151
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Denyer T, Timmermans MCP. Crafting a blueprint for single-cell RNA sequencing. TRENDS IN PLANT SCIENCE 2022; 27:92-103. [PMID: 34580023 DOI: 10.1016/j.tplants.2021.08.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/23/2021] [Accepted: 08/31/2021] [Indexed: 05/05/2023]
Abstract
Droplet-based single-cell RNA sequencing (scRNA-Seq) has moved rapidly from a technology with great potential to a method applied to ever-broader questions. The detailed information that scRNA-Seq offers has proven incredibly powerful in resolving cell responses to developmental and environmental cues. However, to maximize the potential of this technology, a panoply of upstream, practical points require consideration. Principal among these are the optimization of cell-isolation procedures, accommodating biotic/abiotic stress responses, and discerning the number of cells and sequencing reads needed. To complement excellent reviews outlining applications and data analysis tools for scRNA-Seq, we here discuss these considerations and provide practical tips to tailor experimental design and ensure the best possible outcome.
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Affiliation(s)
- Tom Denyer
- Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Marja C P Timmermans
- Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany.
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152
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Xu Z, Wang Q, Zhu X, Wang G, Qin Y, Ding F, Tu L, Daniell H, Zhang X, Jin S. Plant Single Cell Transcriptome Hub (PsctH): an integrated online tool to explore the plant single-cell transcriptome landscape. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:10-12. [PMID: 34651402 PMCID: PMC8710823 DOI: 10.1111/pbi.13725] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/22/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Zhongping Xu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Qiongqiong Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Xiangqian Zhu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Guanying Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Yuan Qin
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Fang Ding
- Hubei Key Laboratory of Plant PathologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Lili Tu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Henry Daniell
- Department of Basic and Translational SciencesSchool of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
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153
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Sanden NC, Schulz A. Identification of new proteins in mature sieve elements. PHYSIOLOGIA PLANTARUM 2022; 174:e13634. [PMID: 35060148 DOI: 10.1111/ppl.13634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 01/16/2022] [Indexed: 06/14/2023]
Abstract
The phloem enables vascular plants to transport photoassimilates from source tissues to heterotrophic sink tissues. In the phloem, unbroken strings of enucleated sieve elements, which lose the majority of their cellular contents upon maturation, provide a low resistance path for mass flow. The protein machinery in mature sieve elements performs vital functions to maintain the flow, transmit systemic signals and defend the sugar stream against pests. However, our knowledge of this particular protein population is very limited since mature sieve elements are difficult to isolate and not amenable to transcriptomic analysis due to their enucleate nature. Here, we used co-expression analysis and published gene clusters from transcriptomic studies to generate a list of sieve element proteins that potentially survive the enucleation process to reside in mature sieve elements. We selected seven candidates and show that they all localize in sieve elements in Arabidopsis roots and six of them in bolting stems. Our results support the idea that nascent sieve elements prior to enucleation translate part of the protein machinery found in mature sieve elements. Our co-expression list and the publicly available gene clusters expressed in late proto- and meta-phloem sieve elements are valuable resources for uncharacterized genes that may function in mature sieve elements.
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Affiliation(s)
- Niels Christian Sanden
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- Section for Transport biology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Alexander Schulz
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- Section for Transport biology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
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154
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Chávez-Hernández EC, Quiroz S, García-Ponce B, Álvarez-Buylla ER. The flowering transition pathways converge into a complex gene regulatory network that underlies the phase changes of the shoot apical meristem in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022; 13:852047. [PMID: 36017258 PMCID: PMC9396034 DOI: 10.3389/fpls.2022.852047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 07/04/2022] [Indexed: 05/08/2023]
Abstract
Post-embryonic plant development is characterized by a period of vegetative growth during which a combination of intrinsic and extrinsic signals triggers the transition to the reproductive phase. To understand how different flowering inducing and repressing signals are associated with phase transitions of the Shoot Apical Meristem (SAM), we incorporated available data into a dynamic gene regulatory network model for Arabidopsis thaliana. This Flowering Transition Gene Regulatory Network (FT-GRN) formally constitutes a dynamic system-level mechanism based on more than three decades of experimental data on flowering. We provide novel experimental data on the regulatory interactions of one of its twenty-three components: a MADS-box transcription factor XAANTAL2 (XAL2). These data complement the information regarding flowering transition under short days and provides an example of the type of questions that can be addressed by the FT-GRN. The resulting FT-GRN is highly connected and integrates developmental, hormonal, and environmental signals that affect developmental transitions at the SAM. The FT-GRN is a dynamic multi-stable Boolean system, with 223 possible initial states, yet it converges into only 32 attractors. The latter are coherent with the expression profiles of the FT-GRN components that have been experimentally described for the developmental stages of the SAM. Furthermore, the attractors are also highly robust to initial states and to simulated perturbations of the interaction functions. The model recovered the meristem phenotypes of previously described single mutants. We also analyzed the attractors landscape that emerges from the postulated FT-GRN, uncovering which set of signals or components are critical for reproductive competence and the time-order transitions observed in the SAM. Finally, in the context of such GRN, the role of XAL2 under short-day conditions could be understood. Therefore, this model constitutes a robust biological module and the first multi-stable, dynamical systems biology mechanism that integrates the genetic flowering pathways to explain SAM phase transitions.
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Affiliation(s)
- Elva C. Chávez-Hernández
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Stella Quiroz
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- *Correspondence: Berenice García-Ponce,
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Elena R. Álvarez-Buylla,
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155
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Roszak P, Heo JO, Blob B, Toyokura K, Sugiyama Y, de Luis Balaguer MA, Lau WWY, Hamey F, Cirrone J, Madej E, Bouatta AM, Wang X, Guichard M, Ursache R, Tavares H, Verstaen K, Wendrich J, Melnyk CW, Oda Y, Shasha D, Ahnert SE, Saeys Y, De Rybel B, Heidstra R, Scheres B, Grossmann G, Mähönen AP, Denninger P, Göttgens B, Sozzani R, Birnbaum KD, Helariutta Y. Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization. Science 2021; 374:eaba5531. [PMID: 34941412 PMCID: PMC8730638 DOI: 10.1126/science.aba5531] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In the plant meristem, tissue-wide maturation gradients are coordinated with specialized cell networks to establish various developmental phases required for indeterminate growth. Here, we used single-cell transcriptomics to reconstruct the protophloem developmental trajectory from the birth of cell progenitors to terminal differentiation in the Arabidopsis thaliana root. PHLOEM EARLY DNA-BINDING-WITH-ONE-FINGER (PEAR) transcription factors mediate lineage bifurcation by activating guanosine triphosphatase signaling and prime a transcriptional differentiation program. This program is initially repressed by a meristem-wide gradient of PLETHORA transcription factors. Only the dissipation of PLETHORA gradient permits activation of the differentiation program that involves mutual inhibition of early versus late meristem regulators. Thus, for phloem development, broad maturation gradients interface with cell-type-specific transcriptional regulators to stage cellular differentiation.
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Affiliation(s)
- Pawel Roszak
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Jung-Ok Heo
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Institute of Biotechnology, HiLIFE/Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Bernhard Blob
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Koichi Toyokura
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
- Faculty of Science and Engineering, Konan University, Kobe, Japan
- GRA&GREEN Inc., Incubation Facility, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Yuki Sugiyama
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
| | | | - Winnie W Y Lau
- Wellcome Trust and MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge, UK
| | - Fiona Hamey
- Wellcome Trust and MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge, UK
| | - Jacopo Cirrone
- Computer Science Department, Courant Institute for Mathematical Sciences, New York University, New York, NY, USA
| | - Ewelina Madej
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Alida M Bouatta
- Plant Systems Biology, Technical University of Munich, Freising, Germany
| | - Xin Wang
- Institute of Biotechnology, HiLIFE/Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Marjorie Guichard
- Institute of Cell and Interaction Biology, CEPLAS, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Robertas Ursache
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Hugo Tavares
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Bioinformatics Training Facility, Department of Genetics, University of Cambridge, Cambridge, UK
| | - Kevin Verstaen
- Data Mining and Modelling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Jos Wendrich
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Charles W Melnyk
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Yoshihisa Oda
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
- Department of Genetics, the Graduate University for Advanced Studies, SOKENDAI, Mishima, Japan
| | - Dennis Shasha
- Computer Science Department, Courant Institute for Mathematical Sciences, New York University, New York, NY, USA
| | - Sebastian E Ahnert
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- The Alan Turing Institute, British Library, London, UK
| | - Yvan Saeys
- Data Mining and Modelling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Renze Heidstra
- Department of Plant Sciences, Wageningen University and Research, Wageningen, Netherlands
| | - Ben Scheres
- Department of Plant Sciences, Wageningen University and Research, Wageningen, Netherlands
- Rijk Zwaan R&D, 4793 Fijnaart, Netherlands
| | - Guido Grossmann
- Institute of Cell and Interaction Biology, CEPLAS, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Ari Pekka Mähönen
- Institute of Biotechnology, HiLIFE/Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Philipp Denninger
- Plant Systems Biology, Technical University of Munich, Freising, Germany
| | - Berthold Göttgens
- Wellcome Trust and MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge, UK
| | - Rosangela Sozzani
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC, USA
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Yrjö Helariutta
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Institute of Biotechnology, HiLIFE/Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
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156
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A Transcriptomic Atlas of the Ectomycorrhizal Fungus Laccaria bicolor. Microorganisms 2021; 9:microorganisms9122612. [PMID: 34946213 PMCID: PMC8708209 DOI: 10.3390/microorganisms9122612] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 02/05/2023] Open
Abstract
Trees are able to colonize, establish and survive in a wide range of soils through associations with ectomycorrhizal (EcM) fungi. Proper functioning of EcM fungi implies the differentiation of structures within the fungal colony. A symbiotic structure is dedicated to nutrient exchange and the extramatricular mycelium explores soil for nutrients. Eventually, basidiocarps develop to assure last stages of sexual reproduction. The aim of this study is to understand how an EcM fungus uses its gene set to support functional differentiation and development of specialized morphological structures. We examined the transcriptomes of Laccaria bicolor under a series of experimental setups, including the growth with Populus tremula x alba at different developmental stages, basidiocarps and free-living mycelium, under various conditions of N, P and C supply. In particular, N supply induced global transcriptional changes, whereas responses to P supply seemed to be independent from it. Symbiosis development with poplar is characterized by transcriptional waves. Basidiocarp development shares transcriptional signatures with other basidiomycetes. Overlaps in transcriptional responses of L. bicolor hyphae to a host plant and N/C supply next to co-regulation of genes in basidiocarps and mature mycorrhiza were detected. Few genes are induced in a single condition only, but functional and morphological differentiation rather involves fine tuning of larger gene sets. Overall, this transcriptomic atlas builds a reference to study the function and stability of EcM symbiosis in distinct conditions using L. bicolor as a model and indicates both similarities and differences with other ectomycorrhizal fungi, allowing researchers to distinguish conserved processes such as basidiocarp development from nutrient homeostasis.
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157
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Thibivilliers SB, Anderson DK, Libault MY. Isolation of Plant Nuclei Compatible with Microfluidic Single-nucleus ATAC-sequencing. Bio Protoc 2021; 11:e4240. [PMID: 35005085 DOI: 10.21769/bioprotoc.4240] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/29/2021] [Accepted: 09/06/2021] [Indexed: 11/02/2022] Open
Abstract
Gene expression depends on the binding of transcription factors with DNA regulatory sequences. The level of accessibility for these sequences varies between cells and cell types. Until recently, using the Tn5 assay for transposase-accessible chromatin for sequencing (ATAC-seq) technology allowed assessing the profiles of chromatin from an entire organ or, when coupled with the isolation of nuclei tagged in specific cell types (INTACT) method, from a cell-type. Recently, ATAC-seq experiments were conducted at the level of individual plant nuclei. Applying single nuclei ATAC-seq (sNucATAC-seq) technology to thousands of individual cells revealed more finely tuned profiles of chromatin accessibility. In this manuscript, we describe a method to isolate nuclei fom plant roots and green tissues, permeabilize the nuclear membrane using detergent to allow the penetration of the Tn5 transposase, and re-suspend them in a nuclei resuspension buffer compatible with the construction of sNucATAC-seq libraries using the 10× Genomic's Chromium technology. This protocol was successfully applied on Arabidopsis thaliana and Glycine max root nuclei.
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Affiliation(s)
- Sandra B Thibivilliers
- Department of Agronomy and Horticulture, Centre for Plant Science Innovation, Center for Root and Rhizobiome Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Dirk K Anderson
- Flow Cytometry Service Center, Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Marc Y Libault
- Department of Agronomy and Horticulture, Centre for Plant Science Innovation, Center for Root and Rhizobiome Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
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158
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Kim JY, Loo EPI, Pang TY, Lercher M, Frommer WB, Wudick MM. Cellular export of sugars and amino acids: role in feeding other cells and organisms. PLANT PHYSIOLOGY 2021; 187:1893-1914. [PMID: 34015139 PMCID: PMC8644676 DOI: 10.1093/plphys/kiab228] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/29/2021] [Indexed: 05/20/2023]
Abstract
Sucrose, hexoses, and raffinose play key roles in the plant metabolism. Sucrose and raffinose, produced by photosynthesis, are translocated from leaves to flowers, developing seeds and roots. Translocation occurs in the sieve elements or sieve tubes of angiosperms. But how is sucrose loaded into and unloaded from the sieve elements? There seem to be two principal routes: one through plasmodesmata and one via the apoplasm. The best-studied transporters are the H+/SUCROSE TRANSPORTERs (SUTs) in the sieve element-companion cell complex. Sucrose is delivered to SUTs by SWEET sugar uniporters that release these key metabolites into the apoplasmic space. The H+/amino acid permeases and the UmamiT amino acid transporters are hypothesized to play analogous roles as the SUT-SWEET pair to transport amino acids. SWEETs and UmamiTs also act in many other important processes-for example, seed filling, nectar secretion, and pollen nutrition. We present information on cell type-specific enrichment of SWEET and UmamiT family members and propose several members to play redundant roles in the efflux of sucrose and amino acids across different cell types in the leaf. Pathogens hijack SWEETs and thus represent a major susceptibility of the plant. Here, we provide an update on the status of research on intercellular and long-distance translocation of key metabolites such as sucrose and amino acids, communication of the plants with the root microbiota via root exudates, discuss the existence of transporters for other important metabolites and provide potential perspectives that may direct future research activities.
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Affiliation(s)
- Ji-Yun Kim
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Eliza P -I Loo
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Tin Yau Pang
- Institute for Computer Science and Department of Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Martin Lercher
- Institute for Computer Science and Department of Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Wolf B Frommer
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Michael M Wudick
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
- Author for communication:
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159
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Cantó-Pastor A, Mason GA, Brady SM, Provart NJ. Arabidopsis bioinformatics: tools and strategies. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1585-1596. [PMID: 34695270 DOI: 10.1111/tpj.15547] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/01/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
The sequencing of the Arabidopsis thaliana genome 21 years ago ushered in the genomics era for plant research. Since then, an incredible variety of bioinformatic tools permit easy access to large repositories of genomic, transcriptomic, proteomic, epigenomic and other '-omic' data. In this review, we cover some more recent tools (and highlight the 'classics') for exploring such data in order to help formulate quality, testable hypotheses, often without having to generate new experimental data. We cover tools for examining gene expression and co-expression patterns, undertaking promoter analyses and gene set enrichment analyses, and exploring protein-protein and protein-DNA interactions. We will touch on tools that integrate different data sets at the end of the article.
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Affiliation(s)
- Alex Cantó-Pastor
- Department of Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - G Alex Mason
- Department of Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
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160
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Chen Y, Tong S, Jiang Y, Ai F, Feng Y, Zhang J, Gong J, Qin J, Zhang Y, Zhu Y, Liu J, Ma T. Transcriptional landscape of highly lignified poplar stems at single-cell resolution. Genome Biol 2021; 22:319. [PMID: 34809675 PMCID: PMC8607660 DOI: 10.1186/s13059-021-02537-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/10/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Plant secondary growth depends on the activity of the vascular cambium, which produces xylem and phloem. Wood derived from xylem is the most abundant form of biomass globally and has played key socio-economic and subsistence roles throughout human history. However, despite intensive study of vascular development, the full diversity of cell types and the gene networks engaged are still poorly understood. RESULTS Here, we have applied an optimized protoplast isolation protocol and RNA sequencing to characterize the high-resolution single-cell transcriptional landscape of highly lignified poplar stems. We identify 20 putative cell clusters with a series of novel cluster-specific marker genes and find that these cells are highly heterogeneous based on the transcriptome. Analysis of these marker genes' expression dynamics enables reconstruction of the cell differentiation trajectories involved in phloem and xylem development. We find that different cell clusters exhibit distinct patterns of phytohormone responses and emphasize the use of our data to predict potential gene redundancy and identify candidate genes related to vascular development in trees. CONCLUSIONS These findings establish the transcriptional landscape of major cell types of poplar stems at single-cell resolution and provide a valuable resource for investigating basic principles of vascular cell specification and differentiation in trees.
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Affiliation(s)
- Yang Chen
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Shaofei Tong
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yuanzhong Jiang
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Fandi Ai
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yanlin Feng
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Junlin Zhang
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jue Gong
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jiajia Qin
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yuanyuan Zhang
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yingying Zhu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Tao Ma
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
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161
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Pasternak T, Pérez-Pérez JM. Methods of In Situ Quantitative Root Biology. PLANTS (BASEL, SWITZERLAND) 2021; 10:2399. [PMID: 34834762 PMCID: PMC8625443 DOI: 10.3390/plants10112399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 11/30/2022]
Abstract
When dealing with plant roots, a multiscale description of the functional root structure is needed. Since the beginning of 21st century, new devices such as laser confocal microscopes have been accessible for coarse root structure measurements, including three-dimensional (3D) reconstruction. Most researchers are familiar with using simple 2D geometry visualization that does not allow quantitative determination of key morphological features from an organ-like perspective. We provide here a detailed description of the quantitative methods available for 3D analysis of root features at single-cell resolution, including root asymmetry, lateral root analysis, cell size and nuclear organization, cell-cycle kinetics, and chromatin structure analysis. Quantitative maps of the root apical meristem (RAM) are shown for different species, including Arabidopsis thaliana (L.), Heynh, Nicotiana tabacum L., Medicago sativa L., and Setaria italica (L.) P. Beauv. The 3D analysis of the RAM in these species showed divergence in chromatin organization and cell volume distribution that might be used to study root zonation for each root tissue. Detailed protocols and possible pitfalls in the usage of the marker lines are discussed. Therefore, researchers who need to improve their quantitative root biology portfolio can use them as a reference.
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Affiliation(s)
- Taras Pasternak
- Centre for BioSystems Analysis, BIOSS Centre for Biological Signalling Studies University of Freiburg, Institute of Biology II/Molecular Plant Physiology, 79104 Freiburg, Germany
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Hadizadeh Esfahani A, Maß J, Hallab A, Schuldt BM, Nevarez D, Usadel B, Ott MC, Buer B, Schuppert A. Plant PhysioSpace: a robust tool to compare stress response across plant species. PLANT PHYSIOLOGY 2021; 187:1795-1811. [PMID: 34734276 PMCID: PMC8566309 DOI: 10.1093/plphys/kiab325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 06/12/2021] [Indexed: 06/13/2023]
Abstract
Generalization of transcriptomics results can be achieved by comparison across experiments. This generalization is based on integration of interrelated transcriptomics studies into a compendium. Such a focus on the bigger picture enables both characterizations of the fate of an organism and distinction between generic and specific responses. Numerous methods for analyzing transcriptomics datasets exist. Yet, most of these methods focus on gene-wise dimension reduction to obtain marker genes and gene sets for, for example, pathway analysis. Relying only on isolated biological modules might result in missing important confounders and relevant contexts. We developed a method called Plant PhysioSpace, which enables researchers to compute experimental conditions across species and platforms without a priori reducing the reference information to specific gene sets. Plant PhysioSpace extracts physiologically relevant signatures from a reference dataset (i.e. a collection of public datasets) by integrating and transforming heterogeneous reference gene expression data into a set of physiology-specific patterns. New experimental data can be mapped to these patterns, resulting in similarity scores between the acquired data and the extracted compendium. Because of its robustness against platform bias and noise, Plant PhysioSpace can function as an inter-species or cross-platform similarity measure. We have demonstrated its success in translating stress responses between different species and platforms, including single-cell technologies. We have also implemented two R packages, one software and one data package, and a Shiny web application to facilitate access to our method and precomputed models.
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Affiliation(s)
- Ali Hadizadeh Esfahani
- Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen 52074, Germany
| | - Janina Maß
- IBG-4: Bioinformatics, Forschungszentrum Jülich, Jülich 52425, Germany
| | - Asis Hallab
- IBG-4: Bioinformatics, Forschungszentrum Jülich, Jülich 52425, Germany
| | | | - David Nevarez
- Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen 52074, Germany
| | - Björn Usadel
- IBG-4: Bioinformatics, Forschungszentrum Jülich, Jülich 52425, Germany
| | | | - Benjamin Buer
- Crop Science Division, Bayer AG, Monheim am Rhein 40789, Germany
| | - Andreas Schuppert
- Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen 52074, Germany
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163
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Hawkins C, Ginzburg D, Zhao K, Dwyer W, Xue B, Xu A, Rice S, Cole B, Paley S, Karp P, Rhee SY. Plant Metabolic Network 15: A resource of genome-wide metabolism databases for 126 plants and algae. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1888-1905. [PMID: 34403192 DOI: 10.1111/jipb.13163] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 08/14/2021] [Indexed: 05/18/2023]
Abstract
To understand and engineer plant metabolism, we need a comprehensive and accurate annotation of all metabolic information across plant species. As a step towards this goal, we generated genome-scale metabolic pathway databases of 126 algal and plant genomes, ranging from model organisms to crops to medicinal plants (https://plantcyc.org). Of these, 104 have not been reported before. We systematically evaluated the quality of the databases, which revealed that our semi-automated validation pipeline dramatically improves the quality. We then compared the metabolic content across the 126 organisms using multiple correspondence analysis and found that Brassicaceae, Poaceae, and Chlorophyta appeared as metabolically distinct groups. To demonstrate the utility of this resource, we used recently published sorghum transcriptomics data to discover previously unreported trends of metabolism underlying drought tolerance. We also used single-cell transcriptomics data from the Arabidopsis root to infer cell type-specific metabolic pathways. This work shows the quality and quantity of our resource and demonstrates its wide-ranging utility in integrating metabolism with other areas of plant biology.
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Affiliation(s)
- Charles Hawkins
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - Daniel Ginzburg
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - Kangmei Zhao
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - William Dwyer
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - Bo Xue
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - Angela Xu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - Selena Rice
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - Benjamin Cole
- DOE-Joint Genome Institute, Lawrence Berkeley Laboratory, Berkeley, California, 94720, USA
| | - Suzanne Paley
- SRI International, Menlo Park, California, 94025, USA
| | - Peter Karp
- SRI International, Menlo Park, California, 94025, USA
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
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164
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Sanden NC, Schulz A. Stationary sieve element proteins. JOURNAL OF PLANT PHYSIOLOGY 2021; 266:153511. [PMID: 34537466 DOI: 10.1016/j.jplph.2021.153511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/13/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
Vascular plants use the phloem to move sugars and other molecules from source leaves to sink organs such as roots and fruits. Within the phloem, enucleate sieve elements provide the low-resistance pipe system that enable bulk flow of sap. In this review, we provide an overview of the highly specific protein machinery that localize to mature sieve elements without entering the phloem translocation stream. Generally, the proteins either maintain the flow, protect the sieve element against pathogens or transmit system wide signals. A notable exception is found in poppy, where part of the opium biosynthesis is compartmentalized in sieve elements. Biosynthesis of sieve element proteins happens either continuously in companion cell or transiently in immature sieve elements before nuclear disintegration. The latter population is translated during differentiation and stays functional without turnover during the entire lifespan of sieve elements. We discuss how protein longevity imposes some interesting restrictions on plants, especially in arborescent monocots with long living sieve elements.
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Affiliation(s)
- Niels Christian Sanden
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark; Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Alexander Schulz
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark; Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
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165
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Liu H, Hu D, Du P, Wang L, Liang X, Li H, Lu Q, Li S, Liu H, Chen X, Varshney RK, Hong Y. Single-cell RNA-seq describes the transcriptome landscape and identifies critical transcription factors in the leaf blade of the allotetraploid peanut (Arachis hypogaea L.). PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2261-2276. [PMID: 34174007 PMCID: PMC8541777 DOI: 10.1111/pbi.13656] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 05/26/2023]
Abstract
Single-cell RNA-seq (scRNA-seq) has been highlighted as a powerful tool for the description of human cell transcriptome, but the technology has not been broadly applied in plant cells. Herein, we describe the successful development of a robust protoplast cell isolation system in the peanut leaf. A total of 6,815 single cells were divided into eight cell clusters based on reported marker genes by applying scRNA-seq. Further, a pseudo-time analysis was used to describe the developmental trajectory and interaction network of transcription factors (TFs) of distinct cell types during leaf growth. The trajectory enabled re-investigation of the primordium-driven development processes of the mesophyll and epidermis. These results suggest that palisade cells likely differentiate into spongy cells, while the epidermal cells originated earlier than the primordium. Subsequently, the developed method integrated multiple technologies to efficiently validate the scRNA-seq result in a homogenous cell population. The expression levels of several TFs were strongly correlated with epidermal ontogeny in accordance with obtained scRNA-seq values. Additionally, peanut AHL23 (AT-HOOK MOTIF NUCLEAR LOCALIZED PROTEIN 23), which is localized in nucleus, promoted leaf growth when ectopically expressed in Arabidopsis by modulating the phytohormone pathway. Together, our study displays that application of scRNA-seq can provide new hypotheses regarding cell differentiation in the leaf blade of Arachis hypogaea. We believe that this approach will enable significant advances in the functional study of leaf blade cells in the allotetraploid peanut and other plant species.
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Affiliation(s)
- Hao Liu
- Guangdong Provincial Key Laboratory of Crop Genetic ImprovementSouth China Peanut Sub‐Center of National Center of Oilseed Crops ImprovementCrops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Dongxiu Hu
- Guangdong Provincial Key Laboratory of Crop Genetic ImprovementSouth China Peanut Sub‐Center of National Center of Oilseed Crops ImprovementCrops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Puxuan Du
- Guangdong Provincial Key Laboratory of Crop Genetic ImprovementSouth China Peanut Sub‐Center of National Center of Oilseed Crops ImprovementCrops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Liping Wang
- Guangdong Provincial Key Laboratory of Crop Genetic ImprovementSouth China Peanut Sub‐Center of National Center of Oilseed Crops ImprovementCrops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Xuanqiang Liang
- Guangdong Provincial Key Laboratory of Crop Genetic ImprovementSouth China Peanut Sub‐Center of National Center of Oilseed Crops ImprovementCrops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Haifen Li
- Guangdong Provincial Key Laboratory of Crop Genetic ImprovementSouth China Peanut Sub‐Center of National Center of Oilseed Crops ImprovementCrops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Qing Lu
- Guangdong Provincial Key Laboratory of Crop Genetic ImprovementSouth China Peanut Sub‐Center of National Center of Oilseed Crops ImprovementCrops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Shaoxiong Li
- Guangdong Provincial Key Laboratory of Crop Genetic ImprovementSouth China Peanut Sub‐Center of National Center of Oilseed Crops ImprovementCrops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Haiyan Liu
- Guangdong Provincial Key Laboratory of Crop Genetic ImprovementSouth China Peanut Sub‐Center of National Center of Oilseed Crops ImprovementCrops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Xiaoping Chen
- Guangdong Provincial Key Laboratory of Crop Genetic ImprovementSouth China Peanut Sub‐Center of National Center of Oilseed Crops ImprovementCrops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadTelanganaIndia
- State Agricultural Biotechnology CentreCentre for Crop and Food InnovationFood Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Yanbin Hong
- Guangdong Provincial Key Laboratory of Crop Genetic ImprovementSouth China Peanut Sub‐Center of National Center of Oilseed Crops ImprovementCrops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
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166
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Sunaga-Franze DY, Muino JM, Braeuning C, Xu X, Zong M, Smaczniak C, Yan W, Fischer C, Vidal R, Kliem M, Kaufmann K, Sauer S. Single-nucleus RNA sequencing of plant tissues using a nanowell-based system. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:859-869. [PMID: 34390289 DOI: 10.1111/tpj.15458] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 07/16/2021] [Accepted: 08/02/2021] [Indexed: 05/25/2023]
Abstract
Single-cell genomics provides unprecedented potential for research on plant development and environmental responses. Here, we introduce a generic procedure for plant nucleus isolation combined with nanowell-based library preparation. Our method enables the transcriptome analysis of thousands of individual plant nuclei. It serves as an alternative to the use of protoplast isolation, which is currently a standard methodology for plant single-cell genomics, although it can be challenging for some plant tissues. We show the applicability of our nucleus isolation method by using different plant materials from different species. The potential of our single-nucleus RNA sequencing method is shown through the characterization of transcriptomes of seedlings and developing flowers from Arabidopsis thaliana. We evaluated the transcriptome dynamics during the early stages of anther development, identified stage-specific activities of transcription factors regulating this process, and predicted potential target genes of these transcription factors. Our nucleus isolation procedure can be applied in different plant species and tissues, thus expanding the toolkit for plant single-cell genomics experiments.
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Affiliation(s)
- Daniele Y Sunaga-Franze
- Genomics Platforms, Max Delbrück Center for Molecular Medicine in the Helmholtz Association/Berlin Institute of Health, Berlin, Germany
| | - Jose M Muino
- Systems Biology of Gene Regulation, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Caroline Braeuning
- Genomics Platforms, Max Delbrück Center for Molecular Medicine in the Helmholtz Association/Berlin Institute of Health, Berlin, Germany
| | - Xiaocai Xu
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Minglei Zong
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Cezary Smaczniak
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Wenhao Yan
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Cornelius Fischer
- Genomics Platforms, Max Delbrück Center for Molecular Medicine in the Helmholtz Association/Berlin Institute of Health, Berlin, Germany
| | - Ramon Vidal
- Genomics Platforms, Max Delbrück Center for Molecular Medicine in the Helmholtz Association/Berlin Institute of Health, Berlin, Germany
| | - Magdalena Kliem
- Genomics Platforms, Max Delbrück Center for Molecular Medicine in the Helmholtz Association/Berlin Institute of Health, Berlin, Germany
| | - Kerstin Kaufmann
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sascha Sauer
- Genomics Platforms, Max Delbrück Center for Molecular Medicine in the Helmholtz Association/Berlin Institute of Health, Berlin, Germany
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167
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Li H, Dai X, Huang X, Xu M, Wang Q, Yan X, Sederoff RR, Li Q. Single-cell RNA sequencing reveals a high-resolution cell atlas of xylem in Populus. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1906-1921. [PMID: 34347368 DOI: 10.1111/jipb.13159] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/02/2021] [Indexed: 05/24/2023]
Abstract
High-throughput single-cell RNA sequencing (scRNA-seq) has advantages over traditional RNA-seq to explore spatiotemporal information on gene dynamic expressions in heterogenous tissues. We performed Drop-seq, a method for the dropwise sequestration of single cells for sequencing, on protoplasts from the differentiating xylem of Populus alba × Populus glandulosa. The scRNA-seq profiled 9,798 cells, which were grouped into 12 clusters. Through characterization of differentially expressed genes in each cluster and RNA in situ hybridizations, we identified vessel cells, fiber cells, ray parenchyma cells and xylem precursor cells. Diffusion pseudotime analyses revealed the differentiating trajectory of vessels, fiber cells and ray parenchyma cells and indicated a different differentiation process between vessels and fiber cells, and a similar differentiation process between fiber cells and ray parenchyma cells. We identified marker genes for each cell type (cluster) and key candidate regulators during developmental stages of xylem cell differentiation. Our study generates a high-resolution expression atlas of wood formation at the single cell level and provides valuable information on wood formation.
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Affiliation(s)
- Hui Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xinren Dai
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xiong Huang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Mengxuan Xu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Qiao Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xiaojing Yan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Ronald R Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
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168
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Sunaga-Franze DY, Muino JM, Braeuning C, Xu X, Zong M, Smaczniak C, Yan W, Fischer C, Vidal R, Kliem M, Kaufmann K, Sauer S. Single-nucleus RNA sequencing of plant tissues using a nanowell-based system. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:859-869. [PMID: 34390289 DOI: 10.1101/2020.11.14.382812] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 07/16/2021] [Accepted: 08/02/2021] [Indexed: 05/22/2023]
Abstract
Single-cell genomics provides unprecedented potential for research on plant development and environmental responses. Here, we introduce a generic procedure for plant nucleus isolation combined with nanowell-based library preparation. Our method enables the transcriptome analysis of thousands of individual plant nuclei. It serves as an alternative to the use of protoplast isolation, which is currently a standard methodology for plant single-cell genomics, although it can be challenging for some plant tissues. We show the applicability of our nucleus isolation method by using different plant materials from different species. The potential of our single-nucleus RNA sequencing method is shown through the characterization of transcriptomes of seedlings and developing flowers from Arabidopsis thaliana. We evaluated the transcriptome dynamics during the early stages of anther development, identified stage-specific activities of transcription factors regulating this process, and predicted potential target genes of these transcription factors. Our nucleus isolation procedure can be applied in different plant species and tissues, thus expanding the toolkit for plant single-cell genomics experiments.
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Affiliation(s)
- Daniele Y Sunaga-Franze
- Genomics Platforms, Max Delbrück Center for Molecular Medicine in the Helmholtz Association/Berlin Institute of Health, Berlin, Germany
| | - Jose M Muino
- Systems Biology of Gene Regulation, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Caroline Braeuning
- Genomics Platforms, Max Delbrück Center for Molecular Medicine in the Helmholtz Association/Berlin Institute of Health, Berlin, Germany
| | - Xiaocai Xu
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Minglei Zong
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Cezary Smaczniak
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Wenhao Yan
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Cornelius Fischer
- Genomics Platforms, Max Delbrück Center for Molecular Medicine in the Helmholtz Association/Berlin Institute of Health, Berlin, Germany
| | - Ramon Vidal
- Genomics Platforms, Max Delbrück Center for Molecular Medicine in the Helmholtz Association/Berlin Institute of Health, Berlin, Germany
| | - Magdalena Kliem
- Genomics Platforms, Max Delbrück Center for Molecular Medicine in the Helmholtz Association/Berlin Institute of Health, Berlin, Germany
| | - Kerstin Kaufmann
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sascha Sauer
- Genomics Platforms, Max Delbrück Center for Molecular Medicine in the Helmholtz Association/Berlin Institute of Health, Berlin, Germany
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169
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Wu J, Fang Z, Liu T, Hu W, Wu Y, Li S. Maximizing the Utility of Transcriptomics Data in Inflammatory Skin Diseases. Front Immunol 2021; 12:761890. [PMID: 34777377 PMCID: PMC8586455 DOI: 10.3389/fimmu.2021.761890] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022] Open
Abstract
Inflammatory skin diseases are induced by disorders of the host defense system of the skin, which is composed of a barrier, innate and acquired immunity, as well as the cutaneous microbiome. These disorders are characterized by recurrent cutaneous lesions and intense itch, which seriously affecting life quality of people across all ages and ethnicities. To elucidate molecular factors for typical inflammatory skin diseases (such as psoriasis and atopic dermatitis), transcriptomic profiling assays have been largely performed. Additionally, single-cell RNA sequencing (scRNA-seq) as well as spatial transcriptomic profiling have revealed multiple potential translational targets and offered guides to improve diagnosis and treatment strategies for inflammatory skin diseases. High-throughput transcriptomics data has shown unprecedented power to disclose the complex pathophysiology of inflammatory skin diseases. Here, we will summarize discoveries from transcriptomics data and discuss how to maximize the transcriptomics data to propel the development of diagnostic biomarkers and therapeutic targets in inflammatory skin diseases.
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Affiliation(s)
- Jingni Wu
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhixiao Fang
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Teng Liu
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Hu
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yangjun Wu
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Shengli Li
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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170
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Jin J, Lu P, Xu Y, Tao J, Li Z, Wang S, Yu S, Wang C, Xie X, Gao J, Chen Q, Wang L, Pu W, Cao P. PCMDB: a curated and comprehensive resource of plant cell markers. Nucleic Acids Res 2021; 50:D1448-D1455. [PMID: 34718712 PMCID: PMC8728192 DOI: 10.1093/nar/gkab949] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/29/2021] [Accepted: 10/02/2021] [Indexed: 11/12/2022] Open
Abstract
The advent of single-cell sequencing opened a new era in transcriptomic and genomic research. To understand cell composition using single-cell studies, a variety of cell markers have been widely used to label individual cell types. However, the specific database of cell markers for use by the plant research community remains very limited. To overcome this problem, we developed the Plant Cell Marker DataBase (PCMDB, http://www.tobaccodb.org/pcmdb/), which is based on a uniform annotation pipeline. By manually curating over 130 000 research publications, we collected a total of 81 117 cell marker genes of 263 cell types in 22 tissues across six plant species. Tissue- and cell-specific expression patterns can be visualized using multiple tools: eFP Browser, Bar, and UMAP/TSNE graph. The PCMDB also supports several analysis tools, including SCSA and SingleR, which allows for user annotation of cell types. To provide information about plant species currently unsupported in PCMDB, potential marker genes for other plant species can be searched based on homology with the supported species. PCMDB is a user-friendly hierarchical platform that contains five built-in search engines. We believe PCMDB will constitute a useful resource for researchers working on cell type annotation and the prediction of the biological function of individual cells.
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Affiliation(s)
- Jingjing Jin
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Peng Lu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Yalong Xu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Jiemeng Tao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Zefeng Li
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Shuaibin Wang
- China Tobacco Hunan Industrial Co., Ltd., Changsha 410007, China
| | - Shizhou Yu
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China
| | - Chen Wang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Xiaodong Xie
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Junping Gao
- China Tobacco Hunan Industrial Co., Ltd., Changsha 410007, China
| | - Qiansi Chen
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Lin Wang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Wenxuan Pu
- China Tobacco Hunan Industrial Co., Ltd., Changsha 410007, China
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
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171
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Wang Y, Huan Q, Li K, Qian W. Single-cell transcriptome atlas of the leaf and root of rice seedlings. J Genet Genomics 2021; 48:881-898. [PMID: 34340913 DOI: 10.1016/j.jgg.2021.06.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 12/14/2022]
Abstract
As a multicellular organism, rice flourishes relying on gene expression diversity among cells of various functions. However, cellular-resolution transcriptome features are yet to be fully recognized, let alone cell-specific transcriptional responses to environmental stimuli. In this study, we apply single-cell RNA sequencing to both shoot and root of rice seedlings growing in Kimura B nutrient solution or exposed to various abiotic stresses and characterize transcriptomes for a total of 237,431 individual cells. We identify 15 and 9 cell types in the leaf and root, respectively, and observe that common transcriptome features are often shared between leaves and roots in the same tissue layer, except for endodermis or epidermis. Abiotic stress stimuli alter gene expression largely in a cell type-specific manner, but for a given cell type, different stresses often trigger transcriptional regulation of roughly the same set of genes. Besides, we detect proportional changes in cell populations in response to abiotic stress and investigate the underlying molecular mechanisms through single-cell reconstruction of the developmental trajectory. Collectively, our study represents a benchmark-setting data resource of single-cell transcriptome atlas for rice seedlings and an illustration of exploiting such resources to drive discoveries in plant biology.
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Affiliation(s)
- Yu Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing Huan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Ke Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenfeng Qian
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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172
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Effects of Sample Size on Plant Single-Cell RNA Profiling. Curr Issues Mol Biol 2021; 43:1685-1697. [PMID: 34698115 PMCID: PMC8929096 DOI: 10.3390/cimb43030119] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/17/2021] [Accepted: 10/15/2021] [Indexed: 01/01/2023] Open
Abstract
Single-cell RNA (scRNA) profiling or scRNA-sequencing (scRNA-seq) makes it possible to parallelly investigate diverse molecular features of multiple types of cells in a given plant tissue and discover cell developmental processes. In this study, we evaluated the effects of sample size (i.e., cell number) on the outcome of single-cell transcriptome analysis by sampling different numbers of cells from a pool of ~57,000 Arabidopsis thaliana root cells integrated from five published studies. Our results indicated that the most significant principal components could be achieved when 20,000–30,000 cells were sampled, a relatively high reliability of cell clustering could be achieved by using ~20,000 cells with little further improvement by using more cells, 96% of the differentially expressed genes could be successfully identified with no more than 20,000 cells, and a relatively stable pseudotime could be estimated in the subsample with 5000 cells. Finally, our results provide a general guide for optimizing sample size to be used in plant scRNA-seq studies.
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173
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Desvoyes B, Echevarría C, Gutierrez C. A perspective on cell proliferation kinetics in the root apical meristem. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6708-6715. [PMID: 34159378 PMCID: PMC8513163 DOI: 10.1093/jxb/erab303] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/22/2021] [Indexed: 06/13/2023]
Abstract
Organogenesis in plants is primarily postembryonic and relies on a strict balance between cell division and cell expansion. The root is a particularly well-suited model to study cell proliferation in detail since the two processes are spatially and temporally separated for all the different tissues. In addition, the root is amenable to detailed microscopic analysis to identify cells progressing through the cell cycle. While it is clear that cell proliferation activity is restricted to the root apical meristem (RAM), understanding cell proliferation kinetics and identifying its parameters have required much effort over many years. Here, we review the main concepts, experimental settings, and findings aimed at obtaining a detailed knowledge of how cells proliferate within the RAM. The combination of novel tools, experimental strategies, and mathematical models has contributed to our current view of cell proliferation in the RAM. We also discuss several lines of research that need to be explored in the future.
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Affiliation(s)
- Bénédicte Desvoyes
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Clara Echevarría
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Crisanto Gutierrez
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
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174
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Shahan R, Nolan TM, Benfey PN. Single-cell analysis of cell identity in the Arabidopsis root apical meristem: insights and opportunities. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6679-6686. [PMID: 34018001 PMCID: PMC8513161 DOI: 10.1093/jxb/erab228] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/18/2021] [Indexed: 05/06/2023]
Abstract
A fundamental question in developmental biology is how the progeny of stem cells become differentiated tissues. The Arabidopsis root is a tractable model to address this question due to its simple organization and defined cell lineages. In particular, the zone of dividing cells at the root tip-the root apical meristem-presents an opportunity to map the gene regulatory networks underlying stem cell niche maintenance, tissue patterning, and cell identity acquisition. To identify molecular regulators of these processes, studies over the last 20 years employed global profiling of gene expression patterns. However, these technologies are prone to information loss due to averaging gene expression signatures over multiple cell types and/or developmental stages. Recently developed high-throughput methods to profile gene expression at single-cell resolution have been successfully applied to plants. Here, we review insights from the first published single-cell mRNA sequencing and chromatin accessibility datasets generated from Arabidopsis roots. These studies successfully reconstruct developmental trajectories, phenotype cell identity mutants at unprecedented resolution, and reveal cell type-specific responses to environmental stimuli. The experimental insight gained from Arabidopsis paves the way to profile roots from additional species.
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Affiliation(s)
- Rachel Shahan
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Trevor M Nolan
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Philip N Benfey
- Department of Biology, Duke University, Durham, NC 27708, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
- Correspondence:
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175
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Shojaee A, Saavedra M, Huang SSC. Potentials of single-cell genomics in deciphering cellular phenotypes. CURRENT OPINION IN PLANT BIOLOGY 2021; 63:102059. [PMID: 34116424 PMCID: PMC8545747 DOI: 10.1016/j.pbi.2021.102059] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/26/2021] [Accepted: 04/25/2021] [Indexed: 06/05/2023]
Abstract
Single-cell genomics, particularly single-cell transcriptome profiling by RNA sequencing have transformed the possibilities to relate genes to functions, structures, and eventually phenotypes. We can now observe changes in each cell's transcriptome and among its neighborhoods, interrogate the sequence of transcriptional events, and assess their influence on subsequent events. This paradigm shift in biology enables us to infer causal relationships in these events with high accuracy. Here we review the latest single-cell studies in plants that uncover how cellular phenotypes emerge as a result of the transcriptome process such as waves of expression, trajectories of development and responses to the environment, and spatial information. With an eye on the advances made in animal and human studies, we further highlight some of the needed areas for future research and development, including computational methods.
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Affiliation(s)
- Abbas Shojaee
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Pl, New York, NY 10003, United States
| | - Michelle Saavedra
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Pl, New York, NY 10003, United States
| | - Shao-Shan Carol Huang
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Pl, New York, NY 10003, United States.
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176
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Cui L, Li HZ, Yang K, Zhu LJ, Xu F, Zhu YG. Raman biosensor and molecular tools for integrated monitoring of pathogens and antimicrobial resistance in wastewater. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116415] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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177
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Hou Z, Liu Y, Zhang M, Zhao L, Jin X, Liu L, Su Z, Cai H, Qin Y. High-throughput single-cell transcriptomics reveals the female germline differentiation trajectory in Arabidopsis thaliana. Commun Biol 2021; 4:1149. [PMID: 34599277 PMCID: PMC8486858 DOI: 10.1038/s42003-021-02676-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 09/15/2021] [Indexed: 12/20/2022] Open
Abstract
Female germline cells in flowering plants differentiate from somatic cells to produce specialized reproductive organs, called ovules, embedded deep inside the flowers. We investigated the molecular basis of this distinctive developmental program by performing single-cell RNA sequencing (scRNA-seq) of 16,872 single cells of Arabidopsis thaliana ovule primordia at three developmental time points during female germline differentiation. This allowed us to identify the characteristic expression patterns of the main cell types, including the female germline and its surrounding nucellus. We then reconstructed the continuous trajectory of female germline differentiation and observed dynamic waves of gene expression along the developmental trajectory. A focused analysis revealed transcriptional cascades and identified key transcriptional factors that showed distinct expression patterns along the germline differentiation trajectory. Our study provides a valuable reference dataset of the transcriptional process during female germline differentiation at single-cell resolution, shedding light on the mechanisms underlying germline cell fate determination. Zhimin Hou, Yanhui Liu et al. used single cell RNA-seq to analyze the model organism, Arabidopsis thaliana, at three stages during female germline differentiation. They reconstructed the continuous trajectory of female germline differentiation, providing a valuable reference for future investigation of germline cell fate determination in A. thaliana.
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Affiliation(s)
- Zhimin Hou
- College of Life Sciences, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Plant Protection, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Yanhui Liu
- College of Life Sciences, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Plant Protection, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Man Zhang
- College of Life Sciences, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Plant Protection, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Lihua Zhao
- College of Life Sciences, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Plant Protection, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Xingyue Jin
- College of Life Sciences, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Plant Protection, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Liping Liu
- College of Life Sciences, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Plant Protection, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Zhenxia Su
- College of Life Sciences, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Plant Protection, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Hanyang Cai
- College of Life Sciences, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Plant Protection, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Yuan Qin
- College of Life Sciences, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Plant Protection, Fujian Agriculture and Forestry University, 350002, Fuzhou, China. .,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, 530004, Nanning, China.
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178
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Abstract
High-throughput single-cell transcriptomic approaches have revolutionized our view of gene expression at the level of individual cells, providing new insights into their heterogeneity, identities, and functions. Recently, technical challenges to the application of single-cell transcriptomics to plants have been overcome, and many plant organs and tissues have now been subjected to analyses at single-cell resolution. In this review, we describe these studies and their impact on our understanding of the diversity, differentiation, and activities of plant cells. We particularly highlight their impact on plant cell identity, including unprecedented views of cell transitions and definitions of rare and novel cell types. We also point out current challenges and future opportunities for the application and analyses of single-cell transcriptomics in plants. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Kook Hui Ryu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA; , ,
| | - Yan Zhu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA; , ,
| | - John Schiefelbein
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA; , ,
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179
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Abstract
Plant intra-individual and inter-individual variation can be determined by the epigenome, a set of covalent modifications of DNA and chromatin that can alter genome structure and activity without changes to the genome sequence. The epigenome of plant cells is plastic, that is, it can change in response to internal or external cues, such as during development or due to environmental changes, to create a memory of such events. Ongoing advances in technologies to read and write epigenomic patterns with increasing resolution, scale and precision are enabling the extent of plant epigenome variation to be more extensively characterized and functionally interrogated. In this Review, we discuss epigenome dynamics and variation within plants during development and in response to environmental changes, including stress, as well as between plants. We review known or potential functions of such plasticity and emphasize the importance of investigating the causality of epigenomic changes. Finally, we discuss emerging technologies that may underpin future research into plant epigenome plasticity.
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Affiliation(s)
- James P B Lloyd
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
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180
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Jha SG, Borowsky AT, Cole BJ, Fahlgren N, Farmer A, Huang SSC, Karia P, Libault M, Provart NJ, Rice SL, Saura-Sanchez M, Agarwal P, Ahkami AH, Anderton CR, Briggs SP, Brophy JAN, Denolf P, Di Costanzo LF, Exposito-Alonso M, Giacomello S, Gomez-Cano F, Kaufmann K, Ko DK, Kumar S, Malkovskiy AV, Nakayama N, Obata T, Otegui MS, Palfalvi G, Quezada-Rodríguez EH, Singh R, Uhrig RG, Waese J, Van Wijk K, Wright RC, Ehrhardt DW, Birnbaum KD, Rhee SY. Vision, challenges and opportunities for a Plant Cell Atlas. eLife 2021; 10:e66877. [PMID: 34491200 PMCID: PMC8423441 DOI: 10.7554/elife.66877] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 08/26/2021] [Indexed: 02/06/2023] Open
Abstract
With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.
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Affiliation(s)
- Suryatapa Ghosh Jha
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Alexander T Borowsky
- Department of Botany and Plant Sciences, University of California, RiversideRiversideUnited States
| | - Benjamin J Cole
- Joint Genome Institute, Lawrence Berkeley National LaboratoryWalnut CreekUnited States
| | - Noah Fahlgren
- Donald Danforth Plant Science CenterSt. LouisUnited States
| | - Andrew Farmer
- National Center for Genome ResourcesSanta FeUnited States
| | | | - Purva Karia
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
- Department of Cell and Systems Biology, University of TorontoTorontoCanada
| | - Marc Libault
- Department of Agronomy and Horticulture, University of Nebraska-LincolnLincolnUnited States
| | - Nicholas J Provart
- Department of Cell and Systems Biology and the Centre for the Analysis of Genome Evolution and Function, University of TorontoTorontoCanada
| | - Selena L Rice
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Maite Saura-Sanchez
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Facultad de Agronomía, Universidad de Buenos AiresBuenos AiresArgentina
| | - Pinky Agarwal
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Amir H Ahkami
- Environmental Molecular Sciences Division, Pacific Northwest National LaboratoryRichlandUnited States
| | - Christopher R Anderton
- Environmental Molecular Sciences Division, Pacific Northwest National LaboratoryRichlandUnited States
| | - Steven P Briggs
- Department of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | | | | | - Luigi F Di Costanzo
- Department of Agricultural Sciences, University of Naples Federico IINapoliItaly
| | - Moises Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
- Department of Plant Biology, Carnegie Institution for ScienceTübingenGermany
| | | | - Fabio Gomez-Cano
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast LansingUnited States
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universitaet zu BerlinBerlinGermany
| | - Dae Kwan Ko
- Great Lakes Bioenergy Research Center, Michigan State UniversityEast LansingUnited States
| | - Sagar Kumar
- Department of Plant Breeding & Genetics, Mata Gujri College, Fatehgarh Sahib, Punjabi UniversityPatialaIndia
| | - Andrey V Malkovskiy
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Naomi Nakayama
- Department of Bioengineering, Imperial College LondonLondonUnited Kingdom
| | - Toshihiro Obata
- Department of Biochemistry, University of Nebraska-LincolnMadisonUnited States
| | - Marisa S Otegui
- Department of Botany, University of Wisconsin-MadisonMadisonUnited States
| | - Gergo Palfalvi
- Division of Evolutionary Biology, National Institute for Basic BiologyOkazakiJapan
| | - Elsa H Quezada-Rodríguez
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de MéxicoLeónMexico
| | - Rajveer Singh
- School of Agricultural Biotechnology, Punjab Agricultural UniversityLudhianaIndia
| | - R Glen Uhrig
- Department of Science, University of AlbertaEdmontonCanada
| | - Jamie Waese
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of TorontoTorontoCanada
| | - Klaas Van Wijk
- School of Integrated Plant Science, Plant Biology Section, Cornell UniversityIthacaUnited States
| | - R Clay Wright
- Department of Biological Systems Engineering, Virginia TechBlacksburgUnited States
| | - David W Ehrhardt
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
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181
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Cole B, Bergmann D, Blaby-Haas CE, Blaby IK, Bouchard KE, Brady SM, Ciobanu D, Coleman-Derr D, Leiboff S, Mortimer JC, Nobori T, Rhee SY, Schmutz J, Simmons BA, Singh AK, Sinha N, Vogel JP, O'Malley RC, Visel A, Dickel DE. Plant single-cell solutions for energy and the environment. Commun Biol 2021; 4:962. [PMID: 34385583 PMCID: PMC8361165 DOI: 10.1038/s42003-021-02477-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 07/22/2021] [Indexed: 01/26/2023] Open
Abstract
Progress in sequencing, microfluidics, and analysis strategies has revolutionized the granularity at which multicellular organisms can be studied. In particular, single-cell transcriptomics has led to fundamental new insights into animal biology, such as the discovery of new cell types and cell type-specific disease processes. However, the application of single-cell approaches to plants, fungi, algae, or bacteria (environmental organisms) has been far more limited, largely due to the challenges posed by polysaccharide walls surrounding these species' cells. In this perspective, we discuss opportunities afforded by single-cell technologies for energy and environmental science and grand challenges that must be tackled to apply these approaches to plants, fungi and algae. We highlight the need to develop better and more comprehensive single-cell technologies, analysis and visualization tools, and tissue preparation methods. We advocate for the creation of a centralized, open-access database to house plant single-cell data. Finally, we consider how such efforts should balance the need for deep characterization of select model species while still capturing the diversity in the plant kingdom. Investments into the development of methods, their application to relevant species, and the creation of resources to support data dissemination will enable groundbreaking insights to propel energy and environmental science forward.
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Affiliation(s)
- Benjamin Cole
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Dominique Bergmann
- Department of Biology, Stanford University and Howard Hughes Medical Institute, Stanford, CA, USA
| | - Crysten E Blaby-Haas
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | - Ian K Blaby
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kristofer E Bouchard
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Helen Wills Neuroscience Institute & Redwood Center for Theoretical Neuroscience, University of California, Berkeley, CA, USA
| | - Siobhan M Brady
- Department of Plant Biology, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
| | - Doina Ciobanu
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Samuel Leiboff
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Jenny C Mortimer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Emeryville, CA, USA
- School of Agriculture, Food and Wine, Waite Research Institute, Waite Research Precinct, University of Adelaide, Glen Osmond, SA, Australia
| | - Tatsuya Nobori
- Plant Biology Laboratory and Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Seung Y Rhee
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, USA
| | - Jeremy Schmutz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Blake A Simmons
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Emeryville, CA, USA
| | - Anup K Singh
- Sandia National Laboratories, Livermore, CA, USA
| | - Neelima Sinha
- Department of Plant Biology, University of California, Davis, CA, USA
| | - John P Vogel
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Ronan C O'Malley
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Axel Visel
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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182
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Thibivilliers S, Libault M. Enhancing Our Understanding of Plant Cell-to-Cell Interactions Using Single-Cell Omics. FRONTIERS IN PLANT SCIENCE 2021; 12:696811. [PMID: 34421948 PMCID: PMC8375048 DOI: 10.3389/fpls.2021.696811] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/07/2021] [Indexed: 05/05/2023]
Abstract
Plants are composed of cells that physically interact and constantly adapt to their environment. To reveal the contribution of each plant cells to the biology of the entire organism, their molecular, morphological, and physiological attributes must be quantified and analyzed in the context of the morphology of the plant organs. The emergence of single-cell/nucleus omics technologies now allows plant biologists to access different modalities of individual cells including their epigenome and transcriptome to reveal the unique molecular properties of each cell composing the plant and their dynamic regulation during cell differentiation and in response to their environment. In this manuscript, we provide a perspective regarding the challenges and strategies to collect plant single-cell biological datasets and their analysis in the context of cellular interactions. As an example, we provide an analysis of the transcriptional regulation of the Arabidopsis genes controlling the differentiation of the root hair cells at the single-cell level. We also discuss the perspective of the use of spatial profiling to complement existing plant single-cell omics.
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Affiliation(s)
| | - Marc Libault
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
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183
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Serrano-Ron L, Perez-Garcia P, Sanchez-Corrionero A, Gude I, Cabrera J, Ip PL, Birnbaum KD, Moreno-Risueno MA. Reconstruction of lateral root formation through single-cell RNA sequencing reveals order of tissue initiation. MOLECULAR PLANT 2021; 14:1362-1378. [PMID: 34062316 PMCID: PMC8338891 DOI: 10.1016/j.molp.2021.05.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 05/01/2021] [Accepted: 05/26/2021] [Indexed: 05/13/2023]
Abstract
Postembryonic organogenesis is critical for plant development. Underground, lateral roots (LRs) form the bulk of mature root systems, yet the ontogeny of the LR primordium (LRP) is not clear. In this study, we performed the single-cell RNA sequencing through the first four stages of LR formation in Arabidopsis. Our analysis led to a model in which a single group of precursor cells, with a cell identity different from their pericycle origins, rapidly reprograms and splits into a mixed ground tissue/stem cell niche fate and a vascular precursor fate. The ground tissue and stem cell niche fates soon separate and a subset of more specialized vascular cells form sucrose transporting phloem cells that appear to connect to the primary root. We did not detect cells resembling epidermis or root cap, suggesting that outer tissues may form later, preceding LR emergence. At this stage, some remaining initial precursor cells form the primordium flanks, while the rest create a reservoir of pluripotent cells that are able to replace the LR if damaged. Laser ablation of the central and lateral LRP regions showed that remaining cells restart the sequence of tissue initiation to form a LR. Collectively, our study reveals an ontological hierarchy for LR formation with an early and sequential split of main root tissues and stem cells.
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Affiliation(s)
- Laura Serrano-Ron
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Pablo Perez-Garcia
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain.
| | - Alvaro Sanchez-Corrionero
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Inmaculada Gude
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Javier Cabrera
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Pui-Leng Ip
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Miguel A Moreno-Risueno
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, 28223 Madrid, Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain.
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184
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Mishra B, Kumar N, Mukhtar MS. Network biology to uncover functional and structural properties of the plant immune system. CURRENT OPINION IN PLANT BIOLOGY 2021; 62:102057. [PMID: 34102601 DOI: 10.1016/j.pbi.2021.102057] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 04/15/2021] [Accepted: 04/18/2021] [Indexed: 06/12/2023]
Abstract
In the last two decades, advances in network science have facilitated the discovery of important systems' entities in diverse biological networks. This graph-based technique has revealed numerous emergent properties of a system that enable us to understand several complex biological processes including plant immune systems. With the accumulation of multiomics data sets, the comprehensive understanding of plant-pathogen interactions can be achieved through the analyses and efficacious integration of multidimensional qualitative and quantitative relationships among the components of hosts and their microbes. This review highlights comparative network topology analyses in plant-pathogen co-expression networks and interactomes, outlines dynamic network modeling for cell-specific immune regulatory networks, and discusses the new frontiers of single-cell sequencing as well as multiomics data integration that are necessary for unraveling the intricacies of plant immune systems.
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Affiliation(s)
- Bharat Mishra
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd., Birmingham, AL, 35294, USA
| | - Nilesh Kumar
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd., Birmingham, AL, 35294, USA
| | - M Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd., Birmingham, AL, 35294, USA.
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185
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Berkowitz O, Xu Y, Liew LC, Wang Y, Zhu Y, Hurgobin B, Lewsey MG, Whelan J. RNA-seq analysis of laser microdissected Arabidopsis thaliana leaf epidermis, mesophyll and vasculature defines tissue-specific transcriptional responses to multiple stress treatments. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:938-955. [PMID: 33974297 DOI: 10.1111/tpj.15314] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/28/2021] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
Acclimation of plants to adverse conditions requires the coordination of gene expression and signalling pathways between tissues and cell types. As the energy and carbon capturing organs, leaves are significantly affected by abiotic and biotic stresses. However, tissue- or cell type-specific analyses of stress responses have focussed on the Arabidopsis root. Here, we comparatively explore the transcriptomes of three leaf tissues (epidermis, mesophyll, vasculature) after induction of diverse stress pathways by chemical stimuli (antimycin A, 3-amino-1,2,4-triazole, methyl viologen, salicylic acid) and ultraviolet light in Arabidopsis using laser capture microdissection followed by RNA sequencing. Stimulation of stress pathways caused an overall reduction in the number of genes expressed in a tissue-specific manner, though a small subset gained or changed their tissue specificity. We find no evidence of a common stress response, with only a few genes consistently responsive to two or more treatments in the analysed tissues. However, differentially expressed genes overlap between tissues for individual treatments. A focussed analysis provided evidence for an interaction of auxin and ethylene that mediates retrograde signalling during mitochondrial dysfunction specifically in the epidermis, and a gene regulatory network defined the hierarchy of interactions. Taken together, we have generated an extensive reference dataset that will be valuable for future experiments analysing transcriptional responses on a tissue or single-cell level. Our results will enable the tailoring of the tissue-specific engineering of stress-tolerant plants.
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Affiliation(s)
- Oliver Berkowitz
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Yue Xu
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Lim Chee Liew
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Yan Wang
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Yanqiao Zhu
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Bhavna Hurgobin
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Mathew G Lewsey
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - James Whelan
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
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186
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Kao P, Schon MA, Mosiolek M, Enugutti B, Nodine MD. Gene expression variation in Arabidopsis embryos at single-nucleus resolution. Development 2021; 148:dev199589. [PMID: 34142712 PMCID: PMC8276985 DOI: 10.1242/dev.199589] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/24/2021] [Indexed: 12/17/2022]
Abstract
Soon after fertilization of egg and sperm, plant genomes become transcriptionally activated and drive a series of coordinated cell divisions to form the basic body plan during embryogenesis. Early embryonic cells rapidly diversify from each other, and investigation of the corresponding gene expression dynamics can help elucidate underlying cellular differentiation programs. However, current plant embryonic transcriptome datasets either lack cell-specific information or have RNA contamination from surrounding non-embryonic tissues. We have coupled fluorescence-activated nuclei sorting together with single-nucleus mRNA-sequencing to construct a gene expression atlas of Arabidopsis thaliana early embryos at single-cell resolution. In addition to characterizing cell-specific transcriptomes, we found evidence that distinct epigenetic and transcriptional regulatory mechanisms operate across emerging embryonic cell types. These datasets and analyses, as well as the approach we devised, are expected to facilitate the discovery of molecular mechanisms underlying pattern formation in plant embryos. This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Ping Kao
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Bio Center (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Michael A. Schon
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Bio Center (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Magdalena Mosiolek
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Bio Center (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Balaji Enugutti
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Bio Center (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Michael D. Nodine
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Bio Center (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
- Laboratory of Molecular Biology, Wageningen University, Wageningen 6708 PB, The Netherlands
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187
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Feng Z, Bartholomew ES, Liu Z, Cui Y, Dong Y, Li S, Wu H, Ren H, Liu X. Glandular trichomes: new focus on horticultural crops. HORTICULTURE RESEARCH 2021; 8:158. [PMID: 34193839 PMCID: PMC8245418 DOI: 10.1038/s41438-021-00592-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/07/2021] [Accepted: 05/10/2021] [Indexed: 05/31/2023]
Abstract
Plant glandular trichomes (GTs) are epidermal outgrowths with the capacity to biosynthesize and secrete specialized metabolites, that are of great scientific and practical significance. Our understanding of the developmental process of GTs is limited, and no single plant species serves as a unique model. Here, we review the genetic mechanisms of GT initiation and development and provide a summary of the biosynthetic pathways of GT-specialized metabolites in nonmodel plant species, especially horticultural crops. We discuss the morphology and classification of GT types. Moreover, we highlight technological advancements in methods employed for investigating GTs. Understanding the molecular basis of GT development and specialized metabolites not only offers useful avenues for research in plant breeding that will lead to the improved production of desirable metabolites, but also provides insights for plant epidermal development research.
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Affiliation(s)
- Zhongxuan Feng
- Engineering Research Center of the Ministry of Education for Horticultural Crops Breeding and Propagation, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China
| | - Ezra S Bartholomew
- Engineering Research Center of the Ministry of Education for Horticultural Crops Breeding and Propagation, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China
| | - Ziyu Liu
- Library of China Agricultural University, China Agricultural University, 100193, Beijing, P. R. China
| | - Yuanyuan Cui
- Engineering Research Center of the Ministry of Education for Horticultural Crops Breeding and Propagation, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China
| | - Yuming Dong
- Engineering Research Center of the Ministry of Education for Horticultural Crops Breeding and Propagation, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China
| | - Sen Li
- Engineering Research Center of the Ministry of Education for Horticultural Crops Breeding and Propagation, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China
| | - Haoying Wu
- Engineering Research Center of the Ministry of Education for Horticultural Crops Breeding and Propagation, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China
| | - Huazhong Ren
- Engineering Research Center of the Ministry of Education for Horticultural Crops Breeding and Propagation, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China.
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China.
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin, China.
| | - Xingwang Liu
- Engineering Research Center of the Ministry of Education for Horticultural Crops Breeding and Propagation, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China.
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, 100193, Beijing, P. R. China.
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188
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Tripathi RK, Wilkins O. Single cell gene regulatory networks in plants: Opportunities for enhancing climate change stress resilience. PLANT, CELL & ENVIRONMENT 2021; 44:2006-2017. [PMID: 33522607 PMCID: PMC8359182 DOI: 10.1111/pce.14012] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 05/05/2023]
Abstract
Global warming poses major challenges for plant survival and agricultural productivity. Thus, efforts to enhance stress resilience in plants are key strategies for protecting food security. Gene regulatory networks (GRNs) are a critical mechanism conferring stress resilience. Until recently, predicting GRNs of the individual cells that make up plants and other multicellular organisms was impeded by aggregate population scale measurements of transcriptome and other genome-scale features. With the advancement of high-throughput single cell RNA-seq and other single cell assays, learning GRNs for individual cells is now possible, in principle. In this article, we report on recent advances in experimental and analytical methodologies for single cell sequencing assays especially as they have been applied to the study of plants. We highlight recent advances and ongoing challenges for scGRN prediction, and finally, we highlight the opportunity to use scGRN discovery for studying and ultimately enhancing abiotic stress resilience in plants.
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Affiliation(s)
- Rajiv K. Tripathi
- Department of Biological SciencesUniversity of ManitobaWinnipegManitobaCanada
| | - Olivia Wilkins
- Department of Biological SciencesUniversity of ManitobaWinnipegManitobaCanada
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189
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Seyed Rahmani R, Shi T, Zhang D, Gou X, Yi J, Miclotte G, Marchal K, Li J. Genome-wide expression and network analyses of mutants in key brassinosteroid signaling genes. BMC Genomics 2021; 22:465. [PMID: 34157989 PMCID: PMC8220701 DOI: 10.1186/s12864-021-07778-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 06/07/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Brassinosteroid (BR) signaling regulates plant growth and development in concert with other signaling pathways. Although many genes have been identified that play a role in BR signaling, the biological and functional consequences of disrupting those key BR genes still require detailed investigation. RESULTS Here we performed phenotypic and transcriptomic comparisons of A. thaliana lines carrying a loss-of-function mutation in BRI1 gene, bri1-5, that exhibits a dwarf phenotype and its three activation-tag suppressor lines that were able to partially revert the bri1-5 mutant phenotype to a WS2 phenotype, namely bri1-5/bri1-1D, bri1-5/brs1-1D, and bri1-5/bak1-1D. From the three investigated bri1-5 suppressors, bri1-5/bak1-1D was the most effective suppressor at the transcriptional level. All three bri1-5 suppressors showed altered expression of the genes in the abscisic acid (ABA signaling) pathway, indicating that ABA likely contributes to the partial recovery of the wild-type phenotype in these bri1-5 suppressors. Network analysis revealed crosstalk between BR and other phytohormone signaling pathways, suggesting that interference with one hormone signaling pathway affects other hormone signaling pathways. In addition, differential expression analysis suggested the existence of a strong negative feedback from BR signaling on BR biosynthesis and also predicted that BRS1, rather than being directly involved in signaling, might be responsible for providing an optimal environment for the interaction between BRI1 and its ligand. CONCLUSIONS Our study provides insights into the molecular mechanisms and functions of key brassinosteroid (BR) signaling genes, especially BRS1.
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Affiliation(s)
- Razgar Seyed Rahmani
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Department of Information Technology, IDLab, imec, Ghent University, Ghent, Belgium
| | - Tao Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Dongzhi Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Xiaoping Gou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jing Yi
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Giles Miclotte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Department of Information Technology, IDLab, imec, Ghent University, Ghent, Belgium
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. .,Department of Information Technology, IDLab, imec, Ghent University, Ghent, Belgium. .,Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
| | - Jia Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
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190
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Alvarez JM, Brooks MD, Swift J, Coruzzi GM. Time-Based Systems Biology Approaches to Capture and Model Dynamic Gene Regulatory Networks. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:105-131. [PMID: 33667112 PMCID: PMC9312366 DOI: 10.1146/annurev-arplant-081320-090914] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
All aspects of transcription and its regulation involve dynamic events. However, capturing these dynamic events in gene regulatory networks (GRNs) offers both a promise and a challenge. The promise is that capturing and modeling the dynamic changes in GRNs will allow us to understand how organisms adapt to a changing environment. The ability to mount a rapid transcriptional response to environmental changes is especially important in nonmotile organisms such as plants. The challenge is to capture these dynamic, genome-wide events and model them in GRNs. In this review, we cover recent progress in capturing dynamic interactions of transcription factors with their targets-at both the local and genome-wide levels-and how they are used to learn how GRNs operate as a function of time. We also discuss recent advances that employ time-based machine learning approaches to forecast gene expression at future time points, a key goal of systems biology.
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Affiliation(s)
- Jose M Alvarez
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Matthew D Brooks
- Global Change and Photosynthesis Research Unit, US Department of Agriculture Agricultural Research Service, Urbana, Illinois 61801, USA
| | - Joseph Swift
- Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA;
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191
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Seyfferth C, Renema J, Wendrich JR, Eekhout T, Seurinck R, Vandamme N, Blob B, Saeys Y, Helariutta Y, Birnbaum KD, De Rybel B. Advances and Opportunities in Single-Cell Transcriptomics for Plant Research. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:847-866. [PMID: 33730513 PMCID: PMC7611048 DOI: 10.1146/annurev-arplant-081720-010120] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Single-cell approaches are quickly changing our view on biological systems by increasing the spatiotemporal resolution of our analyses to the level of the individual cell. The field of plant biology has fully embraced single-cell transcriptomics and is rapidly expanding the portfolio of available technologies and applications. In this review, we give an overview of the main advances in plant single-cell transcriptomics over the past few years and provide the reader with an accessible guideline covering all steps, from sample preparation to data analysis. We end by offering a glimpse of how these technologies will shape and accelerate plant-specific research in the near future.
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Affiliation(s)
- Carolin Seyfferth
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Jim Renema
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Jos R Wendrich
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Thomas Eekhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Ruth Seurinck
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, 9052 Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium
| | - Niels Vandamme
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, 9052 Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium
| | - Bernhard Blob
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
- Viikki Plant Science Centre, HiLIFE/Organismal and Evolutionary Biology Research Program, Institute of Biotechnology, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Yvan Saeys
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, 9052 Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium
| | - Yrjo Helariutta
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
- Viikki Plant Science Centre, HiLIFE/Organismal and Evolutionary Biology Research Program, Institute of Biotechnology, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA;
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
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192
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Lhamo D, Luan S. Potential Networks of Nitrogen-Phosphorus-Potassium Channels and Transporters in Arabidopsis Roots at a Single Cell Resolution. FRONTIERS IN PLANT SCIENCE 2021; 12:689545. [PMID: 34220911 PMCID: PMC8242960 DOI: 10.3389/fpls.2021.689545] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/24/2021] [Indexed: 05/08/2023]
Abstract
Nitrogen (N), phosphorus (P), and potassium (K) are three major macronutrients essential for plant life. These nutrients are acquired and transported by several large families of transporters expressed in plant roots. However, it remains largely unknown how these transporters are distributed in different cell-types that work together to transfer the nutrients from the soil to different layers of root cells and eventually reach vasculature for massive flow. Using the single cell transcriptomics data from Arabidopsis roots, we profiled the transcriptional patterns of putative nutrient transporters in different root cell-types. Such analyses identified a number of uncharacterized NPK transporters expressed in the root epidermis to mediate NPK uptake and distribution to the adjacent cells. Some transport genes showed cortex- and endodermis-specific expression to direct the nutrient flow toward the vasculature. For long-distance transport, a variety of transporters were shown to express and potentially function in the xylem and phloem. In the context of subcellular distribution of mineral nutrients, the NPK transporters at subcellular compartments were often found to show ubiquitous expression patterns, which suggests function in house-keeping processes. Overall, these single cell transcriptomic analyses provide working models of nutrient transport from the epidermis across the cortex to the vasculature, which can be further tested experimentally in the future.
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Affiliation(s)
- Dhondup Lhamo
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
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193
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Chen H, Yin X, Guo L, Yao J, Ding Y, Xu X, Liu L, Zhu QH, Chu Q, Fan L. PlantscRNAdb: A database for plant single-cell RNA analysis. MOLECULAR PLANT 2021; 14:855-857. [PMID: 33962062 DOI: 10.1016/j.molp.2021.05.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/14/2021] [Accepted: 04/30/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Hongyu Chen
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Xinxin Yin
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Longbiao Guo
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Jie Yao
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Yiwen Ding
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Xiaoxu Xu
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Lu Liu
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Qinjie Chu
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.
| | - Longjiang Fan
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China; Shandong (Linyi) Institute of Modern Agriculture of Zhejiang University, Fengyi Street, Linyi, Shandong Province, China.
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194
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Moison M, Pacheco JM, Lucero L, Fonouni-Farde C, Rodríguez-Melo J, Mansilla N, Christ A, Bazin J, Benhamed M, Ibañez F, Crespi M, Estevez JM, Ariel F. The lncRNA APOLO interacts with the transcription factor WRKY42 to trigger root hair cell expansion in response to cold. MOLECULAR PLANT 2021; 14:937-948. [PMID: 33689931 DOI: 10.1016/j.molp.2021.03.008] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 02/08/2021] [Accepted: 03/03/2021] [Indexed: 05/25/2023]
Abstract
Plant long noncoding RNAs (lncRNAs) have emerged as important regulators of chromatin dynamics, impacting on transcriptional programs leading to different developmental outputs. The lncRNA AUXIN-REGULATED PROMOTER LOOP (APOLO) directly recognizes multiple independent loci across the Arabidopsis genome and modulates their three-dimensional chromatin conformation, leading to transcriptional shifts. Here, we show that APOLO recognizes the locus encoding the root hair (RH) master regulator ROOT HAIR DEFECTIVE 6 (RHD6) and controls RHD6 transcriptional activity, leading to cold-enhanced RH elongation through the consequent activation of the transcription factor gene RHD6-like RSL4. Furthermore, we demonstrate that APOLO interacts with the transcription factor WRKY42 and modulates its binding to the RHD6 promoter. WRKY42 is required for the activation of RHD6 by low temperatures and WRKY42 deregulation impairs cold-induced RH expansion. Collectively, our results indicate that a novel ribonucleoprotein complex with APOLO and WRKY42 forms a regulatory hub to activate RHD6 by shaping its epigenetic environment and integrate signals governing RH growth and development.
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Affiliation(s)
- Michaël Moison
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB/FHUC, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, Santa Fe 3000, Argentina
| | - Javier Martínez Pacheco
- Fundación Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, Buenos Aires CP C1405BWE, Argentina
| | - Leandro Lucero
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB/FHUC, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, Santa Fe 3000, Argentina
| | - Camille Fonouni-Farde
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB/FHUC, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, Santa Fe 3000, Argentina
| | - Johan Rodríguez-Melo
- Instituto de Investigaciones Agrobiotecnológicas, CONICET, Universidad Nacional de Río Cuarto, Río Cuarto 5800, Argentina
| | - Natanael Mansilla
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB/FHUC, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, Santa Fe 3000, Argentina
| | - Aurélie Christ
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Saclay and University of Paris Bâtiment 630, 91192 Gif sur Yvette, France
| | - Jérémie Bazin
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Saclay and University of Paris Bâtiment 630, 91192 Gif sur Yvette, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Saclay and University of Paris Bâtiment 630, 91192 Gif sur Yvette, France
| | - Fernando Ibañez
- Instituto de Investigaciones Agrobiotecnológicas, CONICET, Universidad Nacional de Río Cuarto, Río Cuarto 5800, Argentina
| | - Martin Crespi
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Saclay and University of Paris Bâtiment 630, 91192 Gif sur Yvette, France
| | - José M Estevez
- Fundación Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, Buenos Aires CP C1405BWE, Argentina; Centro de Biotecnología Vegetal (CBV), Facultad de Ciencias de la Vida (FCsV), Universidad Andres Bello, Santiago, Chile and Millennium Institute for Integrative Biology (iBio), Santiago, Chile.
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB/FHUC, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, Santa Fe 3000, Argentina.
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195
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Dorrity MW, Alexandre CM, Hamm MO, Vigil AL, Fields S, Queitsch C, Cuperus JT. The regulatory landscape of Arabidopsis thaliana roots at single-cell resolution. Nat Commun 2021; 12:3334. [PMID: 34099698 DOI: 10.1101/2020.07.17.204792] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 05/10/2021] [Indexed: 05/21/2023] Open
Abstract
The scarcity of accessible sites that are dynamic or cell type-specific in plants may be due in part to tissue heterogeneity in bulk studies. To assess the effects of tissue heterogeneity, we apply single-cell ATAC-seq to Arabidopsis thaliana roots and identify thousands of differentially accessible sites, sufficient to resolve all major cell types of the root. We find that the entirety of a cell's regulatory landscape and its transcriptome independently capture cell type identity. We leverage this shared information on cell identity to integrate accessibility and transcriptome data to characterize developmental progression, endoreduplication and cell division. We further use the combined data to characterize cell type-specific motif enrichments of transcription factor families and link the expression of family members to changing accessibility at specific loci, resolving direct and indirect effects that shape expression. Our approach provides an analytical framework to infer the gene regulatory networks that execute plant development.
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Affiliation(s)
- Michael W Dorrity
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Morgan O Hamm
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Anna-Lena Vigil
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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196
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Dorrity MW, Alexandre CM, Hamm MO, Vigil AL, Fields S, Queitsch C, Cuperus JT. The regulatory landscape of Arabidopsis thaliana roots at single-cell resolution. Nat Commun 2021; 12:3334. [PMID: 34099698 PMCID: PMC8184767 DOI: 10.1038/s41467-021-23675-y] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 05/10/2021] [Indexed: 02/05/2023] Open
Abstract
The scarcity of accessible sites that are dynamic or cell type-specific in plants may be due in part to tissue heterogeneity in bulk studies. To assess the effects of tissue heterogeneity, we apply single-cell ATAC-seq to Arabidopsis thaliana roots and identify thousands of differentially accessible sites, sufficient to resolve all major cell types of the root. We find that the entirety of a cell's regulatory landscape and its transcriptome independently capture cell type identity. We leverage this shared information on cell identity to integrate accessibility and transcriptome data to characterize developmental progression, endoreduplication and cell division. We further use the combined data to characterize cell type-specific motif enrichments of transcription factor families and link the expression of family members to changing accessibility at specific loci, resolving direct and indirect effects that shape expression. Our approach provides an analytical framework to infer the gene regulatory networks that execute plant development.
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Affiliation(s)
- Michael W. Dorrity
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, WA USA
| | - Cristina M. Alexandre
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, WA USA
| | - Morgan O. Hamm
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, WA USA
| | - Anna-Lena Vigil
- grid.272362.00000 0001 0806 6926School of Life Sciences, University of Nevada, Las Vegas, NV USA
| | - Stanley Fields
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, WA USA ,grid.34477.330000000122986657Department of Medicine, University of Washington, Seattle, WA USA
| | - Christine Queitsch
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, WA USA
| | - Josh T. Cuperus
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, WA USA
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197
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Thibivilliers S, Libault M. Plant Single-Cell Multiomics: Cracking the Molecular Profiles of Plant Cells. TRENDS IN PLANT SCIENCE 2021; 26:662-663. [PMID: 33745785 DOI: 10.1016/j.tplants.2021.03.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/03/2021] [Indexed: 05/22/2023]
Affiliation(s)
- Sandra Thibivilliers
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Beadle Center, Lincoln, NE 68503, USA
| | - Marc Libault
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Beadle Center, Lincoln, NE 68503, USA.
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198
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Provart NJ, Brady SM, Parry G, Schmitz RJ, Queitsch C, Bonetta D, Waese J, Schneeberger K, Loraine AE. Anno genominis XX: 20 years of Arabidopsis genomics. THE PLANT CELL 2021; 33:832-845. [PMID: 33793861 PMCID: PMC8226293 DOI: 10.1093/plcell/koaa038] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/09/2020] [Indexed: 05/04/2023]
Abstract
Twenty years ago, the Arabidopsis thaliana genome sequence was published. This was an important moment as it was the first sequenced plant genome and explicitly brought plant science into the genomics era. At the time, this was not only an outstanding technological achievement, but it was characterized by a superb global collaboration. The Arabidopsis genome was the seed for plant genomic research. Here, we review the development of numerous resources based on the genome that have enabled discoveries across plant species, which has enhanced our understanding of how plants function and interact with their environments.
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Affiliation(s)
- Nicholas J Provart
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, California, 95616, USA
| | - Geraint Parry
- GARNet, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Georgia, 30602, USA
| | - Christine Queitsch
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington, 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, 98195, USA
| | - Dario Bonetta
- Faculty of Science, Ontario Tech University, Oshawa, Ontario, L1G 0C5, Canada
| | - Jamie Waese
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, D-50829, Cologne, Germany
- Faculty of Biology, LMU Munich, 82152 Munich, Germany
| | - Ann E Loraine
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
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199
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Gaillochet C, Develtere W, Jacobs TB. CRISPR screens in plants: approaches, guidelines, and future prospects. THE PLANT CELL 2021; 33:794-813. [PMID: 33823021 PMCID: PMC8226290 DOI: 10.1093/plcell/koab099] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/02/2021] [Indexed: 05/20/2023]
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)-associated systems have revolutionized genome engineering by facilitating a wide range of targeted DNA perturbations. These systems have resulted in the development of powerful new screens to test gene functions at the genomic scale. While there is tremendous potential to map and interrogate gene regulatory networks at unprecedented speed and scale using CRISPR screens, their implementation in plants remains in its infancy. Here we discuss the general concepts, tools, and workflows for establishing CRISPR screens in plants and analyze the handful of recent reports describing the use of this strategy to generate mutant knockout collections or to diversify DNA sequences. In addition, we provide insight into how to design CRISPR knockout screens in plants given the current challenges and limitations and examine multiple design options. Finally, we discuss the unique multiplexing capabilities of CRISPR screens to investigate redundant gene functions in highly duplicated plant genomes. Combinatorial mutant screens have the potential to routinely generate higher-order mutant collections and facilitate the characterization of gene networks. By integrating this approach with the numerous genomic profiles that have been generated over the past two decades, the implementation of CRISPR screens offers new opportunities to analyze plant genomes at deeper resolution and will lead to great advances in functional and synthetic biology.
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Affiliation(s)
- Christophe Gaillochet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Ward Develtere
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Thomas B Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
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200
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Ma F, Salomé PA, Merchant SS, Pellegrini M. Single-cell RNA sequencing of batch Chlamydomonas cultures reveals heterogeneity in their diurnal cycle phase. THE PLANT CELL 2021; 33:1042-1057. [PMID: 33585940 PMCID: PMC8226295 DOI: 10.1093/plcell/koab025] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/13/2021] [Indexed: 05/02/2023]
Abstract
The photosynthetic unicellular alga Chlamydomonas (Chlamydomonas reinhardtii) is a versatile reference for algal biology because of its ease of culture in the laboratory. Genomic and systems biology approaches have previously described transcriptome responses to environmental changes using bulk data, thus representing the average behavior from pools of cells. Here, we apply single-cell RNA sequencing (scRNA-seq) to probe the heterogeneity of Chlamydomonas cell populations under three environments and in two genotypes differing by the presence of a cell wall. First, we determined that RNA can be extracted from single algal cells with or without a cell wall, offering the possibility to sample natural algal communities. Second, scRNA-seq successfully separated single cells into nonoverlapping cell clusters according to their growth conditions. Cells exposed to iron or nitrogen deficiency were easily distinguished despite a shared tendency to arrest photosynthesis and cell division to economize resources. Notably, these groups of cells not only recapitulated known patterns observed with bulk RNA-seq but also revealed their inherent heterogeneity. A substantial source of variation between cells originated from their endogenous diurnal phase, although cultures were grown in constant light. We exploited this result to show that circadian iron responses may be conserved from algae to land plants. We document experimentally that bulk RNA-seq data represent an average of typically hidden heterogeneity in the population.
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Affiliation(s)
- Feiyang Ma
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California 90095, USA
| | - Patrice A Salomé
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
- Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, USA
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
- Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, USA
- Departments of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California 90095, USA
- Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, USA
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