Advances and Opportunities in Single-Cell Transcriptomics for Plant Research

被引：127

作者：

Seyfferth, Carolin ^{[1
,2
]}

Renema, Jim ^{[1
,2
]}

Wendrich, Jos R. ^{[1
,2
]}

Eekhout, Thomas ^{[1
,2
]}

Seurinck, Ruth ^{[3
,4
]}

Vandamme, Niels ^{[3
,4
]}

Blob, Bernhard ^{[5
,6
]}

Saeys, Yvan ^{[3
,4
]}

Helariutta, Yrjo ^{[5
,6
]}

Birnbaum, Kenneth D. ^{[7
]}

De Rybel, Bert ^{[1
,2
]}

机构：

[1] Univ Ghent, Dept Plant Biotechnol & Bioinformat, B-9052 Ghent, Belgium

[2] VIB, Ctr Plant Syst Biol, B-9052 Ghent, Belgium

[3] VIB, Ctr Inflammat Res, Data Min & Modeling Biomed, B-9052 Ghent, Belgium

[4] Univ Ghent, Dept Appl Math Comp Sci & Stat, B-9000 Ghent, Belgium

[5] Univ Cambridge, Sainsbury Lab, Cambridge CB2 1LR, England

[6] Univ Helsinki, Fac Biol & Environm Sci, HiLIFE Organismal & Evolutionary Biol Res Program, Viikki Plant Sci Ctr,Inst Biotechnol, FIN-00014 Helsinki, Finland

[7] NYU, Dept Biol, Ctr Genom & Syst Biol, New York, NY 10003 USA

来源：

ANNUAL REVIEW OF PLANT BIOLOGY, VOL 72, 2021 | 2021年 / 72卷

基金：

欧洲研究理事会;

关键词：

scRNA-seq; plant transcriptomics; protoplast; cell atlas; cell trajectory; GENE-EXPRESSION; IN-SITU; RNA; GENOME; MAP; CHROMATIN; SEQUENCE; DIFFERENTIATION; TECHNOLOGIES; LANDSCAPE;

D O I：

10.1146/annurev-arplant-081720-010120

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

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.

引用

页码：847 / 866

页数：20

共 96 条

[21]

Duo Angelo, 2018, F1000Res, V7, P1141, DOI 10.12688/f1000research.15666.3

[22] Root Regeneration Triggers an Embryo-like Sequence Guided by Hormonal Interactions [J].

Efroni, Idan ;

Mello, Alison ;

Nawy, Tal ;

Ip, Pui-Leng ;

Rahni, Ramin ;

DelRose, Nicholas ;

Powers, Ashley ;

Satija, Rahul ;

Birnbaum, Kenneth D. .

CELL, 2016, 165 (07) :1721-1733

[23] Quantification of cell identity from single-cell gene expression profiles [J].

Efroni, Idan ;

Ip, Pui-Leng ;

Nawy, Tal ;

Mello, Alison ;

Birnbaum, Kenneth D. .

GENOME BIOLOGY, 2015, 16

[24] Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH [J].

Eng, Chee-Huat Linus ;

Lawson, Michael ;

Zhu, Qian ;

Dries, Ruben ;

Koulena, Noushin ;

Takei, Yodai ;

Yun, Jina ;

Cronin, Christopher ;

Karp, Christoph ;

Yuan, Guo-Cheng ;

Cai, Long .

NATURE, 2019, 568 (7751) :235-+

[25] Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell level [J].

Farmer, Andrew ;

Thibivilliers, Sandra ;

Ryu, Kook Hui ;

Schiefelbein, John ;

Libault, Marc .

MOLECULAR PLANT, 2021, 14 (03) :372-383

[26]

Freytag Saskia, 2018, F1000Res, V7, P1297, DOI 10.12688/f1000research.15809.1

[27]

Gala HP, 2020, SINGLE CELL IEW TRAN, V2020

[28] Cell-specific nitrogen responses mediate developmental plasticity [J].

Gifford, Miriam L. ;

Dean, Alexis ;

Gutierrez, Rodrigo A. ;

Coruzzi, Gloria M. ;

Birnbaum, Kenneth D. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (02) :803-808

[29]

Gong, 2020, SINGLE CELL RESOLUTI, V56, DOI DOI 10.1101/2020.09.08.288498

[30] Single-cell transcriptional diversity is a hallmark of developmental potential [J].

Gulati, Gunsagar S. ;

Sikandar, Shaheen S. ;

Wesche, Daniel J. ;

Manjunath, Anoop ;

Bharadwaj, Anjan ;

Berger, Mark J. ;

Ilagan, Francisco ;

Kuo, Angera H. ;

Hsieh, Robert W. ;

Cai, Shang ;

Zabala, Maider ;

Scheeren, Ferenc A. ;

Lobo, Neethan A. ;

Qian, Dalong ;

Yu, Feiqiao B. ;

Dirbas, Frederick M. ;

Clarke, Michael F. ;

Newman, Aaron M. .

SCIENCE, 2020, 367 (6476) :405-+

← 1 2 3 4 5 6 7 8 9 10 →