1
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Lee S, Park YS, Rhee JH, Chu H, Frost JM, Choi Y. Insights into plant regeneration: cellular pathways and DNA methylation dynamics. PLANT CELL REPORTS 2024; 43:120. [PMID: 38634973 PMCID: PMC11026228 DOI: 10.1007/s00299-024-03216-9] [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: 02/26/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024]
Abstract
Plants, known for their immobility, employ various mechanisms against stress and damage. A prominent feature is the formation of callus tissue-a cellular growth phenomenon that remains insufficiently explored, despite its distinctive cellular plasticity compared to vertebrates. Callus formation involves dedifferentiated cells, with a subset attaining pluripotency. Calluses exhibit an extraordinary capacity to reinitiate cellular division and undergo structural transformations, generating de novo shoots and roots, thereby developing into regenerated plants-a testament to the heightened developmental plasticity inherent in plants. In this way, plant regeneration through clonal propagation is a widely employed technique for vegetative reproduction. Thus, exploration of the biological components involved in regaining pluripotency contributes to the foundation upon which methods of somatic plant propagation can be advanced. This review provides an overview of the cellular pathway involved in callus and subsequent de novo shoot formation from already differentiated plant tissue, highlighting key genes critical to this process. In addition, it explores the intricate realm of epigenetic regulatory processes, emphasizing the nuanced dynamics of DNA methylation that contribute to plant regeneration. Finally, we briefly discuss somaclonal variation, examining its relation to DNA methylation, and investigating the heritability of epigenomic changes in crops.
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Affiliation(s)
- Seunga Lee
- Department of Biological Sciences, Seoul National University, Seoul, Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, Korea
| | - Young Seo Park
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Ji Hoon Rhee
- Department of Biological Sciences, Seoul National University, Seoul, Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, Korea
| | - Hyojeong Chu
- Department of Biological Sciences, Seoul National University, Seoul, Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, Korea
- The Research Institute of Basic Sciences, Seoul National University, Seoul, Korea
| | - Jennifer M Frost
- Genomics and Child Health, The Blizard Institute, Queen Mary University of London, London, UK
| | - Yeonhee Choi
- Department of Biological Sciences, Seoul National University, Seoul, Korea.
- Research Center for Plant Plasticity, Seoul National University, Seoul, Korea.
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2
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Šmeringai J, Schrumpfová PP, Pernisová M. Cytokinins - regulators of de novo shoot organogenesis. FRONTIERS IN PLANT SCIENCE 2023; 14:1239133. [PMID: 37662179 PMCID: PMC10471832 DOI: 10.3389/fpls.2023.1239133] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023]
Abstract
Plants, unlike animals, possess a unique developmental plasticity, that allows them to adapt to changing environmental conditions. A fundamental aspect of this plasticity is their ability to undergo postembryonic de novo organogenesis. This requires the presence of regulators that trigger and mediate specific spatiotemporal changes in developmental programs. The phytohormone cytokinin has been known as a principal regulator of plant development for more than six decades. In de novo shoot organogenesis and in vitro shoot regeneration, cytokinins are the prime candidates for the signal that determines shoot identity. Both processes of de novo shoot apical meristem development are accompanied by changes in gene expression, cell fate reprogramming, and the switching-on of the shoot-specific homeodomain regulator, WUSCHEL. Current understanding about the role of cytokinins in the shoot regeneration will be discussed.
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Affiliation(s)
- Ján Šmeringai
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Petra Procházková Schrumpfová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Markéta Pernisová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
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3
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Kaszler N, Benkő P, Molnár Á, Zámbori A, Fehér A, Gémes K. Absence of Arabidopsis Polyamine Oxidase 5 Influences the Cytokinin-Induced Shoot Meristem Formation from Lateral Root Primordia. PLANTS (BASEL, SWITZERLAND) 2023; 12:454. [PMID: 36771539 PMCID: PMC9920396 DOI: 10.3390/plants12030454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Lateral root primordia (LRPs) of Arabidopsis can be directly converted to shoot meristems (SMs) by the application of exogenous cytokinin. Here, we report that Arabidopsis POLYAMINE OXIDASE 5 (AtPAO5) contributes to this process, since the rate of SM formation from LRPs was significantly lower in the pao5-2 knockout mutant. Furthermore, the presented experiments showed that AtPAO5 influences SM formation via controlling the thermospermine (T-Spm) level. Gene expression analyses supported the view that the pao5-2 mutation as well as exogenous T-Spm downregulate the expression of the class 3 haemoglobin coding genes AtGLB1 and AtGLB2. AtGLB1 and 2 have been reported to augment cytokinin sensitivity, indirectly inhibiting the expression of type-A ARABIDOPSIS RESPONSE REGULATORs (ARRs). In agreement, the same ARR-coding genes were found to be upregulated in the pao5-2 mutant. Although GLB proteins might also control cytokinin-induced nitric oxide (NO) accumulation, we could not find experimental evidence for it. Rather, the negative effect of NO-donor treatment on AtPAO5 gene expression and SM formation was seen. Nevertheless, a hypothetical pathway is set up explaining how AtPAO5 may affect direct shoot meristem formation, controlling cytokinin sensitivity through T-Spm and GLBs.
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Affiliation(s)
- Nikolett Kaszler
- Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network, 62. Temesvári krt., H-6726 Szeged, Hungary
- Doctoral School of Biology, University of Szeged, 52. Közép fasor, H-6726 Szeged, Hungary
- Department of Plant Biology, University of Szeged, 52. Közép fasor, H-6726 Szeged, Hungary
| | - Péter Benkő
- Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network, 62. Temesvári krt., H-6726 Szeged, Hungary
- Department of Plant Biology, University of Szeged, 52. Közép fasor, H-6726 Szeged, Hungary
| | - Árpád Molnár
- Department of Plant Biology, University of Szeged, 52. Közép fasor, H-6726 Szeged, Hungary
| | - Abigél Zámbori
- Department of Plant Biology, University of Szeged, 52. Közép fasor, H-6726 Szeged, Hungary
| | - Attila Fehér
- Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network, 62. Temesvári krt., H-6726 Szeged, Hungary
- Department of Plant Biology, University of Szeged, 52. Közép fasor, H-6726 Szeged, Hungary
| | - Katalin Gémes
- Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network, 62. Temesvári krt., H-6726 Szeged, Hungary
- Department of Plant Biology, University of Szeged, 52. Közép fasor, H-6726 Szeged, Hungary
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4
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Transcriptome Analysis Reveals the Molecular Regularity Mechanism Underlying Stem Bulblet Formation in Oriental Lily 'Siberia'; Functional Characterization of the LoLOB18 Gene. Int J Mol Sci 2022; 23:ijms232315246. [PMID: 36499579 PMCID: PMC9738039 DOI: 10.3390/ijms232315246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/09/2022] Open
Abstract
The formation of underground stem bulblets in lilies is a complex biological process which is key in their micropropagation. Generally, it involves a stem-to-bulblet transition; however, the underlying mechanism remains elusive. It is important to understand the regulatory mechanism of bulblet formation for the reproductive efficiency of Lilium. In this study, we investigated the regulatory mechanism of underground stem bulblet formation under different conditions regarding the gravity point angle of the stem, i.e., vertical (control), horizontal, and slanting. The horizontal and slanting group displayed better formation of bulblets in terms of quality and quantity compared with the control group. A transcriptome analysis revealed that sucrose and starch were key energy sources for bulblet formation, auxin and cytokinin likely promoted bulblet formation, and gibberellin inhibited bulblet formation. Based on transcriptome analysis, we identified the LoLOB18 gene, a homolog to AtLOB18, which has been proven to be related to embryogenic development. We established the stem bud growth tissue culture system of Lilium and silenced the LoLOb18 gene using the VIGS system. The results showed that the bulblet induction was reduced with down-regulation of LoLOb18, indicating the involvement of LoLOb18 in stem bulblet formation in lilies. Our research lays a solid foundation for further molecular studies on stem bulblet formation of lilies.
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Varapparambath V, Mathew MM, Shanmukhan AP, Radhakrishnan D, Kareem A, Verma S, Ramalho JJ, Manoj B, Vellandath AR, Aiyaz M, Radha RK, Landge AN, Mähönen AP, Heisler MG, Weijers D, Prasad K. Mechanical conflict caused by a cell-wall-loosening enzyme activates de novo shoot regeneration. Dev Cell 2022; 57:2063-2080.e10. [PMID: 36002002 DOI: 10.1016/j.devcel.2022.07.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/10/2022] [Accepted: 07/27/2022] [Indexed: 01/02/2023]
Abstract
Cellular heterogeneity is a hallmark of multicellular organisms. During shoot regeneration from undifferentiated callus, only a select few cells, called progenitors, develop into shoot. How these cells are selected and what governs their subsequent progression to a patterned organ system is unknown. Using Arabidopsis thaliana, we show that it is not just the abundance of stem cell regulators but rather the localization pattern of polarity proteins that predicts the progenitor's fate. A shoot-promoting factor, CUC2, activated the expression of the cell-wall-loosening enzyme, XTH9, solely in a shell of cells surrounding the progenitor, causing different mechanical stresses in these cells. This mechanical conflict then activates cell polarity in progenitors to promote meristem formation. Interestingly, genetic or physical perturbations to cells surrounding the progenitor impaired the progenitor and vice versa. These suggest a feedback loop between progenitors and their neighbors for shoot regeneration in the absence of tissue-patterning cues.
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Affiliation(s)
- Vijina Varapparambath
- Indian Institute of Science Education and Research (IISER)-Pune, Pune 411008, India; IISER-Thiruvananthapuram, Thiruvananthapuram, India
| | - Mabel Maria Mathew
- Indian Institute of Science Education and Research (IISER)-Pune, Pune 411008, India; IISER-Thiruvananthapuram, Thiruvananthapuram, India.
| | - Anju Pallipurath Shanmukhan
- Indian Institute of Science Education and Research (IISER)-Pune, Pune 411008, India; IISER-Thiruvananthapuram, Thiruvananthapuram, India
| | | | - Abdul Kareem
- IISER-Thiruvananthapuram, Thiruvananthapuram, India
| | - Shubham Verma
- Indian Institute of Science Education and Research (IISER)-Pune, Pune 411008, India
| | - João Jacob Ramalho
- Laboratory of Biochemistry, Wageningen University, Wageningen, the Netherlands
| | - Bejoy Manoj
- IISER-Thiruvananthapuram, Thiruvananthapuram, India
| | | | - Mohammed Aiyaz
- Indian Institute of Science Education and Research (IISER)-Pune, Pune 411008, India; IISER-Thiruvananthapuram, Thiruvananthapuram, India
| | | | | | - Ari Pekka Mähönen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Marcus G Heisler
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Wageningen, the Netherlands
| | - Kalika Prasad
- Indian Institute of Science Education and Research (IISER)-Pune, Pune 411008, India; IISER-Thiruvananthapuram, Thiruvananthapuram, India.
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6
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Rapid and Efficient Regeneration of Populus ussuriensis Kom. from Root Explants through Direct De Novo Shoot Organogenesis. FORESTS 2022. [DOI: 10.3390/f13050806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Populus ussuriensis is an important tree species with high economic and ecologic values. However, traditional sexual propagation is time-consuming and inefficient, challenging afforestation and wood production using P. ussuriensis, and requires a rapid and efficient regeneration system. The present study established a rapid, efficient, and stable shoot regeneration method from root explants in P. ussuriensis using several plant growth regulators. Most shoot buds (15.2 per explant) were induced at high efficiency under WPM medium supplemented with 221.98 μM 6-BA, 147.61 μM IBA, and 4.54 μM TDZ within two weeks. The shoot buds were further multiplicated and elongated under WPM medium supplemented with 221.98 μM 6-BA, 147.61 μM IBA, and 57.74 μM GA3 for four weeks. The average number and efficiency of elongation of multiplication and elongation for induced shoot buds were 75.2 and 78%, respectively. All the shoots were rooted within a week and none of them showed abnormality in rooting. The time spent for the entire regeneration of this direct shoot organogenesis was seven weeks, much shorter than conventional indirect organogenesis with the callus induction phase, and no abnormal growth was observed. This novel regeneration system will not only promote the massive propagation, but also accelerate the genetic engineering studies for trait improvement of P. ussuriensis species.
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7
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Integrating the Roles for Cytokinin and Auxin in De Novo Shoot Organogenesis: From Hormone Uptake to Signaling Outputs. Int J Mol Sci 2021; 22:ijms22168554. [PMID: 34445260 PMCID: PMC8395325 DOI: 10.3390/ijms22168554] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/01/2021] [Accepted: 08/03/2021] [Indexed: 12/01/2022] Open
Abstract
De novo shoot organogenesis (DNSO) is a procedure commonly used for the in vitro regeneration of shoots from a variety of plant tissues. Shoot regeneration occurs on nutrient media supplemented with the plant hormones cytokinin (CK) and auxin, which play essential roles in this process, and genes involved in their signaling cascades act as master regulators of the different phases of shoot regeneration. In the last 20 years, the genetic regulation of DNSO has been characterized in detail. However, as of today, the CK and auxin signaling events associated with shoot regeneration are often interpreted as a consequence of these hormones simply being present in the regeneration media, whereas the roles for their prior uptake and transport into the cultivated plant tissues are generally overlooked. Additionally, sucrose, commonly added to the regeneration media as a carbon source, plays a signaling role and has been recently shown to interact with CK and auxin and to affect the efficiency of shoot regeneration. In this review, we provide an integrative interpretation of the roles for CK and auxin in the process of DNSO, adding emphasis on their uptake from the regeneration media and their interaction with sucrose present in the media to their complex signaling outputs that mediate shoot regeneration.
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8
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Cytokinins initiate secondary growth in the Arabidopsis root through a set of LBD genes. Curr Biol 2021; 31:3365-3373.e7. [PMID: 34129827 PMCID: PMC8360765 DOI: 10.1016/j.cub.2021.05.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/24/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022]
Abstract
During primary growth, plant tissues increase their length, and as these tissues mature, they initiate secondary growth to increase thickness.1 It is not known what activates this transition to secondary growth. Cytokinins are key plant hormones regulating vascular development during both primary and secondary growth. During primary growth of Arabidopsis roots, cytokinins promote procambial cell proliferation2,3 and vascular patterning together with the hormone auxin.4-7 In the absence of cytokinins, secondary growth fails to initiate.8 Enhanced cytokinin levels, in turn, promote secondary growth.8,9 Despite the importance of cytokinins, little is known about the downstream signaling events in this process. Here, we show that cytokinins and a few downstream LATERAL ORGAN BOUNDARIES DOMAIN (LBD) family of transcription factors are rate-limiting components in activating and further promoting secondary growth in Arabidopsis roots. Cytokinins directly activate transcription of two homologous LBD genes, LBD3 and LBD4. Two other homologous LBDs, LBD1 and LBD11, are induced only after prolonged cytokinin treatment. Our genetic studies revealed a two-stage mechanism downstream of cytokinin signaling: while LBD3 and LBD4 regulate activation of secondary growth, LBD1, LBD3, LBD4, and LBD11 together promote further radial growth and maintenance of cambial stem cells. LBD overexpression promoted rapid cell growth followed by accelerated cell divisions, thus leading to enhanced secondary growth. Finally, we show that LBDs rapidly inhibit cytokinin signaling. Together, our data suggest that the cambium-promoting LBDs negatively feed back into cytokinin signaling to keep root secondary growth in balance.
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9
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Abstract
Plants encompass unparalleled multi-scale regenerative potential. Despite lacking specialized cells that are recruited to injured sites, and despite their cells being encased in rigid cell walls, plants exhibit a variety of regenerative responses ranging from the regeneration of specific cell types, tissues and organs, to the rebuilding of an entire organism. Over the years, extensive studies on embryo, shoot and root development in the model plant species Arabidopsis thaliana have provided insights into the mechanisms underlying plant regeneration. These studies highlight how Arabidopsis, with its wide array of refined molecular, genetic and cell biological tools, provides a perfect model to interrogate the cellular and molecular mechanisms of reprogramming during regeneration.
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Affiliation(s)
- Mabel Maria Mathew
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, 695551, India
| | - Kalika Prasad
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, 695551, India
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Kaszler N, Benkő P, Bernula D, Szepesi Á, Fehér A, Gémes K. Polyamine Metabolism Is Involved in the Direct Regeneration of Shoots from Arabidopsis Lateral Root Primordia. PLANTS 2021; 10:plants10020305. [PMID: 33562616 PMCID: PMC7915173 DOI: 10.3390/plants10020305] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/29/2021] [Accepted: 02/02/2021] [Indexed: 11/16/2022]
Abstract
Plants can be regenerated from various explants/tissues via de novo shoot meristem formation. Most of these regeneration pathways are indirect and involve callus formation. Besides plant hormones, the role of polyamines (PAs) has been implicated in these processes. Interestingly, the lateral root primordia (LRPs) of Arabidopsis can be directly converted to shoot meristems by exogenous cytokinin application. In this system, no callus formation takes place. We report that the level of PAs, especially that of spermidine (Spd), increased during meristem conversion and the application of exogenous Spd improved its efficiency. The high endogenous Spd level could be due to enhanced synthesis as indicated by the augmented relative expression of PA synthesis genes (AtADC1,2, AtSAMDC2,4, AtSPDS1,2) during the process. However, the effect of PAs on shoot meristem formation might also be dependent on their catabolism. The expression of Arabidopsis POLYAMINE OXIDASE 5 (AtPAO5) was shown to be specifically high during the process and its ectopic overexpression increased the LRP-to-shoot conversion efficiency. This was correlated with Spd accumulation in the roots and ROS accumulation in the converting LRPs. The potential ways how PAO5 may influence direct shoot organogenesis from Arabidopsis LRPs are discussed.
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Affiliation(s)
- Nikolett Kaszler
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, 62. Temesvári krt, H-6726 Szeged, Hungary; (N.K.); (P.B.); (D.B.)
- Doctoral School of Biology, University of Szeged, 52. Közép fasor, H-6726 Szeged, Hungary
- Department of Plant Biology, University of Szeged, 52. Közép fasor, H-6726 Szeged, Hungary;
| | - Péter Benkő
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, 62. Temesvári krt, H-6726 Szeged, Hungary; (N.K.); (P.B.); (D.B.)
- Doctoral School of Biology, University of Szeged, 52. Közép fasor, H-6726 Szeged, Hungary
- Department of Plant Biology, University of Szeged, 52. Közép fasor, H-6726 Szeged, Hungary;
| | - Dóra Bernula
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, 62. Temesvári krt, H-6726 Szeged, Hungary; (N.K.); (P.B.); (D.B.)
- Doctoral School of Biology, University of Szeged, 52. Közép fasor, H-6726 Szeged, Hungary
- Department of Plant Biology, University of Szeged, 52. Közép fasor, H-6726 Szeged, Hungary;
| | - Ágnes Szepesi
- Department of Plant Biology, University of Szeged, 52. Közép fasor, H-6726 Szeged, Hungary;
| | - Attila Fehér
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, 62. Temesvári krt, H-6726 Szeged, Hungary; (N.K.); (P.B.); (D.B.)
- Department of Plant Biology, University of Szeged, 52. Közép fasor, H-6726 Szeged, Hungary;
- Correspondence: author: (A.F.); (K.G.); Tel.: +36-62-546-962 (A.F.); +36-62-544-307 (K.G.)
| | - Katalin Gémes
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, 62. Temesvári krt, H-6726 Szeged, Hungary; (N.K.); (P.B.); (D.B.)
- Department of Plant Biology, University of Szeged, 52. Közép fasor, H-6726 Szeged, Hungary;
- Correspondence: author: (A.F.); (K.G.); Tel.: +36-62-546-962 (A.F.); +36-62-544-307 (K.G.)
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11
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Wang X, Ye L, Lyu M, Ursache R, Löytynoja A, Mähönen AP. An inducible genome editing system for plants. NATURE PLANTS 2020; 6:766-772. [PMID: 32601420 PMCID: PMC7611339 DOI: 10.1038/s41477-020-0695-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 05/17/2020] [Indexed: 05/02/2023]
Abstract
Conditional manipulation of gene expression is a key approach to investigating the primary function of a gene in a biological process. While conditional and cell-type-specific overexpression systems exist for plants, there are currently no systems available to disable a gene completely and conditionally. Here, we present a new tool with which target genes can efficiently and conditionally be knocked out by genome editing at any developmental stage. Target genes can also be knocked out in a cell-type-specific manner. Our tool is easy to construct and will be particularly useful for studying genes having null alleles that are non-viable or show pleiotropic developmental defects.
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Affiliation(s)
- Xin Wang
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Lingling Ye
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Munan Lyu
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Robertas Ursache
- Department of Plant Molecular Biology, Biophore, Campus UNIL-Sorge, University of Lausanne, Lausanne, Switzerland
| | - Ari Löytynoja
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ari Pekka Mähönen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland.
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
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12
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Winnicki K. The Winner Takes It All: Auxin-The Main Player during Plant Embryogenesis. Cells 2020; 9:E606. [PMID: 32138372 PMCID: PMC7140527 DOI: 10.3390/cells9030606] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/21/2020] [Accepted: 02/27/2020] [Indexed: 12/11/2022] Open
Abstract
In plants, the first asymmetrical division of a zygote leads to the formation of two cells with different developmental fates. The establishment of various patterns relies on spatial and temporal gene expression, however the precise mechanism responsible for embryonic patterning still needs elucidation. Auxin seems to be the main player which regulates embryo development and controls expression of various genes in a dose-dependent manner. Thus, local auxin maxima and minima which are provided by polar auxin transport underlie cell fate specification. Diverse auxin concentrations in various regions of an embryo would easily explain distinct cell identities, however the question about the mechanism of cellular patterning in cells exposed to similar auxin concentrations still remains open. Thus, specification of cell fate might result not only from the cell position within an embryo but also from events occurring before and during mitosis. This review presents the impact of auxin on the orientation of the cell division plane and discusses the mechanism of auxin-dependent cytoskeleton alignment. Furthermore, close attention is paid to auxin-induced calcium fluxes, which regulate the activity of MAPKs during postembryonic development and which possibly might also underlie cellular patterning during embryogenesis.
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Affiliation(s)
- Konrad Winnicki
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lódź, Poland
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13
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Zhang K, Zhao L, Yang X, Li M, Sun J, Wang K, Li Y, Zheng Y, Yao Y, Li W. GmRAV1 regulates regeneration of roots and adventitious buds by the cytokinin signaling pathway in Arabidopsis and soybean. PHYSIOLOGIA PLANTARUM 2019; 165:814-829. [PMID: 29923201 DOI: 10.1111/ppl.12788] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 06/12/2018] [Accepted: 06/14/2018] [Indexed: 05/07/2023]
Abstract
The division and differentiation of cells are the basis of growth and development. Cytokinin plays an active role in cell growth division and differentiation. The Related to ABI3/VP1 (RAV) family comprises transcription factors in plants and all contain both AP2- and B3-like domains. In this study, GmRAV1 (Glycine max), which belongs to the AP2/ERF transcription factor family, was isolated and functionally characterized. Subcellular localization showed that GmRAV1 was localized to the nucleus and quantitative real-time polymerase chain reaction (qRT-PCR) analysis indicated that GmRAV1 was induced by cytokinin. Furthermore, compared with wild-type plants, plants overexpressing GmRAV1 showed dwarfism and late maturity. In contrast, the mutant of TEMPRANILLO (tem1) and GmRAV-i plants had an opposite phenotype. More interestingly, a root and shoot regeneration experiment indicated that GmRAV1 is one of the most important positive regulators of the cytokinin signaling pathway, which is involved in promoting root and shoot regeneration. In addition, RNA-seq and qRT-PCR results indicated that GmRAV1 is related to the key factors involved in the cytokinin signaling pathway, namely, cytokinin oxidase (GmCKX6 and GmCKX7), purine permease (GmPUP1), cell cyclin-related genes (GmCycA2;4, GmCycD3 and GmCYC1), cyclin-dependent kinase (GmCDKB2), cell division cycle (GmCDC20), E2F transcription factors (GmE2FE) and authentic response regulator (GmARR9). In conclusion, GmRAV1, one of the most important positive regulators involved in promoting root and shoot regeneration, was induced by cytokinin and is related to the key factors of the cytokinin signaling pathways.
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Affiliation(s)
- Kexin Zhang
- Key Laboratory of Soybean Biology in the Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural University, Harbin 150030, China
| | - Lin Zhao
- Key Laboratory of Soybean Biology in the Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural University, Harbin 150030, China
| | - Xue Yang
- Key Laboratory of Soybean Biology in the Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural University, Harbin 150030, China
| | - Minmin Li
- Key Laboratory of Soybean Biology in the Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural University, Harbin 150030, China
| | - Jingzhe Sun
- Key Laboratory of Soybean Biology in the Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural University, Harbin 150030, China
| | - Kuo Wang
- Key Laboratory of Soybean Biology in the Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural University, Harbin 150030, China
| | - Yinghua Li
- Key Laboratory of Soybean Biology in the Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural University, Harbin 150030, China
| | - Yanhong Zheng
- Key Laboratory of Soybean Biology in the Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural University, Harbin 150030, China
| | - Yuheng Yao
- Key Laboratory of Soybean Biology in the Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural University, Harbin 150030, China
| | - Wenbin Li
- Key Laboratory of Soybean Biology in the Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural University, Harbin 150030, China
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14
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Tian X, Zhang C, Xu J. Control of Cell Fate Reprogramming Towards De Novo Shoot Organogenesis. PLANT & CELL PHYSIOLOGY 2018; 59:708-714. [PMID: 29294130 DOI: 10.1093/pcp/pcx207] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/18/2017] [Indexed: 06/07/2023]
Abstract
Many plants have a high regenerative capacity, which can be used to induce de novo organogenesis and produce various valuable plant species and products. In the classic two-step protocol for de novo shoot organogenesis, small pieces of plant parts or tissues known as explants are initially cultured on an auxin-rich medium to produce a cell mass called callus. Upon transfer to a cytokinin-rich medium, a subpopulation of cells within the callus acquire shoot cell fate and subsequently develop into a fertile shoot. Cell fate reprogramming during de novo organogenesis is thus recognized as the decisive step to acquire new cell types progressively, in response to a change in the levels of plant hormones auxin and cytokinin. Currently, the molecular mechanisms underlying the onset and completion of cell fate reprogramming remains partly understood. In this review, we sought to summarize the most recent progress made in the study of cell fate reprogramming during de novo shoot organogenesis, and highlight the critical roles of epigenetic and transcription factors in the developmental timing of cell fate reprogramming.
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Affiliation(s)
- Xin Tian
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Chen Zhang
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Jian Xu
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
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15
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Landge AN, Radhakrishnan D, Kareem A, Prasad K. Intermediate Developmental Phases During Regeneration. PLANT & CELL PHYSIOLOGY 2018; 59:702-707. [PMID: 29361166 DOI: 10.1093/pcp/pcy011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 01/08/2018] [Indexed: 06/07/2023]
Abstract
The initial view that regeneration can be a continuum in terms of regulatory mechanisms is gradually changing, and recent evidence points towards the presence of discrete regulatory steps and intermediate phases. Furthermore, regeneration presents an excellent example of a process generating order and pattern, i.e. a self-organization process. It is likely that the process traverses a set of intermediate phases before reaching an endpoint. Although some progress has been made in deciphering the identity of these intermediate phases, a lot more work is needed to derive a comprehensive and complete picture. Here, we discuss the intermediate developmental phases in plant regeneration and compare them with the possible intermediate developmental phases in animal regeneration.
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Affiliation(s)
- Amit N Landge
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, 695016, India
| | - Dhanya Radhakrishnan
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, 695016, India
| | - Abdul Kareem
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, 695016, India
| | - Kalika Prasad
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, 695016, India
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16
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Efroni I. A Conceptual Framework for Cell Identity Transitions in Plants. PLANT & CELL PHYSIOLOGY 2018; 59:691-701. [PMID: 29136202 PMCID: PMC6018971 DOI: 10.1093/pcp/pcx172] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/27/2017] [Indexed: 05/19/2023]
Abstract
Multicellular organisms develop from a single cell that proliferates to form different cell types with specialized functions. Sixty years ago, Waddington suggested the 'epigenetic landscape' as a useful metaphor for the process. According to this view, cells move through a rugged identity space along genetically encoded trajectories, until arriving at one of the possible final fates. In plants in particular, these trajectories have strong spatial correlates, as cell identity is intimately linked to its relative position within the plant. During regeneration, however, positional signals are severely disrupted and differentiated cells are able to undergo rapid non-canonical identity changes. Moreover, while pluripotent properties have long been ascribed to plant cells, the introduction of induced pluripotent stem cells in animal studies suggests such plasticity may not be unique to plants. As a result, current concepts of differentiation as a gradual and hierarchical process are being reformulated across biological fields. Traditional studies of plant regeneration have placed strong emphasis on the emergence of patterns and tissue organization, and information regarding the events occurring at the level of individual cells is only now beginning to emerge. Here, I review the historical and current concepts of cell identity and identity transitions, and discuss how new views and tools may instruct the future understanding of differentiation and plant regeneration.
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Affiliation(s)
- Idan Efroni
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University, Rehovot, Israel
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17
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Liu J, Hu X, Qin P, Prasad K, Hu Y, Xu L. The WOX11-LBD16 Pathway Promotes Pluripotency Acquisition in Callus Cells During De Novo Shoot Regeneration in Tissue Culture. PLANT & CELL PHYSIOLOGY 2018; 59:734-743. [PMID: 29361138 DOI: 10.1093/pcp/pcy010] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 01/08/2018] [Indexed: 05/04/2023]
Abstract
De novo shoot regeneration in tissue culture undergoes at least two phases. Explants are first cultured on auxin-rich callus-inducing medium (CIM) to produce a group of pluripotent cells termed callus; the callus is then transferred to cytokinin rich shoot-inducing medium (SIM) to promote the formation of shoot progenitor cells, from which adventitious shoots may differentiate. Here, we show that the Arabidopsis thaliana transcription factor gene LATERAL ORGAN BOUNDARIES DOMAIN16 (LBD16) is involved in pluripotency acquisition in callus cells. LBD16, which is activated by WUSCHEL RELATED HOMEOBOX11 (WOX11), is specifically expressed in the newly formed callus on CIM and its expression decreases quickly when callus is moved to SIM. Blocking the WOX11-LBD16 pathway results in the loss of pluripotency in callus cultured on CIM, leading to shooting defects on SIM. Further analysis showed that LBD16 may function in the establishment of the root primordium-like identity in the newly formed callus, indicating that the root primordium-like identity is the cellular nature of pluripotency in callus cells. Additionally, LBD16 promotes cell division during callus initiation. Our study clarified that the WOX11-LBD16 pathway promotes pluripotency acquisition in callus cells.
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Affiliation(s)
- Jie 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 200032, China
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Xiaomei Hu
- 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 200032, China
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Peng Qin
- Department of Instrument Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Kalika Prasad
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695016, India
| | - Yuxin Hu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Lin Xu
- 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 200032, China
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18
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Radhakrishnan D, Kareem A, Durgaprasad K, Sreeraj E, Sugimoto K, Prasad K. Shoot regeneration: a journey from acquisition of competence to completion. CURRENT OPINION IN PLANT BIOLOGY 2018; 41:23-31. [PMID: 28843861 DOI: 10.1016/j.pbi.2017.08.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 08/07/2017] [Accepted: 08/08/2017] [Indexed: 05/12/2023]
Abstract
Plants display an extraordinary ability to regenerate complete shoot systems from a tissue fragment or even from a single cell. Upregulation of the determinants of pluripotency during a precise window of time in response to external inductive cues is a key decisive factor for shoot regeneration. A burst of recent studies has begun to provide an understanding of signaling molecules that are instrumental in the making of the regenerative mass, as well as the developmental regulators that are seminal in shaping the pluripotent state. Here, we discuss how signaling molecules, waves of mutually exclusive stem cell regulators and epigenetic modifiers could contribute to cellular heterogeneity in an island of regenerative mass, thus leading to de novo shoot regeneration.
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Affiliation(s)
- Dhanya Radhakrishnan
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695016, India
| | - Abdul Kareem
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695016, India
| | - Kavya Durgaprasad
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695016, India
| | - E Sreeraj
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695016, India
| | - Kaoru Sugimoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Kalika Prasad
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695016, India.
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19
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Pernisova M, Grochova M, Konecny T, Plackova L, Harustiakova D, Kakimoto T, Heisler MG, Novak O, Hejatko J. Cytokinin signalling regulates organ identity via AHK4 receptor in Arabidopsis. Development 2018; 145:dev.163907. [DOI: 10.1242/dev.163907] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/22/2018] [Indexed: 01/19/2023]
Abstract
Mutual interactions of the phytohormones cytokinins and auxin determine root or shoot identity during postembryonic de novo organogenesis in plants. However, our understanding to the role of hormonal metabolism and perception during early stages of cell fate reprograming is still elusive.
In the hypocotyl explant assay, auxin activated root formation while cytokinins mediated early loss of the root identity, primordia disorganization and initiation of shoot development. Exogenous but also endogenous cytokinins influenced the initiation of newly formed organs as well as the pace of organ developmental sequence. The process of de novo shoot apical meristem establishment was accompanied by accumulation of endogenous cytokinins, differential regulation of genes for individual cytokinin receptors, strong activation of AHK4-mediated signalling and induction of shoot-specific homeodomain regulator WUSCHEL. The latter associated with upregulation of isopentenyladenine-type cytokinins, revealing higher shoot-forming potential when compared with trans-zeatin. Moreover, AHK4-controlled cytokinin signalling negatively regulated root stem cell organizer WUSCHEL RELATED HOMEOBOX 5 in the root quiescent centre. We propose an important role of endogenous cytokinin biosynthesis and AHK4-mediated cytokinin signalling in the control of de novo induced organ identity.
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Affiliation(s)
- Marketa Pernisova
- CEITEC - Central European Institute of Technology and Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Martina Grochova
- CEITEC - Central European Institute of Technology and Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Tomas Konecny
- CEITEC - Central European Institute of Technology and Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lenka Plackova
- Laboratory of Growth Regulators, CRH, Institute of Experimental Botany AS CR and Faculty of Science of Palacký University, Olomouc, Czech Republic
| | - Danka Harustiakova
- Institute of Biostatistics and Analyses, Faculty of Medicine and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Tatsuo Kakimoto
- Department of Biological Science, Graduate School of Science, Osaka University, Osaka, Japan
| | | | - Ondrej Novak
- Laboratory of Growth Regulators, CRH, Institute of Experimental Botany AS CR and Faculty of Science of Palacký University, Olomouc, Czech Republic
| | - Jan Hejatko
- CEITEC - Central European Institute of Technology and Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
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20
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Kareem A, Radhakrishnan D, Sondhi Y, Aiyaz M, Roy MV, Sugimoto K, Prasad K. De novo assembly of plant body plan: a step ahead of Deadpool. REGENERATION (OXFORD, ENGLAND) 2016; 3:182-197. [PMID: 27800169 PMCID: PMC5084358 DOI: 10.1002/reg2.68] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 08/12/2016] [Accepted: 08/24/2016] [Indexed: 12/20/2022]
Abstract
While in the movie Deadpool it is possible for a human to recreate an arm from scratch, in reality plants can even surpass that. Not only can they regenerate lost parts, but also the whole plant body can be reborn from a few existing cells. Despite the decades old realization that plant cells possess the ability to regenerate a complete shoot and root system, it is only now that the underlying mechanisms are being unraveled. De novo plant regeneration involves the initiation of regenerative mass, acquisition of the pluripotent state, reconstitution of stem cells and assembly of regulatory interactions. Recent studies have furthered our understanding on the making of a complete plant system in the absence of embryonic positional cues. We review the recent studies probing the molecular mechanisms of de novo plant regeneration in response to external inductive cues and our current knowledge of direct reprogramming of root to shoot and vice versa. We further discuss how de novo regeneration can be exploited to meet the demands of green culture industries and to serve as a general model to address the fundamental questions of regeneration across the plant kingdom.
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Affiliation(s)
- Abdul Kareem
- School of BiologyIndian Institute of Science Education and ResearchThiruvananthapuramKerala695016India
| | - Dhanya Radhakrishnan
- School of BiologyIndian Institute of Science Education and ResearchThiruvananthapuramKerala695016India
| | - Yash Sondhi
- School of BiologyIndian Institute of Science Education and ResearchThiruvananthapuramKerala695016India
| | - Mohammed Aiyaz
- School of BiologyIndian Institute of Science Education and ResearchThiruvananthapuramKerala695016India
| | - Merin V. Roy
- School of BiologyIndian Institute of Science Education and ResearchThiruvananthapuramKerala695016India
| | - Kaoru Sugimoto
- Department of Applied Biological ScienceFaculty of Science and TechnologyTokyo University of Science2641 YamazakiNodaChiba278‐8510Japan
| | - Kalika Prasad
- School of BiologyIndian Institute of Science Education and ResearchThiruvananthapuramKerala695016India
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