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Liu Z, Yu X, Qin A, Zhao Z, Liu Y, Sun S, Liu H, Guo C, Wu R, Yang J, Hu M, Bawa G, Sun X. Research strategies for single-cell transcriptome analysis in plant leaves. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:27-37. [PMID: 35904970 DOI: 10.1111/tpj.15927] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/23/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
The recent and continuous improvement in single-cell RNA sequencing (scRNA-seq) technology has led to its emergence as an efficient experimental approach in plant research. However, compared with single-cell research in animals and humans, the application of scRNA-seq in plant research is limited by several challenges, including cell separation, cell type annotation, cellular function analysis, and cell-cell communication networks. In addition, the unavailability of corresponding reliable and stable analysis methods and standards has resulted in the relative decentralization of plant single-cell research. Considering these shortcomings, this review summarizes the research progress in plant leaf using scRNA-seq. In addition, it describes the corresponding feasible analytical methods and associated difficulties and problems encountered in the current research. In the end, we provide a speculative overview of the development of plant single-cell transcriptome research in the future.
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Affiliation(s)
- Zhixin Liu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Xiaole Yu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Aizhi Qin
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Zihao Zhao
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Yumeng Liu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Susu Sun
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Hao Liu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Chenxi Guo
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Rui Wu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Jincheng Yang
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Mengke Hu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - George Bawa
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Xuwu Sun
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
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Ricachenevsky FK, Punshon T, Salt DE, Fett JP, Guerinot ML. Arabidopsis thaliana zinc accumulation in leaf trichomes is correlated with zinc concentration in leaves. Sci Rep 2021; 11:5278. [PMID: 33674630 PMCID: PMC7935932 DOI: 10.1038/s41598-021-84508-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/17/2021] [Indexed: 11/21/2022] Open
Abstract
Zinc (Zn) is a key micronutrient for plants and animals, and understanding Zn homeostasis in plants can improve both agriculture and human health. While root Zn transporters in plant model species have been characterized in detail, comparatively little is known about shoot processes controlling Zn concentrations and spatial distribution. Previous work showed that Zn hyperaccumulator species such as Arabidopsis halleri accumulate Zn and other metals in leaf trichomes. To date there is no systematic study regarding Zn accumulation in the trichomes of the non-accumulating, genetic model species A. thaliana. Here, we used Synchrotron X-Ray Fluorescence mapping to show that Zn accumulates at the base of trichomes of A. thaliana. Using transgenic and natural accessions of A thaliana that vary in bulk leaf Zn concentration, we demonstrate that higher leaf Zn increases total Zn found at the base of trichome cells. Our data indicates that Zn accumulation in trichomes is a function of the Zn status of the plant, and provides the basis for future studies on a genetically tractable plant species to understand the molecular steps involved in Zn spatial distribution in leaves.
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Affiliation(s)
- Felipe K Ricachenevsky
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande Do Sul, Porto Alegre, Brazil. .,Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, Porto Alegre, RS, 9500, Brazil. .,Department of Biological Sciences, Life Sciences Center, Dartmouth College, 78 College St, Hanover, NH, 03755, USA.
| | - Tracy Punshon
- Department of Biological Sciences, Life Sciences Center, Dartmouth College, 78 College St, Hanover, NH, 03755, USA
| | - David E Salt
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Janette P Fett
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande Do Sul, Porto Alegre, Brazil.,Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, Porto Alegre, RS, 9500, Brazil
| | - Mary Lou Guerinot
- Department of Biological Sciences, Life Sciences Center, Dartmouth College, 78 College St, Hanover, NH, 03755, USA.
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Cardoso-Gustavson P, Fernandes FF, Alves ES, Victorio MP, Moura BB, Domingos M, Rodrigues CA, Ribeiro AP, Nievola CC, Figueiredo AMG. Tillandsia usneoides: a successful alternative for biomonitoring changes in air quality due to a new highway in São Paulo, Brazil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:1779-1788. [PMID: 26396016 DOI: 10.1007/s11356-015-5449-8] [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: 07/30/2015] [Accepted: 09/16/2015] [Indexed: 06/05/2023]
Abstract
Tillandsia usneoides is an aerial epiphytic bromeliad that absorbs water and nutrients directly from the atmosphere by scales covering its surface. We expanded the use of this species as a broader biomonitor based on chemical and structural markers to detect changes in air quality. The usefulness of such comprehensive approach was tested during the construction and opening of a highway (SP-21) in São Paulo State, Brazil. The biomonitoring study was performed from 2009 to 2012, thus comprising the period during construction and after the highway inauguration. Metal accumulation and structural alterations were assessed, in addition to microscopy analyses to understand the metal chelation in plant tissues and to assess the causes of alterations in the number and shape of scale cells. Altogether, our analyses support the use of this species as a wide biomonitor of air quality in urbanized areas.
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Affiliation(s)
- Poliana Cardoso-Gustavson
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Rua Arcturus 03, Jardim Antares, São Bernardo do Campo, 09606-070, SP, Brazil.
| | - Francine Faia Fernandes
- Programa de Pós-Graduação em Biodiversidade Vegetal e Meio Ambiente, Instituto de Botânica, Av. Miguel Stefano 3687, Água Funda, 04301-902, SP, Brazil.
| | - Edenise Segala Alves
- Núcleo de Pesquisa em Anatomia, Instituto de Botânica, Av. Miguel Stefano 3687, Água Funda, 04301-902, SP, Brazil.
| | - Mariana Pereira Victorio
- Núcleo de Pesquisa em Anatomia, Instituto de Botânica, Av. Miguel Stefano 3687, Água Funda, 04301-902, SP, Brazil.
| | - Barbara Baesso Moura
- Programa de Pós-Graduação em Biodiversidade Vegetal e Meio Ambiente, Instituto de Botânica, Av. Miguel Stefano 3687, Água Funda, 04301-902, SP, Brazil.
| | - Marisa Domingos
- Núcleo de Pesquisa em Anatomia, Instituto de Botânica, Av. Miguel Stefano 3687, Água Funda, 04301-902, SP, Brazil.
| | - Caroline Albuquerque Rodrigues
- Laboratório de Análise por Ativação com Nêutrons, Instituto de Pesquisas Energéticas e Nucleares, Av. Prof. Lineu Prestes, 2242, 05508-000, São Paulo, SP, Brazil.
| | - Andreza Portella Ribeiro
- Mestrado em Cidades Inteligentes e Sustentáveis, Universidade Nove de Julho, Av. Francisco Matarazzo, 612, prédio C, Água Branca, 05001 100, SP, Brazil.
| | - Catarina Carvalho Nievola
- Núcleo de Pesquisa em Anatomia, Instituto de Botânica, Av. Miguel Stefano 3687, Água Funda, 04301-902, SP, Brazil.
| | - Ana Maria G Figueiredo
- Laboratório de Análise por Ativação com Nêutrons, Instituto de Pesquisas Energéticas e Nucleares, Av. Prof. Lineu Prestes, 2242, 05508-000, São Paulo, SP, Brazil.
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Bergau N, Navarette Santos A, Henning A, Balcke GU, Tissier A. Autofluorescence as a Signal to Sort Developing Glandular Trichomes by Flow Cytometry. FRONTIERS IN PLANT SCIENCE 2016; 7:949. [PMID: 27446176 PMCID: PMC4923063 DOI: 10.3389/fpls.2016.00949] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/14/2016] [Indexed: 05/04/2023]
Abstract
The industrial relevance of a number of metabolites produced in plant glandular trichomes (GTs) has spurred research on these specialized organs for a number of years. Most of the research, however, has focused on the elucidation of secondary metabolite pathways and comparatively little has been undertaken on the development and differentiation of GTs. One way to gain insight into these developmental processes is to generate stage-specific transcriptome and metabolome data. The difficulty for this resides in the isolation of early stages of development of the GTs. Here we describe a method for the separation and isolation of intact young and mature type VI trichomes from the wild tomato species Solanum habrochaites. The final and key step of the method uses cell sorting based on distinct autofluorescence signals of the young and mature trichomes. We demonstrate that sorting by flow cytometry allows recovering pure fractions of young and mature trichomes. Furthermore, we show that the sorted trichomes can be used for transcript and metabolite analyses. Because many plant tissues or cells have distinct autofluorescence components, the principles of this method can be generally applicable for the isolation of specific cell types without prior labeling.
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Affiliation(s)
- Nick Bergau
- Department of Cell and Metabolic Biology, Leibniz-Institute of Plant BiochemistryHalle, Germany
| | | | - Anja Henning
- Department of Cell and Metabolic Biology, Leibniz-Institute of Plant BiochemistryHalle, Germany
| | - Gerd U. Balcke
- Department of Cell and Metabolic Biology, Leibniz-Institute of Plant BiochemistryHalle, Germany
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz-Institute of Plant BiochemistryHalle, Germany
- *Correspondence: Alain Tissier,
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Bergau N, Bennewitz S, Syrowatka F, Hause G, Tissier A. The development of type VI glandular trichomes in the cultivated tomato Solanum lycopersicum and a related wild species S. habrochaites. BMC PLANT BIOLOGY 2015; 15:289. [PMID: 26654876 PMCID: PMC4676884 DOI: 10.1186/s12870-015-0678-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/07/2015] [Indexed: 05/17/2023]
Abstract
BACKGROUND Type VI glandular trichomes represent the most abundant trichome type on leaves and stems of tomato plants and significantly contribute to herbivore resistance, particularly in the wild species. Despite this, their development has been poorly studied so far. The goal of this study is to fill this gap. Using a variety of cell imaging techniques, a detailed record of the anatomy and developmental stages of type VI trichomes in the cultivated tomato (Solanum lycopersicum) and in a related wild species (S. habrochaites) is provided. RESULTS In both species, the development of these structures follows a highly reproducible cell division pattern. The two species differ in the shape of the trichome head which is round in S. habrochaites and like a four-leaf clover in S. lycopersicum, correlating with the presence of a large intercellular cavity in S. habrochaites where the produced metabolites accumulate. In both species, the junction between the intermediate cell and the four glandular cells constitute a breaking point facilitating the decapitation of the trichome and thereby the quick release of the metabolites. A strongly auto-fluorescent compound transiently accumulates in the early stages of development suggesting a potential role in the differentiation process. Finally, immuno-labelling with antibodies recognizing specific cell wall components indicate a key role of pectin and arabinogalactan components in the differentiation of type VI trichomes. CONCLUSIONS Our observations explain the adaptive morphologies of type VI trichomes for metabolite storage and release and provide a framework for further studies of these important metabolic cellular factories. This is required to better exploit their potential, in particular for the breeding of pest resistance in tomato.
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Affiliation(s)
- Nick Bergau
- Department of Cell and Metabolic Biology, Leibniz-Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany.
| | - Stefan Bennewitz
- Department of Cell and Metabolic Biology, Leibniz-Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany.
| | - Frank Syrowatka
- Interdisciplinary Center for Material Sciences, Martin-Luther University Halle-Wittenberg, Heinrich-Damerow-Str. 4, 06120, Halle, Saale, Germany.
| | - Gerd Hause
- Biocenter of the Martin-Luther University Halle-Wittenberg, Weinbergweg 22, 06120, Halle, Saale, Germany.
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz-Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany.
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