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Han SY, Park SY, Won KH, Park SI, Park JH, Shim D, Hwang I, Jeong DH, Kim H. Elucidating the callus-to-shoot-forming mechanism in Capsicum annuum 'Dempsey' through comparative transcriptome analyses. BMC PLANT BIOLOGY 2024; 24:367. [PMID: 38711041 DOI: 10.1186/s12870-024-05033-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/17/2024] [Indexed: 05/08/2024]
Abstract
BACKGROUND The formation of shoots plays a pivotal role in plant organogenesis and productivity. Despite its significance, the underlying molecular mechanism of de novo regeneration has not been extensively elucidated in Capsicum annuum 'Dempsey', a bell pepper cultivar. To address this, we performed a comparative transcriptome analysis focusing on the differential expression in C. annuum 'Dempsey' shoot, callus, and leaf tissue. We further investigated phytohormone-related biological processes and their interacting genes in the C. annuum 'Dempsey' transcriptome based on comparative transcriptomic analysis across five species. RESULTS We provided a comprehensive view of the gene networks regulating shoot formation on the callus, revealing a strong involvement of hypoxia responses and oxidative stress. Our comparative transcriptome analysis revealed a significant conservation in the increase of gene expression patterns related to auxin and defense mechanisms in both callus and shoot tissues. Consequently, hypoxia response and defense mechanism emerged as critical regulators in callus and shoot formation in C. annuum 'Dempsey'. Current transcriptome data also indicated a substantial decline in gene expression linked to photosynthesis within regenerative tissues, implying a deactivation of the regulatory system governing photosynthesis in C. annuum 'Dempsey'. CONCLUSION Coupled with defense mechanisms, we thus considered spatial redistribution of auxin to play a critical role in the shoot morphogenesis via primordia outgrowth. Our findings shed light on shoot formation mechanisms in C. annuum 'Dempsey' explants, important information for regeneration programs, and have broader implications for precise molecular breeding in recalcitrant crops.
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Affiliation(s)
- Sang-Yun Han
- Department of Biological Sciences, Institute for Life Sciences, Kangwon National University, Chuncheon, 24341, Korea
| | - So Young Park
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon, 24252, Korea
| | - Kang-Hee Won
- Department of Biological Sciences, Institute for Life Sciences, Kangwon National University, Chuncheon, 24341, Korea
| | - Sung-Il Park
- Department of BIT Medical Convergence, Kangwon National University, Chuncheon, 24341, Korea
| | - Jae-Hyeong Park
- Department of BIT Medical Convergence, Kangwon National University, Chuncheon, 24341, Korea
| | - Donghwan Shim
- Department of Biological Sciences, Chungnam National University, Daejeon, 34134, Korea
| | - Inhwan Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Dong-Hoon Jeong
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon, 24252, Korea.
| | - Hyeran Kim
- Department of Biological Sciences, Institute for Life Sciences, Kangwon National University, Chuncheon, 24341, Korea.
- Department of BIT Medical Convergence, Kangwon National University, Chuncheon, 24341, Korea.
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2
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Osborne R, Rehneke L, Lehmann S, Roberts J, Altmann M, Altmann S, Zhang Y, Köpff E, Dominguez-Ferreras A, Okechukwu E, Sergaki C, Rich-Griffin C, Ntoukakis V, Eichmann R, Shan W, Falter-Braun P, Schäfer P. Symbiont-host interactome mapping reveals effector-targeted modulation of hormone networks and activation of growth promotion. Nat Commun 2023; 14:4065. [PMID: 37429856 DOI: 10.1038/s41467-023-39885-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 06/27/2023] [Indexed: 07/12/2023] Open
Abstract
Plants have benefited from interactions with symbionts for coping with challenging environments since the colonisation of land. The mechanisms of symbiont-mediated beneficial effects and similarities and differences to pathogen strategies are mostly unknown. Here, we use 106 (effector-) proteins, secreted by the symbiont Serendipita indica (Si) to modulate host physiology, to map interactions with Arabidopsis thaliana host proteins. Using integrative network analysis, we show significant convergence on target-proteins shared with pathogens and exclusive targeting of Arabidopsis proteins in the phytohormone signalling network. Functional in planta screening and phenotyping of Si effectors and interacting proteins reveals previously unknown hormone functions of Arabidopsis proteins and direct beneficial activities mediated by effectors in Arabidopsis. Thus, symbionts and pathogens target a shared molecular microbe-host interface. At the same time Si effectors specifically target the plant hormone network and constitute a powerful resource for elucidating the signalling network function and boosting plant productivity.
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Affiliation(s)
- Rory Osborne
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Laura Rehneke
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Silke Lehmann
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Laboratory of Biotechnology and Marine Chemistry LBCM, EA3884, IUEM, Southern Brittany University, 56000, Vannes, France
| | - Jemma Roberts
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Melina Altmann
- Institute of Network Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, 85764, Munich-Neuherberg, Germany
| | - Stefan Altmann
- Institute of Network Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, 85764, Munich-Neuherberg, Germany
| | - Yingqi Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Eva Köpff
- Institute of Molecular Botany, Ulm University, 89069, Ulm, Germany
| | | | - Emeka Okechukwu
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Chrysi Sergaki
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Vardis Ntoukakis
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Ruth Eichmann
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Weixing Shan
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Pascal Falter-Braun
- Institute of Network Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, 85764, Munich-Neuherberg, Germany.
- Microbe-Host Interactions, Faculty of Biology, Ludwig-Maximilians-University München, 82152, Planegg-Martinsried, Germany.
| | - Patrick Schäfer
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany.
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3
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Saidi MN, Mahjoubi H, Yacoubi I. Transcriptome meta-analysis of abiotic stresses-responsive genes and identification of candidate transcription factors for broad stress tolerance in wheat. PROTOPLASMA 2023; 260:707-721. [PMID: 36063229 DOI: 10.1007/s00709-022-01807-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Under field conditions, wheat is subjected to single or multiple stress conditions. The elucidation of the molecular mechanism of stress response is a key step to identify candidate genes for stress resistance in plants. In this study, RNA-seq data analysis identified 17.324, 10.562, 5.510, and 8.653 differentially expressed genes (DEGs) under salt, drought, heat, and cold stress, respectively. Moreover, the comparison of DEGs from each stress revealed 2374 shared genes from which 40% showed highly conserved expression patterns. Moreover, co-expression network analysis and GO enrichment revealed co-expression modules enriched with genes involved in transcription regulation, protein kinase pathway, and genes responding to phytohormones or modulating hormone levels. The expression of 15 selected transcription factor encoding genes was analyzed under abiotic stresses and ABA treatment in durum wheat. The identified transcription factor genes are excellent candidates for genetic engineering of stress tolerance in wheat.
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Affiliation(s)
- Mohamed Najib Saidi
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, Road Sidi Mansour 6 km, P.O. Box 1177, 3018, Sfax, Tunisia.
| | - Habib Mahjoubi
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, Road Sidi Mansour 6 km, P.O. Box 1177, 3018, Sfax, Tunisia
| | - Ines Yacoubi
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, Road Sidi Mansour 6 km, P.O. Box 1177, 3018, Sfax, Tunisia
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4
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Fang Y, Qin X, Liao Q, Du R, Luo X, Zhou Q, Li Z, Chen H, Jin W, Yuan Y, Sun P, Zhang R, Zhang J, Wang L, Cheng S, Yang X, Yan Y, Zhang X, Zhang Z, Bai S, Van de Peer Y, Lucas WJ, Huang S, Yan J. The genome of homosporous maidenhair fern sheds light on the euphyllophyte evolution and defences. NATURE PLANTS 2022; 8:1024-1037. [PMID: 36050462 PMCID: PMC7613604 DOI: 10.1038/s41477-022-01222-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 07/13/2022] [Indexed: 05/06/2023]
Abstract
Euphyllophytes encompass almost all extant plants, including two sister clades, ferns and seed plants. Decoding genomes of ferns is the key to deep insight into the origin of euphyllophytes and the evolution of seed plants. Here we report a chromosome-level genome assembly of Adiantum capillus-veneris L., a model homosporous fern. This fern genome comprises 30 pseudochromosomes with a size of 4.8-gigabase and a contig N50 length of 16.22 Mb. Gene co-expression network analysis uncovered that homospore development in ferns has relatively high genetic similarities with that of the pollen in seed plants. Analysing fern defence response expands understanding of evolution and diversity in endogenous bioactive jasmonates in plants. Moreover, comparing fern genomes with those of other land plants reveals changes in gene families important for the evolutionary novelties within the euphyllophyte clade. These results lay a foundation for studies on fern genome evolution and function, as well as the origin and evolution of euphyllophytes.
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Affiliation(s)
- Yuhan Fang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Xing Qin
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qinggang Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Ran Du
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xizhi Luo
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qian Zhou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Peng Cheng Laboratory, Artificial Intelligence Research Center, Shenzhen, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hengchi Chen
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Wanting Jin
- State Key Laboratory of Protein and Plant Gene Research, Quantitative Biology Center, College of Life Sciences, Peking University, Beijing, China
| | - Yaning Yuan
- State Key Laboratory of Protein and Plant Gene Research, Quantitative Biology Center, College of Life Sciences, Peking University, Beijing, China
| | - Pengbo Sun
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Rui Zhang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Jiao Zhang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Li Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xueyong Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuehong Yan
- The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China
| | - Xingtan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhonghua Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Shunong Bai
- State Key Laboratory of Protein and Plant Gene Research, Quantitative Biology Center, College of Life Sciences, Peking University, Beijing, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB Center for Plant Systems Biology, Ghent, Belgium
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - William John Lucas
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA, USA
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jianbin Yan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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5
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Carvalho TLG, Rosman AC, Grativol C, de M. Nogueira E, Baldani JI, Hemerly AS. Sugarcane Genotypes with Contrasting Biological Nitrogen Fixation Efficiencies Differentially Modulate Nitrogen Metabolism, Auxin Signaling, and Microorganism Perception Pathways. PLANTS (BASEL, SWITZERLAND) 2022; 11:1971. [PMID: 35956449 PMCID: PMC9370643 DOI: 10.3390/plants11151971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Sugarcane is an economically important crop that is used for the production of fuel ethanol. Diazotrophic bacteria have been isolated from sugarcane tissues, without causing visible plant anatomical changes or disease symptoms. These bacteria can be beneficial to the plant by promoting root growth and an increase in plant yield. Different rates of Biological Nitrogen Fixation (BNF) were observed in different genotypes. The aim of this work was to conduct a comprehensive molecular and physiological analysis of two model genotypes for contrasting BNF efficiency in order to unravel plant genes that are differentially regulated during a natural association with diazotrophic bacteria. A next-generation sequencing of RNA samples from the genotypes SP70-1143 (high-BNF) and Chunee (low-BNF) was performed. A differential transcriptome analysis showed that several pathways were differentially regulated among the two BNF-contrasting genotypes, including nitrogen metabolism, hormone regulation and bacteria recognition. Physiological analyses, such as nitrogenase and GS activity quantification, bacterial colonization, auxin response and root architecture evaluation, supported the transcriptome expression analyses. The differences observed between the genotypes may explain, at least in part, the differences in BNF contributions. Some of the identified genes might be involved in key regulatory processes for a beneficial association and could be further used as tools for obtaining more efficient BNF genotypes.
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Affiliation(s)
- Thais Louise G. Carvalho
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, RJ, Brazil; (T.L.G.C.); (A.C.R.); (C.G.); (E.d.M.N.)
| | - Aline C. Rosman
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, RJ, Brazil; (T.L.G.C.); (A.C.R.); (C.G.); (E.d.M.N.)
| | - Clícia Grativol
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, RJ, Brazil; (T.L.G.C.); (A.C.R.); (C.G.); (E.d.M.N.)
- Laboratório de Química e Funções de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes 28015-622, RJ, Brazil
| | - Eduardo de M. Nogueira
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, RJ, Brazil; (T.L.G.C.); (A.C.R.); (C.G.); (E.d.M.N.)
| | - José Ivo Baldani
- Laboratório de Genética e Bioquímica, Centro Nacional de Pesquisa de Agrobiologia, Embrapa Agrobiologia, Rio de Janeiro 23897-970, RJ, Brazil;
| | - Adriana S. Hemerly
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, RJ, Brazil; (T.L.G.C.); (A.C.R.); (C.G.); (E.d.M.N.)
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6
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Utsumi Y, Tanaka M, Utsumi C, Takahashi S, Matsui A, Fukushima A, Kobayashi M, Sasaki R, Oikawa A, Kusano M, Saito K, Kojima M, Sakakibara H, Sojikul P, Narangajavana J, Seki M. Integrative omics approaches revealed a crosstalk among phytohormones during tuberous root development in cassava. PLANT MOLECULAR BIOLOGY 2022; 109:249-269. [PMID: 32757126 DOI: 10.1007/s11103-020-01033-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 07/06/2020] [Indexed: 05/23/2023]
Abstract
Integrative omics approaches revealed a crosstalk among phytohormones during tuberous root development in cassava. Tuberous root formation is a complex process consisting of phase changes as well as cell division and elongation for radial growth. We performed an integrated analysis to clarify the relationships among metabolites, phytohormones, and gene transcription during tuberous root formation in cassava (Manihot esculenta Crantz). We also confirmed the effects of the auxin (AUX), cytokinin (CK), abscisic acid (ABA), jasmonic acid (JA), gibberellin (GA), brassinosteroid (BR), salicylic acid, and indole-3-acetic acid conjugated with aspartic acid on tuberous root development. An integrated analysis of metabolites and gene expression indicated the expression levels of several genes encoding enzymes involved in starch biosynthesis and sucrose metabolism are up-regulated during tuberous root development, which is consistent with the accumulation of starch, sugar phosphates, and nucleotides. An integrated analysis of phytohormones and gene transcripts revealed a relationship among AUX signaling, CK signaling, and BR signaling, with AUX, CK, and BR inducing tuberous root development. In contrast, ABA and JA inhibited tuberous root development. These phenomena might represent the differences between stem tubers (e.g., potato) and root tubers (e.g., cassava). On the basis of these results, a phytohormonal regulatory model for tuberous root development was constructed. This model may be useful for future phytohormonal studies involving cassava.
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Affiliation(s)
- Yoshinori Utsumi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
| | - Maho Tanaka
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Chikako Utsumi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Satoshi Takahashi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Akihiro Matsui
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Atsushi Fukushima
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Makoto Kobayashi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Ryosuke Sasaki
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Akira Oikawa
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Faculty of Agriculture, Yamagata University, Tsuruoka, Japan
| | - Miyako Kusano
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Chiba, 260-8675, Japan
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Punchapat Sojikul
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Jarunya Narangajavana
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Motoaki Seki
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
- RIKEN Cluster for Pioneering Research, 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.
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7
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Liu J, Chen LY, Zhou P, Liao Z, Lin H, Yu Q, Ming R. Sex biased expression of hormone related genes at early stage of sex differentiation in papaya flowers. HORTICULTURE RESEARCH 2021; 8:147. [PMID: 34193826 PMCID: PMC8245580 DOI: 10.1038/s41438-021-00581-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 04/18/2021] [Accepted: 04/26/2021] [Indexed: 06/13/2023]
Abstract
Sex types of papaya are controlled by a pair of nascent sex chromosomes, but molecular genetic mechanisms of sex determination and sex differentiation in papaya are still unclear. We performed comparative analysis of transcriptomic profiles of male and female floral buds at the early development stage before the initiation of reproductive organ primordia at which there is no morphological difference between male and female flowers. A total of 1734 differentially expressed genes (DEGs) were identified, of which 923 showed female-biased expression and 811 showed male-biased expression. Functional annotation revealed that genes related to plant hormone biosynthesis and signaling pathways, especially in abscisic acid and auxin pathways, were overrepresented in the DEGs. Transcription factor binding motifs, such as MYB2, GAMYB, and AP2/EREBP, were enriched in the promoters of the hormone-related DEGs, and transcription factors with those motifs also exhibited differential expression between sex types. Among these DEGs, we also identified 11 genes in the non-recombining region of the papaya sex chromosomes and 9 genes involved in stamen and carpel development. Our results suggested that sex differentiation in papaya may be regulated by multiple layers of regulation and coordination and involved transcriptional, epigenetic, and phytohormone regulation. Hormones, especially ABA and auxin, transcription factors, and genes in the non-recombination region of the sex chromosome could be involved in this process. Our findings may facilitate the elucidation of signal transduction and gene interaction in sex differentiation of unisexual flowers in papaya.
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Affiliation(s)
- Juan Liu
- FAFU and UIUC Joint Center for Genomics and Biotechnology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan, 430074, China
| | - Li-Yu Chen
- FAFU and UIUC Joint Center for Genomics and Biotechnology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Ping Zhou
- FAFU and UIUC Joint Center for Genomics and Biotechnology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Zhenyang Liao
- FAFU and UIUC Joint Center for Genomics and Biotechnology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Hai Lin
- FAFU and UIUC Joint Center for Genomics and Biotechnology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Qingyi Yu
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, 77843, USA
| | - Ray Ming
- FAFU and UIUC Joint Center for Genomics and Biotechnology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
- Department of Plant Biology, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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8
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Ding Y, Yu S, Wang J, Li M, Qu C, Li J, Liu L. Comparative transcriptomic analysis of seed coats with high and low lignin contents reveals lignin and flavonoid biosynthesis in Brassica napus. BMC PLANT BIOLOGY 2021; 21:246. [PMID: 34051742 PMCID: PMC8164251 DOI: 10.1186/s12870-021-03030-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/29/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Brassica napus L. (2n = 38, AACC) is one of the most important oil crops and sources of protein for animal feed worldwide. Lignin is a large molecule aromatic polymer and a major cell wall component. However, lignin in the seed coat reduces the availability and restricts the development of rapeseed cake. Therefore, it is critical to reduce the lignin content of the seed coat. Here, high-lignin (H-lignin) and low-lignin (L-lignin) content recombinant inbred lines (RILs) were selected from an RIL population for analysis. RESULTS The cross-section results indicated that the seed coat of the H-lignin lines was thicker than that of the L-lignin lines, especially the palisade layer. The seed coats and embryos at 35, 40 and 46 days after flowering (DAF) were subjected to RNA sequencing (RNA-Seq), and the expression of the BnPAL and BnC4H gene families in the lignin pathway was significantly higher in the H-lignin seed coat than in the L-lignin seed coat. The Bn4CL gene family also showed this trend. In addition, among the genes related to plant hormone synthesis, BnaC02g01710D was upregulated and BnaA07g11700D and BnaC09g00190D were downregulated in H-lignin lines. Some transcription factors were upregulated, such as BnNAC080, BnNAC083, BnMYB9, BnMYB9-1, BnMYB60 and BnMYB60-1, while BnMYB91 was downregulated in H-lignin lines. Moreover, most genes of the flavonoid pathway, such as BnCHS and BnDFR, were strongly expressed in H-lignin seed coat. CONCLUSIONS In Our study, some key genes such as hormone synthesis genes, transcription factors and miRNAs related to lignin and flavonoid biosynthesis were identified. A regulatory model of B. napus seed coat lignin was proposed. These results provide new insight into lignin and flavonoid biosynthesis in B. napus.
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Affiliation(s)
- Yiran Ding
- College of Agronomy and Biotechnology, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Shizhou Yu
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guizhou, 550008, China
| | - Jia Wang
- College of Agronomy and Biotechnology, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Maoteng Li
- Institute of Resource Biology and Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430070, Hubei, China
| | - Cunmin Qu
- College of Agronomy and Biotechnology, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China.
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9
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The Anaerobic Product Ethanol Promotes Autophagy-Dependent Submergence Tolerance in Arabidopsis. Int J Mol Sci 2020; 21:ijms21197361. [PMID: 33028029 PMCID: PMC7583018 DOI: 10.3390/ijms21197361] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/29/2020] [Accepted: 10/02/2020] [Indexed: 02/07/2023] Open
Abstract
In response to hypoxia under submergence, plants switch from aerobic respiration to anaerobic fermentation, which leads to the accumulation of the end product, ethanol. We previously reported that Arabidopsis thaliana autophagy-deficient mutants show increased sensitivity to ethanol treatment, indicating that ethanol is likely involved in regulating the autophagy-mediated hypoxia response. Here, using a transcriptomic analysis, we identified 3909 genes in Arabidopsis seedlings that were differentially expressed in response to ethanol treatment, including 2487 upregulated and 1422 downregulated genes. Ethanol treatment significantly upregulated genes involved in autophagy and the detoxification of reactive oxygen species. Using transgenic lines expressing AUTOPHAGY-RELATED PROTEIN 8e fused to green fluorescent protein (GFP-ATG8e), we confirmed that exogenous ethanol treatment promotes autophagosome formation in vivo. Phenotypic analysis showed that deletions in the alcohol dehydrogenase gene in adh1 mutants result in attenuated submergence tolerance, decreased accumulation of ATG proteins, and diminished submergence-induced autophagosome formation. Compared to the submergence-tolerant Arabidopsis accession Columbia (Col-0), the submergence-intolerant accession Landsberg erecta (Ler) displayed hypersensitivity to ethanol treatment; we linked these phenotypes to differences in the functions of ADH1 and the autophagy machinery between these accessions. Thus, ethanol promotes autophagy-mediated submergence tolerance in Arabidopsis.
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10
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Extensive signal integration by the phytohormone protein network. Nature 2020; 583:271-276. [PMID: 32612234 DOI: 10.1038/s41586-020-2460-0] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 04/14/2020] [Indexed: 12/31/2022]
Abstract
Plant hormones coordinate responses to environmental cues with developmental programs1, and are fundamental for stress resilience and agronomic yield2. The core signalling pathways underlying the effects of phytohormones have been elucidated by genetic screens and hypothesis-driven approaches, and extended by interactome studies of select pathways3. However, fundamental questions remain about how information from different pathways is integrated. Genetically, most phenotypes seem to be regulated by several hormones, but transcriptional profiling suggests that hormones trigger largely exclusive transcriptional programs4. We hypothesized that protein-protein interactions have an important role in phytohormone signal integration. Here, we experimentally generated a systems-level map of the Arabidopsis phytohormone signalling network, consisting of more than 2,000 binary protein-protein interactions. In the highly interconnected network, we identify pathway communities and hundreds of previously unknown pathway contacts that represent potential points of crosstalk. Functional validation of candidates in seven hormone pathways reveals new functions for 74% of tested proteins in 84% of candidate interactions, and indicates that a large majority of signalling proteins function pleiotropically in several pathways. Moreover, we identify several hundred largely small-molecule-dependent interactions of hormone receptors. Comparison with previous reports suggests that noncanonical and nontranscription-mediated receptor signalling is more common than hitherto appreciated.
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11
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Yu L, Chen Q, Peng Y, Xie L, Liu D, Han M, Chen F, Xiao S, Huang J, Li J. Arabidopsis thaliana Plants Engineered To Produce Astaxanthin Show Enhanced Oxidative Stress Tolerance and Bacterial Pathogen Resistance. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:12590-12598. [PMID: 31639305 DOI: 10.1021/acs.jafc.9b04589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Carotenoids play key roles in photosynthesis and photoprotection. Few multicellular plants produce the ketocarotenoid astaxanthin, a strong antioxidant; however, Arabidopsis thaliana lines overexpressing the Chlamydomonas reinhardtii β-carotene ketolase (CrBKT) accumulated high amounts of astaxanthin in the leaves. In this study, we investigated the changed regulation of key metabolic pathways and the tolerance of the engineered plants to biotic and abiotic stresses resulting from the heterologous expression of CrBKT. Transcriptome analysis identified 1633 and 1722 genes that were differentially expressed in the leaves and siliques, respectively, of CrBKT-overexpressing plants (line CR5) as compared to wild-type Arabidopsis. These genes were enriched in the carotenoid biosynthetic pathways, and plant hormone biosynthesis and signaling pathways. In particular, metabolic profiling showed that, as compared to the wild-type leaves and siliques, overexpression of CrBKT increased the levels of most amino acids, but decreased the contents of sugars and carbohydrates. Furthermore, CR5 plants had lower sensitivity to abscisic acid (ABA) and increased tolerance to oxidative stress. CR5 plants also exhibited enhanced resistance to the bacterial pathogen Pseudomonas syringae pv. tomato DC3000. Our study provides insight into the regulation of carotenoids and the related pathways, which may be involved in plant response to oxidative stress and pathogen infection.
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Affiliation(s)
- Lujun Yu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences , Sun Yat-sen University , Guangzhou 510275 , China
| | - Qinfang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences , Sun Yat-sen University , Guangzhou 510275 , China
| | - Yujun Peng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences , Sun Yat-sen University , Guangzhou 510275 , China
| | - Lijuan Xie
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences , Sun Yat-sen University , Guangzhou 510275 , China
| | - Di Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences , Sun Yat-sen University , Guangzhou 510275 , China
| | - Muqian Han
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences , Sun Yat-sen University , Guangzhou 510275 , China
- College of Agronomy , Hunan Agricultural University , Changsha 410128 China
| | - Feng Chen
- Institute for Advanced Study , Shenzhen University , Shenzhen 518000 , China
| | - Shi Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences , Sun Yat-sen University , Guangzhou 510275 , China
| | - Junchao Huang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201 , China
| | - Juan Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences , Sun Yat-sen University , Guangzhou 510275 , China
- College of Agronomy , Hunan Agricultural University , Changsha 410128 China
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12
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Del Prete S, Molitor A, Charif D, Bessoltane N, Soubigou-Taconnat L, Guichard C, Brunaud V, Granier F, Fransz P, Gaudin V. Extensive nuclear reprogramming and endoreduplication in mature leaf during floral induction. BMC PLANT BIOLOGY 2019; 19:135. [PMID: 30971226 PMCID: PMC6458719 DOI: 10.1186/s12870-019-1738-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 03/24/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND The floral transition is a complex developmental event, fine-tuned by various environmental and endogenous cues to ensure the success of offspring production. Leaves are key organs in sensing floral inductive signals, such as a change in light regime, and in the production of the mobile florigen. CONSTANS and FLOWERING LOCUS T are major players in leaves in response to photoperiod. Morphological and molecular events during the floral transition have been intensively studied in the shoot apical meristem. To better understand the concomitant processes in leaves, which are less described, we investigated the nuclear changes in fully developed leaves during the time course of the floral transition. RESULTS We highlighted new putative regulatory candidates of flowering in leaves. We observed differential expression profiles of genes related to cellular, hormonal and metabolic actions, but also of genes encoding long non-coding RNAs and new natural antisense transcripts. In addition, we detected a significant increase in ploidy level during the floral transition, indicating endoreduplication. CONCLUSIONS Our data indicate that differentiated mature leaves, possess physiological plasticity and undergo extensive nuclear reprogramming during the floral transition. The dynamic events point at functionally related networks of transcription factors and novel regulatory motifs, but also complex hormonal and metabolic changes.
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Affiliation(s)
- Stefania Del Prete
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA Centre de Versailles-Grignon, Bât. 2, RD10 Route de Saint-Cyr, 78000 Versailles, France
| | - Anne Molitor
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA Centre de Versailles-Grignon, Bât. 2, RD10 Route de Saint-Cyr, 78000 Versailles, France
| | - Delphine Charif
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA Centre de Versailles-Grignon, Bât. 2, RD10 Route de Saint-Cyr, 78000 Versailles, France
| | - Nadia Bessoltane
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA Centre de Versailles-Grignon, Bât. 2, RD10 Route de Saint-Cyr, 78000 Versailles, France
| | - Ludivine Soubigou-Taconnat
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, Plateau du Moulon, 91192 Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, Plateau du Moulon, 91192 Gif-sur-Yvette, 91405 Orsay, France
| | - Cécile Guichard
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, Plateau du Moulon, 91192 Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, Plateau du Moulon, 91192 Gif-sur-Yvette, 91405 Orsay, France
| | - Véronique Brunaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, Plateau du Moulon, 91192 Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, Plateau du Moulon, 91192 Gif-sur-Yvette, 91405 Orsay, France
| | - Fabienne Granier
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA Centre de Versailles-Grignon, Bât. 2, RD10 Route de Saint-Cyr, 78000 Versailles, France
| | - Paul Fransz
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1098XH Amsterdam, The Netherlands
| | - Valérie Gaudin
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA Centre de Versailles-Grignon, Bât. 2, RD10 Route de Saint-Cyr, 78000 Versailles, France
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13
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Zhang Y, Xiao Z, Zhan C, Liu M, Xia W, Wang N. Comprehensive analysis of dynamic gene expression and investigation of the roles of hydrogen peroxide during adventitious rooting in poplar. BMC PLANT BIOLOGY 2019; 19:99. [PMID: 30866829 PMCID: PMC6416884 DOI: 10.1186/s12870-019-1700-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 03/06/2019] [Indexed: 05/15/2023]
Abstract
BACKGROUND Adventitious roots (ARs) are roots that are generated from nonrooting tissues. ARs are usually produced both during normal development and in response to stress conditions, such as flooding, nutrient deprivation, heavy metal stress and wounding. The ability of plants to form ARs is a key trait that enables plant propagation, especially for most tree species. RESULTS Here, the kinetics of AR formation in a tissue culture of a hybrid variety of poplar were investigated. AR formation mainly occurred during the first 8 days and both pre- and newly- formed primordia contributed to AR formation in poplar by histological study. RNA-Seq-based transcriptome analysis was performed for stem bases collected at 0, 2, 4, 6 and 8 days after excision (DAE). Based on the data, the expression patterns of 8 phytohormone-related genes were investigated, and their influences on AR formation were considered. Subsequent gene expression cluster analysis showed a number of biological processes involved in AR formation. Among these biological pathways, genes involved in H2O2 homeostasis showed enrichment in one cluster that was highly upregulated from DAE0 to DAE8. Pharmacological assay confirmed that an appropriate content of H2O2 in stem bases could accelerate the formation of ARs in poplar. CONCLUSIONS Based on the results of this study, we were able to predict a regulatory network for 7 phytohormones that are involved in poplar AR formation. The influence of H2O2 on AR formation was also confirmed. These results enhance our understanding of the regulation of AR formation in tree species.
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Affiliation(s)
- Yan Zhang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Zheng’ang Xiao
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Chang Zhan
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Meifeng Liu
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Wenxiu Xia
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Nian Wang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
- Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070 China
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14
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Ilias IA, Negishi K, Yasue K, Jomura N, Morohashi K, Baharum SN, Goh HH. Transcriptome-wide effects of expansin gene manipulation in etiolated Arabidopsis seedling. JOURNAL OF PLANT RESEARCH 2019; 132:159-172. [PMID: 30341720 DOI: 10.1007/s10265-018-1067-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/19/2018] [Indexed: 05/24/2023]
Abstract
Expansin is a non-enzymatic protein which plays a pivotal role in cell wall loosening by inducing stress relaxation and extension in the plant cell wall. Previous studies on Arabidopsis, Petunia × hybrida, and tomato demonstrated that the suppression of expansin gene expression reduced plant growth but expansin overexpression does not necessarily promotes growth. In this study, both expansin gene suppression and overexpression in dark-grown transgenic Arabidopsis seedlings resulted in reduced hypocotyl length at late growth stages with a more pronounced effect for the overexpression. This defect in hypocotyl elongation raises questions about the molecular effect of expansin gene manipulation. RNA-seq analysis of the transcriptomic changes between day 3 and day 5 seedlings for both transgenic lines found numerous differentially expressed genes (DEGs) including transcription factors and hormone-related genes involved in different aspects of cell wall development. These DEGs imply that the observed hypocotyl growth retardation is a consequence of the concerted effect of regulatory factors and multiple cell-wall related genes, which are important for cell wall remodelling during rapid hypocotyl elongation. This is further supported by co-expression analysis through network-centric approach of differential network cluster analysis. This first transcriptome-wide study of expansin manipulation explains why the effect of expansin overexpression is greater than suppression and provides insights into the dynamic nature of molecular regulation during etiolation.
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Affiliation(s)
- Iqmal Asyraf Ilias
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Darul Ehsan, Malaysia
| | - Kohei Negishi
- Faculty of Science and Technology, Tokyo University of Science, Chiba-ken, Tokyo, 278-8510, Japan
| | - Keito Yasue
- Faculty of Science and Technology, Tokyo University of Science, Chiba-ken, Tokyo, 278-8510, Japan
| | - Naohiro Jomura
- Faculty of Science and Technology, Tokyo University of Science, Chiba-ken, Tokyo, 278-8510, Japan
| | - Kengo Morohashi
- Faculty of Science and Technology, Tokyo University of Science, Chiba-ken, Tokyo, 278-8510, Japan
| | - Syarul Nataqain Baharum
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Darul Ehsan, Malaysia
| | - Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Darul Ehsan, Malaysia.
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15
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Yang J, Liu Y, Yan H, Tian T, You Q, Zhang L, Xu W, Su Z. PlantEAR: Functional Analysis Platform for Plant EAR Motif-Containing Proteins. Front Genet 2018; 9:590. [PMID: 30555515 PMCID: PMC6283911 DOI: 10.3389/fgene.2018.00590] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 11/15/2018] [Indexed: 01/05/2023] Open
Abstract
The Ethylene-responsive element binding factor-associated Amphiphilic Repression (EAR) motifs, which were initially identified in members of the Arabidopsis ethylene response factor (ERF) family, are transcriptional repression motifs in plants and are defined by the consensus sequence patterns of either LxLxL or DLNxxP. EAR motif-containing proteins can function as transcription repressors, thus interacting with co-repressors, such as TOPLESS and AtSAP18, affecting the structure of chromatin by histone modifications and thereby repressing gene transcription. EAR motif-containing proteins are highly conserved across diverse plant species and play important roles in hormone signal transduction, stress responses and development, but they have not been identified in most plants. In this study, we identified 20,542 EAR motif-containing proteins from 71 plant species based on a Hidden Markov Model and orthologous gene search, and then we constructed a functional analysis platform for plant EAR motif-containing proteins (PlantEAR, http://structuralbiology.cau.edu.cn/plantEAR) by integrating a variety of functional annotations and processed data. Several tools were provided as functional support for EAR motif-containing proteins, such as browse, search, co-expression and protein-protein interaction (PPI) network analysis as well as cis-element analysis and gene set enrichment analysis (GSEA). In addition, basing on the identified EAR motif-containing proteins, we also explored their distribution in various species and found that the numbers of EAR motif-containing proteins showed an increasing trend in evolution from algae to angiosperms.
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Affiliation(s)
- Jiaotong Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yue Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Hengyu Yan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Tian Tian
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qi You
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Liwei Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
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16
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Xing W, Yuan X, Li L, Hu L, Peng J. Phenotype Extraction Based on Word Embedding to Sentence Embedding Cascaded Approach. IEEE Trans Nanobioscience 2018; 17:172-180. [PMID: 29994536 DOI: 10.1109/tnb.2018.2838137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
As a significant determinant in the development of named entity recognition, phenotypic descriptions are normally presented differently in biomedical literature with the use of complicated semantics. In this paper, a novel approach has been proposed to identify plant phenotypes by adopting word embedding to sentence embedding cascaded approach. We make use of a word embedding method to find high-frequency phenotypes with original sentences used as input in a sentence embedding method. In doing so, a variety of complicated phenotypic expressions can be recognized accurately. Besides, the state-of-the-art word representation models have been compared and among them, skip-gram with negative sampling was selected with the best performance. To evaluate the performance of our approach, we applied it to the dataset composed of 56 748 PubMed abstracts of model organism Arabidopsis thaliana. The experiment results showed that our approach yielded the best performance, as it achieved a 2.588-fold increase in terms of the number of new phenotypic descriptions when compared to the original phenotype ontology.
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17
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Xing W, Qi J, Yuan X, Li L, Zhang X, Fu Y, Xiong S, Hu L, Peng J. A gene-phenotype relationship extraction pipeline from the biomedical literature using a representation learning approach. Bioinformatics 2018; 34:i386-i394. [PMID: 29950017 PMCID: PMC6022650 DOI: 10.1093/bioinformatics/bty263] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Motivation The fundamental challenge of modern genetic analysis is to establish gene-phenotype correlations that are often found in the large-scale publications. Because lexical features of gene are relatively regular in text, the main challenge of these relation extraction is phenotype recognition. Due to phenotypic descriptions are often study- or author-specific, few lexicon can be used to effectively identify the entire phenotypic expressions in text, especially for plants. Results We have proposed a pipeline for extracting phenotype, gene and their relations from biomedical literature. Combined with abbreviation revision and sentence template extraction, we improved the unsupervised word-embedding-to-sentence-embedding cascaded approach as representation learning to recognize the various broad phenotypic information in literature. In addition, the dictionary- and rule-based method was applied for gene recognition. Finally, we integrated one of famous information extraction system OLLIE to identify gene-phenotype relations. To demonstrate the applicability of the pipeline, we established two types of comparison experiment using model organism Arabidopsis thaliana. In the comparison of state-of-the-art baselines, our approach obtained the best performance (F1-Measure of 66.83%). We also applied the pipeline to 481 full-articles from TAIR gene-phenotype manual relationship dataset to prove the validity. The results showed that our proposed pipeline can cover 70.94% of the original dataset and add 373 new relations to expand it. Availability and implementation The source code is available at http://www.wutbiolab.cn: 82/Gene-Phenotype-Relation-Extraction-Pipeline.zip. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Wenhui Xing
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, China
| | - Junsheng Qi
- Department of Plant Science, College of Biological Science, China Agricultural University, Beijing, China
| | - Xiaohui Yuan
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, China
| | - Lin Li
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, China
| | - Xiaoyu Zhang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, China
| | - Yuhua Fu
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, China
| | - Shengwu Xiong
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, China
| | - Lun Hu
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, China
| | - Jing Peng
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, China
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Zhang H, Wang H, Zhu Q, Gao Y, Wang H, Zhao L, Wang Y, Xi F, Wang W, Yang Y, Lin C, Gu L. Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications. BMC PLANT BIOLOGY 2018; 18:125. [PMID: 29925317 PMCID: PMC6011363 DOI: 10.1186/s12870-018-1336-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 05/31/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Moso bamboo (Phyllostachys edulis) is a well-known bamboo species of high economic value in the textile industry due to its rapid growth. Phytohormones, which are master regulators of growth and development, serve as important endogenous signals. However, the mechanisms through which phytohormones regulate growth in moso bamboo remain unknown to date. RESULTS Here, we reported that exogenous gibberellins (GA) applications resulted in a significantly increased internode length and lignin condensation. Transcriptome sequencing revealed that photosynthesis-related genes were enriched in the GA-repressed gene class, which was consistent with the decrease in leaf chlorophyll concentrations and the lower rate of photosynthesis following GA treatment. Exogenous GA applications on seedlings are relatively easy to perform, thus we used 4-week-old whole seedlings of bamboo for GA- treatment followed by high throughput sequencing. In this study, we identified 932 cis-nature antisense transcripts (cis-NATs), and 22,196 alternative splicing (AS) events in total. Among them, 42 cis-nature antisense transcripts (cis-NATs) and 442 AS events were differentially expressed upon exposure to exogenous GA3, suggesting that post-transcriptional regulation might be also involved in the GA3 response. Targets of differential expression of cis-NATs included genes involved in hormone receptor, photosynthesis and cell wall biogenesis. For example, LAC4 and its corresponding cis-NATs were GA3-induced, and may be involved in the accumulation of lignin, thus affecting cell wall composition. CONCLUSIONS This study provides novel insights illustrating how GA alters post-transcriptional regulation and will shed light on the underlying mechanism of growth modulated by GA in moso bamboo.
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Affiliation(s)
- Hangxiao Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Huihui Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Qiang Zhu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yubang Gao
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Huiyuan Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Liangzhen Zhao
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yongsheng Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Feihu Xi
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Wenfei Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yanqiu Yang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Chentao Lin
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Department of Molecular, Cell & Developmental Biology, University of California, CA90095, Los Angeles, USA
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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Liao P, Li S, Cui X, Zheng Y. A comprehensive review of web-based resources of non-coding RNAs for plant science research. Int J Biol Sci 2018; 14:819-832. [PMID: 29989090 PMCID: PMC6036741 DOI: 10.7150/ijbs.24593] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 03/14/2018] [Indexed: 01/06/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are transcribed from genome but not translated into proteins. Many ncRNAs are key regulators of plants growth and development, metabolism and stress tolerance. In order to make the web-based ncRNA resources for plant science research be more easily accessible and understandable, we made a comprehensive review for 83 web-based resources of three types, including genome databases containing ncRNA data, microRNA (miRNA) databases and long non-coding RNA (lncRNA) databases. To facilitate effective usage of these resources, we also suggested some preferred resources of miRNAs and lncRNAs for performing meaningful analysis.
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Affiliation(s)
- Peiran Liao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500,China
| | - Shipeng Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500,China
| | - Xiuming Cui
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500,China
- Yunnan key laboratory of Panax notoginseng, Kunming, Yunnan, 650500, China
| | - Yun Zheng
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
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20
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Ran X, Liu J, Qi M, Wang Y, Cheng J, Zhang Y. GSHR, a Web-Based Platform Provides Gene Set-Level Analyses of Hormone Responses in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:23. [PMID: 29416546 PMCID: PMC5787578 DOI: 10.3389/fpls.2018.00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 01/08/2018] [Indexed: 06/08/2023]
Abstract
Phytohormones regulate diverse aspects of plant growth and environmental responses. Recent high-throughput technologies have promoted a more comprehensive profiling of genes regulated by different hormones. However, these omics data generally result in large gene lists that make it challenging to interpret the data and extract insights into biological significance. With the rapid accumulation of theses large-scale experiments, especially the transcriptomic data available in public databases, a means of using this information to explore the transcriptional networks is needed. Different platforms have different architectures and designs, and even similar studies using the same platform may obtain data with large variances because of the highly dynamic and flexible effects of plant hormones; this makes it difficult to make comparisons across different studies and platforms. Here, we present a web server providing gene set-level analyses of Arabidopsis thaliana hormone responses. GSHR collected 333 RNA-seq and 1,205 microarray datasets from the Gene Expression Omnibus, characterizing transcriptomic changes in Arabidopsis in response to phytohormones including abscisic acid, auxin, brassinosteroids, cytokinins, ethylene, gibberellins, jasmonic acid, salicylic acid, and strigolactones. These data were further processed and organized into 1,368 gene sets regulated by different hormones or hormone-related factors. By comparing input gene lists to these gene sets, GSHR helped to identify gene sets from the input gene list regulated by different phytohormones or related factors. Together, GSHR links prior information regarding transcriptomic changes induced by hormones and related factors to newly generated data and facilities cross-study and cross-platform comparisons; this helps facilitate the mining of biologically significant information from large-scale datasets. The GSHR is freely available at http://bioinfo.sibs.ac.cn/GSHR/.
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Affiliation(s)
- Xiaojuan Ran
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jian Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Meifang Qi
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuejun Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jingfei Cheng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yijing Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
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21
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Ling J, Mao Z, Zhai M, Zeng F, Yang Y, Xie B. Transcriptome profiling of Cucumis metuliferus infected by Meloidogyne incognita provides new insights into putative defense regulatory network in Cucurbitaceae. Sci Rep 2017; 7:3544. [PMID: 28615634 PMCID: PMC5471208 DOI: 10.1038/s41598-017-03563-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 05/02/2017] [Indexed: 12/27/2022] Open
Abstract
Root-knot nematodes (RKN) represent extensive challenges to Cucurbitaceae crops. However, Cucumis metuliferus (Cm) is known to be resistant to Meloidogyne incognita (Mi) infections. Thus, analysis of differentially expressed genes may lead to a comprehensive gene expression profiling of the incompatible Cm-Mi interaction. In this study, the time-course transcriptome of Cm against Mi infection was monitored using RNA-Seq. More than 170000 transcripts were examined in Cm roots, and 2430 genes were subsequently identified as differentially expressed in response to Mi infection. Based on function annotation and orthologs finding, the potential mechanism of transcriptional factor, cytoskeleton, pathogen-related genes and plant hormone were assessed at the transcription level. A comparison of gene expression levels between Mi-infected Cm and cucumber plants revealed that cytoskeleton-related genes are key regulators of Cm resistance to Mi. We herein discuss the dual nature of cytoskeleton-related genes in the susceptibility and resistance of plant hosts to Mi. Our observations provide novel insights into the responses of Cm to Mi at the transcriptome level. The data generated in this study may be useful for elucidating the mechanism underlying resistance to RKNs in cucurbitaceous crops.
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Affiliation(s)
- Jian Ling
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Zhenchuan Mao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Mingjuan Zhai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Feng Zeng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Yuhong Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Bingyan Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China.
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22
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Cunha CP, Roberto GG, Vicentini R, Lembke CG, Souza GM, Ribeiro RV, Machado EC, Lagôa AMMA, Menossi M. Ethylene-induced transcriptional and hormonal responses at the onset of sugarcane ripening. Sci Rep 2017; 7:43364. [PMID: 28266527 PMCID: PMC5339719 DOI: 10.1038/srep43364] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/23/2017] [Indexed: 12/14/2022] Open
Abstract
The effects of ethephon as a sugarcane ripener are attributed to ethylene. However, the role of this phytohormone at the molecular level is unknown. We performed a transcriptome analysis combined with the evaluation of sucrose metabolism and hormone profiling of sugarcane plants sprayed with ethephon or aminoethoxyvinylglycine (AVG), an ethylene inhibitor, at the onset of ripening. The differential response between ethephon and AVG on sucrose level and sucrose synthase activity in internodes indicates ethylene as a potential regulator of sink strength. The correlation between hormone levels and transcriptional changes suggests ethylene as a trigger of multiple hormone signal cascades, with approximately 18% of differentially expressed genes involved in hormone biosynthesis, metabolism, signalling, and response. A defence response elicited in leaves favoured salicylic acid over the ethylene/jasmonic acid pathway, while the upper internode was prone to respond to ethylene with strong stimuli on ethylene biosynthesis and signalling genes. Besides, ethylene acted synergistically with abscisic acid, another ripening factor, and antagonistically with gibberellin and auxin. We identified potential ethylene target genes and characterized the hormonal status during ripening, providing insights into the action of ethylene at the site of sucrose accumulation. A molecular model of ethylene interplay with other hormones is proposed.
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Affiliation(s)
- Camila P. Cunha
- Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, 13083-862, Campinas, Brasil
| | - Guilherme G. Roberto
- Centro de Ecofisiologia e Biofísica, Instituto Agronômico de Campinas, 13001-970, Campinas, Brasil
| | - Renato Vicentini
- Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, 13083-862, Campinas, Brasil
| | - Carolina G. Lembke
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-000, São Paulo, Brasil
| | - Glaucia M. Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-000, São Paulo, Brasil
| | - Rafael V. Ribeiro
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, 13083-862, Campinas, Brasil
| | - Eduardo C. Machado
- Centro de Ecofisiologia e Biofísica, Instituto Agronômico de Campinas, 13001-970, Campinas, Brasil
| | - Ana M. M. A. Lagôa
- Centro de Ecofisiologia e Biofísica, Instituto Agronômico de Campinas, 13001-970, Campinas, Brasil
| | - Marcelo Menossi
- Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, 13083-862, Campinas, Brasil
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23
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Jian H, Yang B, Zhang A, Zhang L, Xu X, Li J, Liu L. Screening of Candidate Leaf Morphology Genes by Integration of QTL Mapping and RNA Sequencing Technologies in Oilseed Rape (Brassica napus L.). PLoS One 2017; 12:e0169641. [PMID: 28068426 PMCID: PMC5222374 DOI: 10.1371/journal.pone.0169641] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 12/20/2016] [Indexed: 11/30/2022] Open
Abstract
Leaf size and shape play important roles in agronomic traits, such as yield, quality and stress responses. Wide variations in leaf morphological traits exist in cultivated varieties of many plant species. By now, the genetics of leaf shape and size have not been characterized in Brassica napus. In this study, a population of 172 recombinant inbred lines (RILs) was used for quantitative trait locus (QTL) analysis of leaf morphology traits. Furthermore, fresh young leaves of extreme lines with more leaf lobes (referred to as ‘A’) and extreme lines with fewer lobes (referred to as ‘B’) selected from the RIL population and leaves of dissected lines (referred to as ‘P’) were used for transcriptional analysis. A total of 31 QTLs for the leaf morphological traits tested in this study were identified on 12 chromosomes, explaining 5.32–39.34% of the phenotypic variation. There were 8, 6, 2, 5, 8, and 2 QTLs for PL (petiole length), PN (lobe number), LW (lamina width), LL (Lamina length), LL/LTL (the lamina size ratio) and LTL (leaf total length), respectively. In addition, 74, 1,166 and 1,272 differentially expressed genes (DEGs) were identified in ‘A vs B’, ‘A vs P’ and ‘B vs P’ comparisons, respectively. The Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were used to predict the functions of these DEGs. Gene regulators of leaf shape and size, such as ASYMMETRIC LEAVES 2, gibberellin 20-oxidase 3, genes encoding gibberellin-regulated family protein, genes encoding growth-regulating factor and KNOTTED1-like homeobox were also detected in DEGs. After integrating the QTL mapping and RNA sequencing data, 33 genes, including a gene encoding auxin-responsive GH3 family protein and a gene encoding sphere organelles protein-related gene, were selected as candidates that may control leaf shape. Our findings should be valuable for studies of the genetic control of leaf morphological trait regulation in B. napus.
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Affiliation(s)
- Hongju Jian
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, P. R. China
| | - Bo Yang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, P. R. China
| | - Aoxiang Zhang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, P. R. China
| | - Li Zhang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, P. R. China
| | - Xinfu Xu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, P. R. China
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, P. R. China
| | - Liezhao Liu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, P. R. China
- * E-mail:
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24
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Simm S, Scharf KD, Jegadeesan S, Chiusano ML, Firon N, Schleiff E. Survey of Genes Involved in Biosynthesis, Transport, and Signaling of Phytohormones with Focus on Solanum lycopersicum. Bioinform Biol Insights 2016; 10:185-207. [PMID: 27695302 PMCID: PMC5038615 DOI: 10.4137/bbi.s38425] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/15/2016] [Accepted: 08/16/2016] [Indexed: 12/19/2022] Open
Abstract
Phytohormones control the development and growth of plants, as well as their response to biotic and abiotic stress. The seven most well-studied phytohormone classes defined today are as follows: auxins, ethylene, cytokinin, abscisic acid, jasmonic acid, gibberellins, and brassinosteroids. The basic principle of hormone regulation is conserved in all plants, but recent results suggest adaptations of synthesis, transport, or signaling pathways to the architecture and growth environment of different plant species. Thus, we aimed to define the extent to which information from the model plant Arabidopsis thaliana is transferable to other plants such as Solanum lycopersicum. We extracted the co-orthologues of genes coding for major pathway enzymes in A. thaliana from the translated genomes of 12 species from the clade Viridiplantae. Based on predicted domain architecture and localization of the identified proteins from all 13 species, we inspected the conservation of phytohormone pathways. The comparison was complemented by expression analysis of (co-) orthologous genes in S. lycopersicum. Altogether, this information allowed the assignment of putative functional equivalents between A. thaliana and S. lycopersicum but also pointed to some variations between the pathways in eudicots, monocots, mosses, and green algae. These results provide first insights into the conservation of the various phytohormone pathways between the model system A. thaliana and crop plants such as tomato. We conclude that orthologue prediction in combination with analysis of functional domain architecture and intracellular localization and expression studies are sufficient tools to transfer information from model plants to other plant species. Our results support the notion that hormone synthesis, transport, and response for most part of the pathways are conserved, and species-specific variations can be found.
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Affiliation(s)
- Stefan Simm
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany.; Cluster of Excellence Macromolecular Complexes, Institute for Molecular Cell Biology of Plants, Frankfurt am Main, Germany
| | - Klaus-Dieter Scharf
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany.; Cluster of Excellence Macromolecular Complexes, Institute for Molecular Cell Biology of Plants, Frankfurt am Main, Germany
| | - Sridharan Jegadeesan
- Department of Vegetable Research, Institute for Plant Sciences, Agricultural Research Organization, Volcani Centre, Bet Dagan, Israel.; The Robert H. Smith Faculty of Agriculture, Food and Environment, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Maria Luisa Chiusano
- Department of Soil, Plants Environmental and Animal Production Sciences, Laboratory of Computer Aided Biosciences, University of Studies of Naples Federico II, Portici, Naples, Italy
| | - Nurit Firon
- Department of Vegetable Research, Institute for Plant Sciences, Agricultural Research Organization, Volcani Centre, Bet Dagan, Israel
| | - Enrico Schleiff
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany.; Cluster of Excellence Macromolecular Complexes, Institute for Molecular Cell Biology of Plants, Frankfurt am Main, Germany
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25
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Yue X, Li XG, Gao XQ, Zhao XY, Dong YX, Zhou C. The Arabidopsis phytohormone crosstalk network involves a consecutive metabolic route and circular control units of transcription factors that regulate enzyme-encoding genes. BMC SYSTEMS BIOLOGY 2016; 10:87. [PMID: 27590055 PMCID: PMC5009710 DOI: 10.1186/s12918-016-0333-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 08/25/2016] [Indexed: 01/26/2023]
Abstract
Background Phytohormone synergies and signaling interdependency are important topics in plant developmental biology. Physiological and genetic experimental evidence for phytohormone crosstalk has been accumulating and a genome-scale enzyme correlation model representing the Arabidopsis metabolic pathway has been published. However, an integrated molecular characterization of phytohormone crosstalk is still not available. Results A novel modeling methodology and advanced computational approaches were used to construct an enzyme-based Arabidopsis phytohormone crosstalk network (EAPCN) at the biosynthesis level. The EAPCN provided the structural connectivity architecture of phytohormone biosynthesis pathways and revealed a surprising result; that enzymes localized at the highly connected nodes formed a consecutive metabolic route. Furthermore, our analysis revealed that the transcription factors (TFs) that regulate enzyme-encoding genes in the consecutive metabolic route formed structures, which we describe as circular control units operating at the transcriptional level. Furthermore, the downstream TFs in phytohormone signal transduction pathways were found to be involved in the circular control units that included the TFs regulating enzyme-encoding genes. In addition, multiple functional enzymes in the EAPCN were found to be involved in ion and pH homeostasis, environmental signal perception, cellular redox homeostasis, and circadian clocks. Last, publicly available transcriptional profiles and a protein expression map of the Arabidopsis root apical meristem were used as a case study to validate the proposed framework. Conclusions Our results revealed multiple scales of coupled mechanisms in that hormonal crosstalk networks that play a central role in coordinating internal developmental processes with environmental signals, and give a broader view of Arabidopsis phytohormone crosstalk. We also uncovered potential key regulators that can be further analyzed in future studies. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0333-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xun Yue
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China. .,State Key Laboratory of Crop Biology, College of Information Sciences and Engineering, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
| | - Xing Guo Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Xin-Qi Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Xiang Yu Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yu Xiu Dong
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Chao Zhou
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
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26
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Davin N, Edger PP, Hefer CA, Mizrachi E, Schuetz M, Smets E, Myburg AA, Douglas CJ, Schranz ME, Lens F. Functional network analysis of genes differentially expressed during xylogenesis in soc1ful woody Arabidopsis plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:376-90. [PMID: 26952251 DOI: 10.1111/tpj.13157] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 02/29/2016] [Accepted: 03/03/2016] [Indexed: 05/21/2023]
Abstract
Many plant genes are known to be involved in the development of cambium and wood, but how the expression and functional interaction of these genes determine the unique biology of wood remains largely unknown. We used the soc1ful loss of function mutant - the woodiest genotype known in the otherwise herbaceous model plant Arabidopsis - to investigate the expression and interactions of genes involved in secondary growth (wood formation). Detailed anatomical observations of the stem in combination with mRNA sequencing were used to assess transcriptome remodeling during xylogenesis in wild-type and woody soc1ful plants. To interpret the transcriptome changes, we constructed functional gene association networks of differentially expressed genes using the STRING database. This analysis revealed functionally enriched gene association hubs that are differentially expressed in herbaceous and woody tissues. In particular, we observed the differential expression of genes related to mechanical stress and jasmonate biosynthesis/signaling during wood formation in soc1ful plants that may be an effect of greater tension within woody tissues. Our results suggest that habit shifts from herbaceous to woody life forms observed in many angiosperm lineages could have evolved convergently by genetic changes that modulate the gene expression and interaction network, and thereby redeploy the conserved wood developmental program.
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Affiliation(s)
- Nicolas Davin
- Naturalis Biodiversity Center, Leiden University, PO Box 9517, 2300 RA Leiden, The Netherlands
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48823, USA
| | - Charles A Hefer
- Department of Botany, University of British Columbia, Department of Botany, 6270 University Blvd, Vancouver BC V6T 1Z4, Canada
- Biotechnology Platform, Agricultural Research Council, Private Bag X5, Onderstepoort, 0110, South Africa
| | - Eshchar Mizrachi
- Department of Genetics, University of Pretoria, PO Box X20, Pretoria, 0028, South Africa
- Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Mathias Schuetz
- Department of Botany, University of British Columbia, Department of Botany, 6270 University Blvd, Vancouver BC V6T 1Z4, Canada
- Michael Smith Laboratories, University of British Columbia, 6270 University boulevard, V6T 1Z4, Vancouver, BC, Canada
| | - Erik Smets
- Naturalis Biodiversity Center, Leiden University, PO Box 9517, 2300 RA Leiden, The Netherlands
- Ecology, Evolution and Biodiversity Conservation Section, Katholieke Universiteit Leuven, Kasteelpark Arenberg 31 box 2435, 3001 Leuven, Belgium
| | - Alexander A Myburg
- Department of Genetics, University of Pretoria, PO Box X20, Pretoria, 0028, South Africa
- Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Carl J Douglas
- Department of Botany, University of British Columbia, Department of Botany, 6270 University Blvd, Vancouver BC V6T 1Z4, Canada
| | - Michael E Schranz
- Biosystematics Group, Wageningen University, PO Box 16, 6700AP Wageningen, The Netherlands
| | - Frederic Lens
- Naturalis Biodiversity Center, Leiden University, PO Box 9517, 2300 RA Leiden, The Netherlands
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Tolerant and Susceptible Sesame Genotypes Reveal Waterlogging Stress Response Patterns. PLoS One 2016; 11:e0149912. [PMID: 26934874 PMCID: PMC4774966 DOI: 10.1371/journal.pone.0149912] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 02/06/2016] [Indexed: 02/07/2023] Open
Abstract
Waterlogging is a common adverse environmental condition that limits plant growth. Sesame (Sesamum indicum) is considered a drought-tolerant oil crop but is typically susceptible to harmful effects from waterlogging. The present study used comparative analysis to explore the waterlogging stress response associated with two sesame genotypes. The RNA-seq dataset generated during a time course of 0, 3, 9 and 15 h of waterlogging as well as 20 h post-drainage indicated that stress gradually suppressed the expression of sesame genes, with 9 h as the critical time point for the response of sesame to waterlogging stress. Of the 19,316 genes expressed during waterlogging, 72.1% were affected significantly. Sesame of both tolerant and susceptible genotypes showed decreased numbers of upregulated differentially expressed genes (DEGs) but increased numbers of downregulated DEGs at the onset of waterlogging. However, the tolerant-genotype sesame exhibited 25.5% more upregulated DEGs and 29.7% fewer downregulated DEGs than those of the susceptible-genotype strain between 3 and 15 h. The results indicated that the tolerant sesame displayed a more positive gene response to waterlogging. A total of 1,379 genes were significantly induced and commonly expressed in sesame under waterlogging conditions from 3 to 15 h regardless of tolerance level; of these genes, 98 are known homologous stress responsive genes, while the remaining 1,281 are newly reported here. This gene set may represent the core genes that function in response to waterlogging, including those related mainly to energy metabolism and phenylpropanoid biosynthesis. Furthermore, a set of 3,016 genes functioning in energy supply and cell repair or formation was activated in sesame recovery from waterlogging stress. A comparative analysis between sesame of the tolerant and susceptible genotypes revealed 66 genes that may be candidates for improving sesame tolerance to waterlogging. This study provided a comprehensive picture of the sesame gene expression pattern in response to waterlogging stress. These results will help dissect the mechanism of the sesame response to waterlogging and identify candidate genes to improve its tolerance.
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Network-Based Comparative Analysis of Arabidopsis Immune Responses to Golovinomyces orontii and Botrytis cinerea Infections. Sci Rep 2016; 6:19149. [PMID: 26750561 PMCID: PMC4707498 DOI: 10.1038/srep19149] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 12/07/2015] [Indexed: 12/14/2022] Open
Abstract
A comprehensive exploration of common and specific plant responses to biotrophs and necrotrophs is necessary for a better understanding of plant immunity. Here, we compared the Arabidopsis defense responses evoked by the biotrophic fungus Golovinomyces orontii and the necrotrophic fungus Botrytis cinerea through integrative network analysis. Two time-course transcriptional datasets were integrated with an Arabidopsis protein-protein interaction (PPI) network to construct a G. orontii conditional PPI sub-network (gCPIN) and a B. cinerea conditional PPI sub-network (bCPIN). We found that hubs in gCPIN and bCPIN played important roles in disease resistance. Hubs in bCPIN evolved faster than hubs in gCPIN, indicating the different selection pressures imposed on plants by different pathogens. By analyzing the common network from gCPIN and bCPIN, we identified two network components in which the genes were heavily involved in defense and development, respectively. The co-expression relationships between interacting proteins connecting the two components were different under G. orontii and B. cinerea infection conditions. Closer inspection revealed that auxin-related genes were overrepresented in the interactions connecting these two components, suggesting a critical role of auxin signaling in regulating the different co-expression relationships. Our work may provide new insights into plant defense responses against pathogens with different lifestyles.
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Fang J, Lin A, Qiu W, Cai H, Umar M, Chen R, Ming R. Transcriptome Profiling Revealed Stress-Induced and Disease Resistance Genes Up-Regulated in PRSV Resistant Transgenic Papaya. FRONTIERS IN PLANT SCIENCE 2016; 7:855. [PMID: 27379138 PMCID: PMC4909764 DOI: 10.3389/fpls.2016.00855] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 05/31/2016] [Indexed: 05/18/2023]
Abstract
Papaya is a productive and nutritious tropical fruit. Papaya Ringspot Virus (PRSV) is the most devastating pathogen threatening papaya production worldwide. Development of transgenic resistant varieties is the most effective strategy to control this disease. However, little is known about the genome-wide functional changes induced by particle bombardment transformation. We conducted transcriptome sequencing of PRSV resistant transgenic papaya SunUp and its PRSV susceptible progenitor Sunset to compare the transcriptional changes in young healthy leaves prior to infection with PRSV. In total, 20,700 transcripts were identified, and 842 differentially expressed genes (DEGs) randomly distributed among papaya chromosomes. Gene ontology (GO) category analysis revealed that microtubule-related categories were highly enriched among these DEGs. Numerous DEGs related to various transcription factors, transporters and hormone biosynthesis showed clear differences between the two cultivars, and most were up-regulated in transgenic papaya. Many known and novel stress-induced and disease-resistance genes were most highly expressed in SunUp, including MYB, WRKY, ERF, NAC, nitrate and zinc transporters, and genes involved in the abscisic acid, salicylic acid, and ethylene signaling pathways. We also identified 67,686 alternative splicing (AS) events in Sunset and 68,455 AS events in SunUp, mapping to 10,994 and 10,995 papaya annotated genes, respectively. GO enrichment for the genes displaying AS events exclusively in Sunset was significantly different from those in SunUp. Transcriptomes in Sunset and transgenic SunUp are very similar with noteworthy differences, which increased PRSV-resistance in transgenic papaya. No detrimental pathways and allergenic or toxic proteins were induced on a genome-wide scale in transgenic SunUp. Our results provide a foundation for unraveling the mechanism of PRSV resistance in transgenic papaya.
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Affiliation(s)
- Jingping Fang
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry UniversityFuzhou, China
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Aiting Lin
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Weijing Qiu
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Hanyang Cai
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Muhammad Umar
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Rukai Chen
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Ray Ming
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry UniversityFuzhou, China
- Department of Plant Biology, University of Illinois at Urbana-ChampaignUrbana, IL, USA
- *Correspondence: Ray Ming
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Dai X, Li J, Liu T, Zhao PX. HRGRN: A Graph Search-Empowered Integrative Database of Arabidopsis Signaling Transduction, Metabolism and Gene Regulation Networks. PLANT & CELL PHYSIOLOGY 2016; 57:e12. [PMID: 26657893 PMCID: PMC4722177 DOI: 10.1093/pcp/pcv200] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/07/2015] [Indexed: 05/10/2023]
Abstract
The biological networks controlling plant signal transduction, metabolism and gene regulation are composed of not only tens of thousands of genes, compounds, proteins and RNAs but also the complicated interactions and co-ordination among them. These networks play critical roles in many fundamental mechanisms, such as plant growth, development and environmental response. Although much is known about these complex interactions, the knowledge and data are currently scattered throughout the published literature, publicly available high-throughput data sets and third-party databases. Many 'unknown' yet important interactions among genes need to be mined and established through extensive computational analysis. However, exploring these complex biological interactions at the network level from existing heterogeneous resources remains challenging and time-consuming for biologists. Here, we introduce HRGRN, a graph search-empowered integrative database of Arabidopsis signal transduction, metabolism and gene regulatory networks. HRGRN utilizes Neo4j, which is a highly scalable graph database management system, to host large-scale biological interactions among genes, proteins, compounds and small RNAs that were either validated experimentally or predicted computationally. The associated biological pathway information was also specially marked for the interactions that are involved in the pathway to facilitate the investigation of cross-talk between pathways. Furthermore, HRGRN integrates a series of graph path search algorithms to discover novel relationships among genes, compounds, RNAs and even pathways from heterogeneous biological interaction data that could be missed by traditional SQL database search methods. Users can also build subnetworks based on known interactions. The outcomes are visualized with rich text, figures and interactive network graphs on web pages. The HRGRN database is freely available at http://plantgrn.noble.org/hrgrn/.
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Affiliation(s)
- Xinbin Dai
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Jun Li
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Tingsong Liu
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Patrick Xuechun Zhao
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
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Sun P, Xiao X, Duan L, Guo Y, Qi J, Liao D, Zhao C, Liu Y, Zhou L, Li X. Dynamic transcriptional profiling provides insights into tuberous root development in Rehmannia glutinosa. FRONTIERS IN PLANT SCIENCE 2015; 6:396. [PMID: 26113849 PMCID: PMC4461823 DOI: 10.3389/fpls.2015.00396] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 05/18/2015] [Indexed: 05/04/2023]
Abstract
Rehmannia glutinosa, an herb of the Scrophulariaceae family, is widely cultivated in the Northern part of China. The tuberous root has well-known medicinal properties; however, yield and quality are threatened by abiotic and biotic stresses. Understanding the molecular process of tuberous root development may help identify novel targets for its control. In the present study, we used Illumina sequencing and de novo assembly strategies to obtain a reference transcriptome that is relevant to tuberous root development. We then conducted RNA-seq quantification analysis to determine gene expression profiles of the adventitious root (AR), thickening adventitious root (TAR), and the developing tuberous root (DTR). Expression profiling identified a total of 6794 differentially expressed unigenes during root development. Bioinformatics analysis and gene expression profiling revealed changes in phenylpropanoid biosynthesis, starch and sucrose metabolism, and plant hormone biosynthesis during root development. Moreover, we identified and allocated putative functions to the genes involved in tuberous root development, including genes related to major carbohydrate metabolism, hormone metabolism, and transcription regulation. The present study provides the initial description of gene expression profiles of AR, TAR, and DTR, which facilitates identification of genes of interest. Moreover, our work provides insights into the molecular mechanisms underlying tuberous root development and may assist in the design and development of improved breeding schemes for different R. glutinosa varieties through genetic manipulation.
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Affiliation(s)
- Peng Sun
- Center for Medicinal Plant Cultivation, Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical SciencesBeijing, China
| | - Xingguo Xiao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural UniversityBeijing, China
| | - Liusheng Duan
- Department of Agronomy, College of Agriculture and Biotechnology, China Agricultural UniversityBeijing, China
| | - Yuhai Guo
- Department of Agronomy, College of Agriculture and Biotechnology, China Agricultural UniversityBeijing, China
| | - Jianjun Qi
- Center for Medicinal Plant Cultivation, Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical SciencesBeijing, China
| | - Dengqun Liao
- Center for Medicinal Plant Cultivation, Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical SciencesBeijing, China
| | - Chunli Zhao
- Center for Medicinal Plant Cultivation, Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical SciencesBeijing, China
| | - Yan Liu
- Center for Medicinal Plant Cultivation, Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical SciencesBeijing, China
| | - Lili Zhou
- Center for Medicinal Plant Cultivation, Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical SciencesBeijing, China
| | - Xianen Li
- Center for Medicinal Plant Cultivation, Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical SciencesBeijing, China
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32
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Amrine KCH, Blanco-Ulate B, Cantu D. Discovery of core biotic stress responsive genes in Arabidopsis by weighted gene co-expression network analysis. PLoS One 2015; 10:e0118731. [PMID: 25730421 PMCID: PMC4346582 DOI: 10.1371/journal.pone.0118731] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Accepted: 01/08/2015] [Indexed: 01/26/2023] Open
Abstract
Intricate signal networks and transcriptional regulators translate the recognition of pathogens into defense responses. In this study, we carried out a gene co-expression analysis of all currently publicly available microarray data, which were generated in experiments that studied the interaction of the model plant Arabidopsis thaliana with microbial pathogens. This work was conducted to identify (i) modules of functionally related co-expressed genes that are differentially expressed in response to multiple biotic stresses, and (ii) hub genes that may function as core regulators of disease responses. Using Weighted Gene Co-expression Network Analysis (WGCNA) we constructed an undirected network leveraging a rich curated expression dataset comprising 272 microarrays that involved microbial infections of Arabidopsis plants with a wide array of fungal and bacterial pathogens with biotrophic, hemibiotrophic, and necrotrophic lifestyles. WGCNA produced a network with scale-free and small-world properties composed of 205 distinct clusters of co-expressed genes. Modules of functionally related co-expressed genes that are differentially regulated in response to multiple pathogens were identified by integrating differential gene expression testing with functional enrichment analyses of gene ontology terms, known disease associated genes, transcriptional regulators, and cis-regulatory elements. The significance of functional enrichments was validated by comparisons with randomly generated networks. Network topology was then analyzed to identify intra- and inter-modular gene hubs. Based on high connectivity, and centrality in meta-modules that are clearly enriched in defense responses, we propose a list of 66 target genes for reverse genetic experiments to further dissect the Arabidopsis immune system. Our results show that statistical-based data trimming prior to network analysis allows the integration of expression datasets generated by different groups, under different experimental conditions and biological systems, into a functionally meaningful co-expression network.
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Affiliation(s)
- Katherine C. H. Amrine
- Department of Viticulture and Enology, University of California Davis, Davis, California, United States of America
| | - Barbara Blanco-Ulate
- Department of Viticulture and Enology, University of California Davis, Davis, California, United States of America
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, California, United States of America
- * E-mail:
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Zaag R, Tamby JP, Guichard C, Tariq Z, Rigaill G, Delannoy E, Renou JP, Balzergue S, Mary-Huard T, Aubourg S, Martin-Magniette ML, Brunaud V. GEM2Net: from gene expression modeling to -omics networks, a new CATdb module to investigate Arabidopsis thaliana genes involved in stress response. Nucleic Acids Res 2014; 43:D1010-7. [PMID: 25392409 PMCID: PMC4383956 DOI: 10.1093/nar/gku1155] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
CATdb (http://urgv.evry.inra.fr/CATdb) is a database providing a public access to a large collection of transcriptomic data, mainly for Arabidopsis but also for other plants. This resource has the rare advantage to contain several thousands of microarray experiments obtained with the same technical protocol and analyzed by the same statistical pipelines. In this paper, we present GEM2Net, a new module of CATdb that takes advantage of this homogeneous dataset to mine co-expression units and decipher Arabidopsis gene functions. GEM2Net explores 387 stress conditions organized into 18 biotic and abiotic stress categories. For each one, a model-based clustering is applied on expression differences to identify clusters of co-expressed genes. To characterize functions associated with these clusters, various resources are analyzed and integrated: Gene Ontology, subcellular localization of proteins, Hormone Families, Transcription Factor Families and a refined stress-related gene list associated to publications. Exploiting protein–protein interactions and transcription factors-targets interactions enables to display gene networks. GEM2Net presents the analysis of the 18 stress categories, in which 17 264 genes are involved and organized within 681 co-expression clusters. The meta-data analyses were stored and organized to compose a dynamic Web resource.
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Affiliation(s)
- Rim Zaag
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Jean Philippe Tamby
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Cécile Guichard
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Zakia Tariq
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Guillem Rigaill
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Etienne Delannoy
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Jean-Pierre Renou
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Sandrine Balzergue
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Tristan Mary-Huard
- INRA, UMR 518 MIA, 75005 Paris, France AgroParisTech, UMR 518 MIA, 75005 Paris, France UMRGV, INRA, Université Paris-Sud, CNRS, F-91190 Gif-sur-Yvette, Paris, France
| | - Sébastien Aubourg
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Marie-Laure Martin-Magniette
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France INRA, UMR 518 MIA, 75005 Paris, France AgroParisTech, UMR 518 MIA, 75005 Paris, France
| | - Véronique Brunaud
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
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Zhang J, Jiang D, Liu B, Luo W, Lu J, Ma T, Wan D. Transcriptome dynamics of a desert poplar (Populus pruinosa) in response to continuous salinity stress. PLANT CELL REPORTS 2014; 33:1565-79. [PMID: 24913126 DOI: 10.1007/s00299-014-1638-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 05/19/2014] [Accepted: 05/20/2014] [Indexed: 05/05/2023]
Abstract
Using RNA sequencing analysis, we identified 9,216 regulatory and salt-related genes with differential expression and temporal expression trends which provide a clear picture of transcriptomic dynamics in response to continuous salinity stress in a desert poplar, Populus pruinosa. Populus pruinosa Schrenk is native to the desert region of western China and extraordinarily well adapted to the local salt stress. Thus, it is an ideal model for studying plants' adaptation to salt stress, but its transcriptomic responses have not been previously characterized. Thus, we analyzed time- courses of these responses via a series of sequencings. In total, we generated 157.4 million 100 bp paired-end clean reads and identified 9,216 differentially expressed genes (DEGs) between salt-stressed calli and controls. Gene ontology classification analysis revealed that salt stress-related categories--including 'oxidation reduction', 'transcription factor activity', 'membrane' and 'ion channel activity'--were highly enriched among these DEGs. In addition, we grouped the 9,216 DEGs by their expression dynamics into four clusters, and the genes in each cluster showed enrichment for particular functional categories. We also found that most DEGs were activated within 24 h of the stress and their expression stabilized after 48 h. All these findings suggest that gene expression rapidly and coordinately changes during this species' adaptation to salt stress. In addition, the identified DEGs provide critical genetic resources for further functional analyses and indications of potential transgenic modifications for developing salt-tolerant poplars.
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Affiliation(s)
- Jian Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000, Gansu, China
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Ding YD, Chang JW, Guo J, Chen D, Li S, Xu Q, Deng XX, Cheng YJ, Chen LL. Prediction and functional analysis of the sweet orange protein-protein interaction network. BMC PLANT BIOLOGY 2014; 14:213. [PMID: 25091279 PMCID: PMC4236729 DOI: 10.1186/s12870-014-0213-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 07/24/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND Sweet orange (Citrus sinensis) is one of the most important fruits world-wide. Because it is a woody plant with a long growth cycle, genetic studies of sweet orange are lagging behind those of other species. RESULTS In this analysis, we employed ortholog identification and domain combination methods to predict the protein-protein interaction (PPI) network for sweet orange. The K-nearest neighbors (KNN) classification method was used to verify and filter the network. The final predicted PPI network, CitrusNet, contained 8,195 proteins with 124,491 interactions. The quality of CitrusNet was evaluated using gene ontology (GO) and Mapman annotations, which confirmed the reliability of the network. In addition, we calculated the expression difference of interacting genes (EDI) in CitrusNet using RNA-seq data from four sweet orange tissues, and also analyzed the EDI distribution and variation in different sub-networks. CONCLUSIONS Gene expression in CitrusNet has significant modular features. Target of rapamycin (TOR) protein served as the central node of the hormone-signaling sub-network. All evidence supported the idea that TOR can integrate various hormone signals and affect plant growth. CitrusNet provides valuable resources for the study of biological functions in sweet orange.
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Affiliation(s)
- Yu-Duan Ding
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - Ji-Wei Chang
- Agricultural Bioinformatics Key laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - Jing Guo
- Agricultural Bioinformatics Key laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - DiJun Chen
- Agricultural Bioinformatics Key laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - Sen Li
- Agricultural Bioinformatics Key laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - Xiu-Xin Deng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - Yun-Jiang Cheng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - Ling-Ling Chen
- Agricultural Bioinformatics Key laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
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36
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Wang Q, Ma B, Qi X, Guo Q, Wang X, Zeng Q, He N. Identification and characterization of genes involved in the jasmonate biosynthetic and signaling pathways in mulberry (Morus notabilis). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:663-672. [PMID: 24428303 DOI: 10.1111/jipb.12166] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 01/13/2014] [Indexed: 06/03/2023]
Abstract
Jasmonate (JA) is an important phytohormone regulating growth, development, and environmental response in plants, particularly defense response against herbivorous insects. Recently, completion of the draft genome of the mulberry (Morus notabilis) in conjunction with genome sequencing of silkworm (Bombyx mori) provides an opportunity to study this unique plant-herbivore interaction. Here, we identified genes involved in JA biosynthetic and signaling pathways in the genome of mulberry for the first time, with the majority of samples showing a tissue-biased expression pattern. The analysis of the representative genes 12-oxophytodienoic acid reductase (OPRs) and jasmonate ZIM-domain (JAZs) was performed and the results indicated that the mulberry genome contains a relatively small number of JA biosynthetic and signaling pathway genes. A gene encoding an important repressor, MnNINJA, was identified as an alternative splicing variant lacking an ethylene-responsive element binding factor-associated amphiphilic repression motif. Having this fundamental information will facilitate future functional study of JA-related genes pertaining to mulberry-silkworm interactions.
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Affiliation(s)
- Qing Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China
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Jones AM, Xuan Y, Xu M, Wang RS, Ho CH, Lalonde S, You CH, Sardi MI, Parsa SA, Smith-Valle E, Su T, Frazer KA, Pilot G, Pratelli R, Grossmann G, Acharya BR, Hu HC, Engineer C, Villiers F, Ju C, Takeda K, Su Z, Dong Q, Assmann SM, Chen J, Kwak JM, Schroeder JI, Albert R, Rhee SY, Frommer WB. Border Control--A Membrane-Linked Interactome of Arabidopsis. Science 2014; 344:711-6. [DOI: 10.1126/science.1251358] [Citation(s) in RCA: 162] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Choi D, Choi J, Kang B, Lee S, Cho YH, Hwang I, Hwang D. iNID: an analytical framework for identifying network models for interplays among developmental signaling in Arabidopsis. MOLECULAR PLANT 2014; 7:792-813. [PMID: 24380880 DOI: 10.1093/mp/sst173] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Integration of internal and external cues into developmental programs is indispensable for growth and development of plants, which involve complex interplays among signaling pathways activated by the internal and external factors (IEFs). However, decoding these complex interplays is still challenging. Here, we present a web-based platform that identifies key regulators and Network models delineating Interplays among Developmental signaling (iNID) in Arabidopsis. iNID provides a comprehensive resource of (1) transcriptomes previously collected under the conditions treated with a broad spectrum of IEFs and (2) protein and genetic interactome data in Arabidopsis. In addition, iNID provides an array of tools for identifying key regulators and network models related to interplays among IEFs using transcriptome and interactome data. To demonstrate the utility of iNID, we investigated the interplays of (1) phytohormones and light and (2) phytohormones and biotic stresses. The results revealed 34 potential regulators of the interplays, some of which have not been reported in association with the interplays, and also network models that delineate the involvement of the 34 regulators in the interplays, providing novel insights into the interplays collectively defined by phytohormones, light, and biotic stresses. We then experimentally verified that BME3 and TEM1, among the selected regulators, are involved in the auxin-brassinosteroid (BR)-blue light interplay. Therefore, iNID serves as a useful tool to provide a basis for understanding interplays among IEFs.
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Affiliation(s)
- Daeseok Choi
- School of Interdisciplinary Bioscience and Bioengineering, POSTECH, 790-784, Pohang, Republic of Korea
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Shaik R, Ramakrishna W. Machine learning approaches distinguish multiple stress conditions using stress-responsive genes and identify candidate genes for broad resistance in rice. PLANT PHYSIOLOGY 2014; 164:481-95. [PMID: 24235132 PMCID: PMC3875824 DOI: 10.1104/pp.113.225862] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 11/13/2013] [Indexed: 05/18/2023]
Abstract
Abiotic and biotic stress responses are traditionally thought to be regulated by discrete signaling mechanisms. Recent experimental evidence revealed a more complex picture where these mechanisms are highly entangled and can have synergistic and antagonistic effects on each other. In this study, we identified shared stress-responsive genes between abiotic and biotic stresses in rice (Oryza sativa) by performing meta-analyses of microarray studies. About 70% of the 1,377 common differentially expressed genes showed conserved expression status, and the majority of the rest were down-regulated in abiotic stresses and up-regulated in biotic stresses. Using dimension reduction techniques, principal component analysis, and partial least squares discriminant analysis, we were able to segregate abiotic and biotic stresses into separate entities. The supervised machine learning model, recursive-support vector machine, could classify abiotic and biotic stresses with 100% accuracy using a subset of differentially expressed genes. Furthermore, using a random forests decision tree model, eight out of 10 stress conditions were classified with high accuracy. Comparison of genes contributing most to the accurate classification by partial least squares discriminant analysis, recursive-support vector machine, and random forests revealed 196 common genes with a dynamic range of expression levels in multiple stresses. Functional enrichment and coexpression network analysis revealed the different roles of transcription factors and genes responding to phytohormones or modulating hormone levels in the regulation of stress responses. We envisage the top-ranked genes identified in this study, which highly discriminate abiotic and biotic stresses, as key components to further our understanding of the inherently complex nature of multiple stress responses in plants.
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Kushwah S, Laxmi A. The interaction between glucose and cytokinin signal transduction pathway in Arabidopsis thaliana. PLANT, CELL & ENVIRONMENT 2014; 37:235-53. [PMID: 23763631 DOI: 10.1111/pce.12149] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Accepted: 05/20/2013] [Indexed: 05/07/2023]
Abstract
Cytokinins (CKs) and glucose (GLC) control a number of common responses in plants. We hypothesize that there may be an extensive overlap between CK- and GLC-signalling pathways. Microarray along with physiological analysis has been performed to find out the interdependence/overlap between CK and GLC signal transduction pathways in Arabidopsis seedlings. GLC could transcriptionally affect 76% of CK-regulated genes at whole genome level, 89% of which are agonistically regulated. GLC may also affect CK-regulated gene expression via non-transcriptional pathways. GLC can regulate several genes involved in CK metabolism and signalling. A number of gene families involved in development and stress are commonly regulated by CK and GLC. Physiologically, both GLC and CK could regulate hypocotyl length in dark. GLC and CK signalling may integrate at the level of type A Arabidopsis response regulators (ARRs) in controlling hypocotyl length. Both GLC and CK signalling cannot alter hypocotyl length in dark in auxin-signalling mutants auxin response2/indole-3-acetic acid7 (AXR2/IAA7) and AXR3/IAA17 suggesting that they may involve auxin-signalling component as a nodal point. Here, we demonstrate that there is an extensive overlap between CK- and GLC-regulated gene expression and physiological responses.
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Affiliation(s)
- Sunita Kushwah
- National Institute of Plant Genome Research, Aruna Asaf Ali Road, New Delhi, 110067, India
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Kudo T, Akiyama K, Kojima M, Makita N, Sakurai T, Sakakibara H. UniVIO: a multiple omics database with hormonome and transcriptome data from rice. PLANT & CELL PHYSIOLOGY 2013; 54:e9. [PMID: 23314752 PMCID: PMC3583028 DOI: 10.1093/pcp/pct003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 01/02/2013] [Indexed: 05/20/2023]
Abstract
Plant hormones play important roles as signaling molecules in the regulation of growth and development by controlling the expression of downstream genes. Since the hormone signaling system represents a complex network involving functional cross-talk through the mutual regulation of signaling and metabolism, a comprehensive and integrative analysis of plant hormone concentrations and gene expression is important for a deeper understanding of hormone actions. We have developed a database named Uniformed Viewer for Integrated Omics (UniVIO: http://univio.psc.riken.jp/), which displays hormone-metabolome (hormonome) and transcriptome data in a single formatted (uniformed) heat map. At the present time, hormonome and transcriptome data obtained from 14 organ parts of rice plants at the reproductive stage and seedling shoots of three gibberellin signaling mutants are included in the database. The hormone concentration and gene expression data can be searched by substance name, probe ID, gene locus ID or gene description. A correlation search function has been implemented to enable users to obtain information of correlated substance accumulation and gene expression. In the correlation search, calculation method, range of correlation coefficient and plant samples can be selected freely.
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Affiliation(s)
- Toru Kudo
- RIKEN Plant Science Center, 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045 Japan
- These authors equally contributed to this study
- Present address: PMCB Program, Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Kenji Akiyama
- RIKEN Plant Science Center, 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045 Japan
- These authors equally contributed to this study
| | - Mikiko Kojima
- RIKEN Plant Science Center, 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045 Japan
| | - Nobue Makita
- RIKEN Plant Science Center, 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045 Japan
| | - Tetsuya Sakurai
- RIKEN Plant Science Center, 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045 Japan
| | - Hitoshi Sakakibara
- RIKEN Plant Science Center, 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045 Japan
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Blanco-Ulate B, Vincenti E, Powell ALT, Cantu D. Tomato transcriptome and mutant analyses suggest a role for plant stress hormones in the interaction between fruit and Botrytis cinerea. FRONTIERS IN PLANT SCIENCE 2013; 4:142. [PMID: 23717322 PMCID: PMC3653111 DOI: 10.3389/fpls.2013.00142] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 04/25/2013] [Indexed: 05/19/2023]
Abstract
Fruit-pathogen interactions are a valuable biological system to study the role of plant development in the transition from resistance to susceptibility. In general, unripe fruit are resistant to pathogen infection but become increasingly more susceptible as they ripen. During ripening, fruit undergo significant physiological and biochemical changes that are coordinated by complex regulatory and hormonal signaling networks. The interplay between multiple plant stress hormones in the interaction between plant vegetative tissues and microbial pathogens has been documented extensively, but the relevance of these hormones during infections of fruit is unclear. In this work, we analyzed a transcriptome study of tomato fruit infected with Botrytis cinerea in order to profile the expression of genes for the biosynthesis, modification and signal transduction of ethylene (ET), salicylic acid (SA), jasmonic acid (JA), and abscisic acid (ABA), hormones that may be not only involved in ripening, but also in fruit interactions with pathogens. The changes in relative expression of key genes during infection and assays of susceptibility of fruit with impaired synthesis or perception of these hormones were used to formulate hypotheses regarding the involvement of these regulators in the outcome of the tomato fruit-B. cinerea interaction.
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Affiliation(s)
- Barbara Blanco-Ulate
- Department of Plant Sciences, University of California, DavisDavis, CA, USA
- Department of Viticulture and Enology, University of California, DavisDavis, CA, USA
| | - Estefania Vincenti
- Department of Plant Sciences, University of California, DavisDavis, CA, USA
| | - Ann L. T. Powell
- Department of Plant Sciences, University of California, DavisDavis, CA, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, DavisDavis, CA, USA
- *Correspondence: Dario Cantu, Department of Viticulture and Enology, University of California, Davis, One Shields Ave., Davis, CA 95616, USA. e-mail:
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Singh K, Singla-Pareek SL, Pareek A. Dissecting out the crosstalk between salinity and hormones in roots of Arabidopsis. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2012; 15:913-24. [PMID: 22181020 DOI: 10.1089/omi.2011.0098] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Phytohormones are chemical messengers that play a leading role in regulating the vital activity of plants, including transcription, posttranscriptional pre-mRNA splicing, translation, and posttranslational modifications by interacting with specific protein receptors. Plant hormones are synthesized in one tissue and act on specific target sites in other tissues at vanishingly low concentrations. High salinity is one of the main factors limiting Arabidopsis growth and productivity. In this study, phytohormones including abscisic acid, auxin, ethylene, and cytokinin responsive genes regulating salinity stress in Arabidopsis roots were monitored using microarray data. We identified phytohormone responsive genes on the basis of their expression pattern at genomic level at various time points. Using publicly available microarray data, we analyzed the effect of salt stress on the transcription of phytohormone responsive genes. Gene ontology (GO) analysis of phytohormone responsive genes showed their role in important biological processes such as signal transduction, hormone metabolism, biosynthetic process, and gene expression. Gene enrichment terms also reveal that transcription regulator activity is the main class of ABA responsive genes under salinity stress. We conclude that expression of ABA responsive genes involves induction of several transcription factors under salt stress treatment in Arabidopsis roots.
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Affiliation(s)
- Khushwant Singh
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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Bonghi C, Trainotti L, Botton A, Tadiello A, Rasori A, Ziliotto F, Zaffalon V, Casadoro G, Ramina A. A microarray approach to identify genes involved in seed-pericarp cross-talk and development in peach. BMC PLANT BIOLOGY 2011; 11:107. [PMID: 21679395 PMCID: PMC3141638 DOI: 10.1186/1471-2229-11-107] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Accepted: 06/16/2011] [Indexed: 05/19/2023]
Abstract
BACKGROUND Field observations and a few physiological studies have demonstrated that peach embryogenesis and fruit development are tightly coupled. In fact, attempts to stimulate parthenocarpic fruit development by means of external tools have failed. Moreover, physiological disturbances during early embryo development lead to seed abortion and fruitlet abscission. Later in embryo development, the interactions between seed and fruit development become less strict. As there is limited genetic and molecular information about seed-pericarp cross-talk and development in peach, a massive gene approach based on the use of the μPEACH 1.0 array platform and quantitative real time RT-PCR (qRT-PCR) was used to study this process. RESULTS A comparative analysis of the transcription profiles conducted in seed and mesocarp (cv Fantasia) throughout different developmental stages (S1, S2, S3 and S4) evidenced that 455 genes are differentially expressed in seed and fruit. Among differentially expressed genes some were validated as markers in two subsequent years and in three different genotypes. Seed markers were a LTP1 (lipid transfer protein), a PR (pathogenesis-related) protein, a prunin and LEA (Late Embryogenesis Abundant) protein, for S1, S2, S3 and S4, respectively. Mesocarp markers were a RD22-like protein, a serin-carboxypeptidase, a senescence related protein and an Aux/IAA, for S1, S2, S3 and S4, respectively.The microarray data, analyzed by using the HORMONOMETER platform, allowed the identification of hormone-responsive genes, some of them putatively involved in seed-pericarp crosstalk. Results indicated that auxin, cytokinins, and gibberellins are good candidates, acting either directly (auxin) or indirectly as signals during early development, when the cross-talk is more active and vital for fruit set, whereas abscisic acid and ethylene may be involved later on. CONCLUSIONS In this research, genes were identified marking different phases of seed and mesocarp development. The selected genes behaved as good seed markers, while for mesocarp their reliability appeared to be dependent upon developmental and ripening traits. Regarding the cross-talk between seed and pericarp, possible candidate signals were identified among hormones.Further investigations relying upon the availability of whole genome platforms will allow the enrichment of a marker genes repertoire and the elucidation of players other than hormones that are involved in seed-pericarp cross-talk (i.e. hormone peptides and microRNAs).
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Affiliation(s)
- Claudio Bonghi
- Department of Environmental Agronomy and Crop Science, University of Padova, Legnaro (PD), Italy
| | - Livio Trainotti
- Department of Biology, University of Padova, Viale G. Colombo, 3 35121 Padova (PD), Italy
| | - Alessandro Botton
- Department of Environmental Agronomy and Crop Science, University of Padova, Legnaro (PD), Italy
| | - Alice Tadiello
- Department of Biology, University of Padova, Viale G. Colombo, 3 35121 Padova (PD), Italy
| | - Angela Rasori
- Department of Environmental Agronomy and Crop Science, University of Padova, Legnaro (PD), Italy
| | - Fiorenza Ziliotto
- Department of Environmental Agronomy and Crop Science, University of Padova, Legnaro (PD), Italy
| | - Valerio Zaffalon
- Department of Environmental Agronomy and Crop Science, University of Padova, Legnaro (PD), Italy
| | - Giorgio Casadoro
- Department of Biology, University of Padova, Viale G. Colombo, 3 35121 Padova (PD), Italy
| | - Angelo Ramina
- Department of Environmental Agronomy and Crop Science, University of Padova, Legnaro (PD), Italy
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