Gigascience 2018; 7:4924998. [PMID: 29697823 PMCID: PMC5915950 DOI: 10.1093/gigascience/giy020] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 03/01/2018] [Indexed: 11/21/2022] Open
Abstract
Background Allopolyploid plants often show wider environmental tolerances than their ancestors; this is expected to be due to the merger of multiple distinct genomes with a fixed heterozygosity. The complex homoeologous gene expression could have been evolutionarily advantageous for the adaptation of allopolyploid plants. Despite multiple previous studies reporting homoeolog-specific gene expression in allopolyploid species, there are no clear examples of homoeolog-specific function in acclimation to a long-term stress condition. Results We found that the allopolyploid grass Brachypodium hybridum and its ancestor Brachypodium stacei show long-term heat stress tolerance, unlike its other ancestor, Brachypodium distachyon. To understand the physiological traits of B. hybridum, we compared the transcriptome of the 3 Brachypodium species grown under normal and heat stress conditions. We found that the expression patterns of approximately 26% and approximately 38% of the homoeolog groups in B. hybridum changed toward nonadditive expression and nonancestral expression, respectively, under normal condition. Moreover, we found that B. distachyon showed similar expression patterns between normal and heat stress conditions, whereas B. hybridum and B. stacei significantly altered their transcriptome in response to heat after 3 days of stress exposure, and homoeologs that were inherited from B. stacei may have contributed to the transcriptional stress response to heat in B. hybridum. After 15 days of heat exposure, B. hybridum and B. stacei maintained transcriptional states similar to those under normal conditions. These results suggest that an earlier response to heat that was specific to homoeologs originating from B. stacei contributed to cellular homeostasis under long-term heat stress in B. hybridum. Conclusions Our results provide insights into different regulatory events of the homoeo-transcriptome that are associated with stress acclimation in allopolyploid plants.
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Affiliation(s)
- Kotaro Takahagi
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa 236-0027, Japan.,Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.,Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Komaki Inoue
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Minami Shimizu
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.,Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yukiko Uehara-Yamaguchi
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshihiko Onda
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.,Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Keiichi Mochida
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa 236-0027, Japan.,Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.,Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan
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7
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Ogita S, Nomura T, Kato Y, Uehara-Yamaguchi Y, Inoue K, Yoshida T, Sakurai T, Shinozaki K, Mochida K. Transcriptional alterations during proliferation and lignification in Phyllostachys nigra cells. Sci Rep 2018; 8:11347. [PMID: 30054534 PMCID: PMC6063902 DOI: 10.1038/s41598-018-29645-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 07/16/2018] [Indexed: 01/24/2023] Open
Abstract
Highly-lignified culms of bamboo show distinctive anatomical and mechanical properties compared with the culms of other grass species. A cell culture system for Phyllostachys nigra has enabled investigating the alterations in cellular states associated with secondary cell wall formation during its proliferation and lignification in woody bamboos. To reveal transcriptional changes related to lignification in bamboo, we analyzed transcriptome in P. nigra cells treated with the synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D) and the synthetic cytokinin benzylaminopurine (BA) by RNA-seq analysis. We found that some genes putatively involved in cell wall biogenesis and cell division were up-regulated in response to the 2,4-D treatment, and the induction of lignification by the BA treatment was correlated with up-regulation of genes involved in the shikimate pathway. We also found that genes encoding MYB transcription factors (TFs) show correlated expression patterns with those encoding cinnamyl alcohol dehydrogenase (CAD), suggesting that MYB TFs presumably regulate secondary cell wall formation in the bamboo cells. These findings suggest that cytokinin signaling may regulate lignification in P. nigra cells through coordinated transcriptional regulation and metabolic alterations. Our results have also produced a useful resource for better understanding of secondary cell wall formation in bamboo plants.
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Affiliation(s)
- Shinjiro Ogita
- Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, 5562 Nanatuka, Shobara, Hiroshima, 727-0023, Japan. .,Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.
| | - Taiji Nomura
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yasuo Kato
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yukiko Uehara-Yamaguchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Komaki Inoue
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Takuhiro Yoshida
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Tetsuya Sakurai
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.,Interdisciplinary Science Unit, Multidisciplinary Science Cluster, Research and Education Faculty, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Kazuo Shinozaki
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Keiichi Mochida
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan. .,RIKEN, Baton Zone Program, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. .,Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan. .,Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, Okayama, 710-0046, Japan.
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Koda S, Onda Y, Matsui H, Takahagi K, Uehara-Yamaguchi Y, Shimizu M, Inoue K, Yoshida T, Sakurai T, Honda H, Eguchi S, Nishii R, Mochida K. Diurnal Transcriptome and Gene Network Represented through Sparse Modeling in Brachypodium distachyon. Front Plant Sci 2017; 8:2055. [PMID: 29234348 PMCID: PMC5712366 DOI: 10.3389/fpls.2017.02055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/16/2017] [Indexed: 05/08/2023]
Abstract
We report the comprehensive identification of periodic genes and their network inference, based on a gene co-expression analysis and an Auto-Regressive eXogenous (ARX) model with a group smoothly clipped absolute deviation (SCAD) method using a time-series transcriptome dataset in a model grass, Brachypodium distachyon. To reveal the diurnal changes in the transcriptome in B. distachyon, we performed RNA-seq analysis of its leaves sampled through a diurnal cycle of over 48 h at 4 h intervals using three biological replications, and identified 3,621 periodic genes through our wavelet analysis. The expression data are feasible to infer network sparsity based on ARX models. We found that genes involved in biological processes such as transcriptional regulation, protein degradation, and post-transcriptional modification and photosynthesis are significantly enriched in the periodic genes, suggesting that these processes might be regulated by circadian rhythm in B. distachyon. On the basis of the time-series expression patterns of the periodic genes, we constructed a chronological gene co-expression network and identified putative transcription factors encoding genes that might be involved in the time-specific regulatory transcriptional network. Moreover, we inferred a transcriptional network composed of the periodic genes in B. distachyon, aiming to identify genes associated with other genes through variable selection by grouping time points for each gene. Based on the ARX model with the group SCAD regularization using our time-series expression datasets of the periodic genes, we constructed gene networks and found that the networks represent typical scale-free structure. Our findings demonstrate that the diurnal changes in the transcriptome in B. distachyon leaves have a sparse network structure, demonstrating the spatiotemporal gene regulatory network over the cyclic phase transitions in B. distachyon diurnal growth.
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Affiliation(s)
- Satoru Koda
- Graduate School of Mathematics, Kyushu University, Fukuoka, Japan
| | - Yoshihiko Onda
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | | | - Kotaro Takahagi
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa, Japan
| | - Yukiko Uehara-Yamaguchi
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Minami Shimizu
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Komaki Inoue
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Takuhiro Yoshida
- Integrated Genome Informatics Research Unit, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Tetsuya Sakurai
- Integrated Genome Informatics Research Unit, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
- Research and Education Faculty, Multidisciplinary Science Cluster, Interdisciplinary Science Unit, Kochi University, Kochi, Japan
| | - Hiroshi Honda
- Graduate School of Mathematics, Kyushu University, Fukuoka, Japan
| | - Shinto Eguchi
- The Institute of Statistical Mathematics, Tokyo, Japan
| | - Ryuei Nishii
- Institute of Mathematics for Industry, Kyushu University, Fukuoka, Japan
- *Correspondence: Keiichi Mochida, Ryuei Nishii,
| | - Keiichi Mochida
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa, Japan
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
- *Correspondence: Keiichi Mochida, Ryuei Nishii,
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Mochida K, Uehara-Yamaguchi Y, Takahashi F, Yoshida T, Sakurai T, Shinozaki K. Large-scale collection and analysis of full-length cDNAs from Brachypodium distachyon and integration with Pooideae sequence resources. PLoS One 2013; 8:e75265. [PMID: 24130698 PMCID: PMC3793998 DOI: 10.1371/journal.pone.0075265] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 08/14/2013] [Indexed: 01/09/2023] Open
Abstract
A comprehensive collection of full-length cDNAs is essential for correct structural gene annotation and functional analyses of genes. We constructed a mixed full-length cDNA library from 21 different tissues of Brachypodium distachyon Bd21, and obtained 78,163 high quality expressed sequence tags (ESTs) from both ends of ca. 40,000 clones (including 16,079 contigs). We updated gene structure annotations of Brachypodium genes based on full-length cDNA sequences in comparison with the latest publicly available annotations. About 10,000 non-redundant gene models were supported by full-length cDNAs; ca. 6,000 showed some transcription unit modifications. We also found ca. 580 novel gene models, including 362 newly identified in Bd21. Using the updated transcription start sites, we searched a total of 580 plant cis-motifs in the −3 kb promoter regions and determined a genome-wide Brachypodium promoter architecture. Furthermore, we integrated the Brachypodium full-length cDNAs and updated gene structures with available sequence resources in wheat and barley in a web-accessible database, the RIKEN Brachypodium FL cDNA database. The database represents a “one-stop” information resource for all genomic information in the Pooideae, facilitating functional analysis of genes in this model grass plant and seamless knowledge transfer to the Triticeae crops.
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Affiliation(s)
- Keiichi Mochida
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, Kanagawa, Japan
- * E-mail:
| | - Yukiko Uehara-Yamaguchi
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Fuminori Takahashi
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Takuhiro Yoshida
- Integrated Genome Informatics Research Unit, RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Tetsuya Sakurai
- Integrated Genome Informatics Research Unit, RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Kazuo Shinozaki
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
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Mochida K, Uehara-Yamaguchi Y, Yoshida T, Sakurai T, Shinozaki K. Global landscape of a co-expressed gene network in barley and its application to gene discovery in Triticeae crops. Plant Cell Physiol 2011; 52:785-803. [PMID: 21441235 PMCID: PMC3093127 DOI: 10.1093/pcp/pcr035] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Accumulated transcriptome data can be used to investigate regulatory networks of genes involved in various biological systems. Co-expression analysis data sets generated from comprehensively collected transcriptome data sets now represent efficient resources that are capable of facilitating the discovery of genes with closely correlated expression patterns. In order to construct a co-expression network for barley, we analyzed 45 publicly available experimental series, which are composed of 1,347 sets of GeneChip data for barley. On the basis of a gene-to-gene weighted correlation coefficient, we constructed a global barley co-expression network and classified it into clusters of subnetwork modules. The resulting clusters are candidates for functional regulatory modules in the barley transcriptome. To annotate each of the modules, we performed comparative annotation using genes in Arabidopsis and Brachypodium distachyon. On the basis of a comparative analysis between barley and two model species, we investigated functional properties from the representative distributions of the gene ontology (GO) terms. Modules putatively involved in drought stress response and cellulose biogenesis have been identified. These modules are discussed to demonstrate the effectiveness of the co-expression analysis. Furthermore, we applied the data set of co-expressed genes coupled with comparative analysis in attempts to discover potentially Triticeae-specific network modules. These results demonstrate that analysis of the co-expression network of the barley transcriptome together with comparative analysis should promote the process of gene discovery in barley. Furthermore, the insights obtained should be transferable to investigations of Triticeae plants. The associated data set generated in this analysis is publicly accessible at http://coexpression.psc.riken.jp/barley/.
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Affiliation(s)
- Keiichi Mochida
- RIKEN Biomass Engineering Program, Yokohama 230-0045, Japan.
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