Single-cell transcriptomics is revolutionizing the improvement of plant biotechnology research: recent advances and future opportunities

被引:13
作者
Kaur, Harmeet [1 ,2 ]
Jha, Priyanka [2 ,3 ]
Ochatt, Sergio J. [4 ]
Kumar, Vijay [1 ,2 ]
机构
[1] Lovely Profess Univ, Div Res & Dev, Plant Biotechnol Lab, Phagwara, Punjab, India
[2] Lovely Profess Univ, Lovely Fac Technol & Sci, Dept Biotechnol, Phagwara, Punjab, India
[3] Lovely Profess Univ, Dept Res Facilitat, Div Res & Dev, Phagwara, Punjab, India
[4] Univ Bourgogne Franche Comte, Agroecol, InstitutAgro Dijon, INRAE, Dijon, France
关键词
Plants; plant transcriptomics; single-cell technology; scRNA-seq; GENOME-WIDE EXPRESSION; MESSENGER-RNA-SEQ; GENE-EXPRESSION; STOMATAL LINEAGE; MAIZE; ATLAS; ROOT; RESOLUTION; PROTEINS; SEQUENCE;
D O I
10.1080/07388551.2023.2165900
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Single-cell approaches are a promising way to obtain high-resolution transcriptomics data and have the potential to revolutionize the study of plant growth and development. Recent years have seen the advent of unprecedented technological advances in the field of plant biology to study the transcriptional information of individual cells by single-cell RNA sequencing (scRNA-seq). This review focuses on the modern advancements of single-cell transcriptomics in plants over the past few years. In addition, it also offers a new insight of how these emerging methods will expedite advance research in plant biotechnology in the near future. Lastly, the various technological hurdles and inherent limitations of single-cell technology that need to be conquered to develop such outstanding possible knowledge gain is critically analyzed and discussed.
引用
收藏
页码:202 / 217
页数:16
相关论文
共 173 条
[1]   Host-Multi-Pathogen Warfare: Pathogen Interactions in Co-infected Plants [J].
Abdullah, Araz S. ;
Moffat, Caroline S. ;
Lopez-Ruiz, Francisco J. ;
Gibberd, Mark R. ;
Hamblin, John ;
Zerihun, Ayalsew .
FRONTIERS IN PLANT SCIENCE, 2017, 8
[2]  
Alberts B., 2002, Molecular biology of the cell, V4th
[3]   Single cell transcriptomics comes of age [J].
Aldridge, Sarah ;
Teichmann, Sarah A. .
NATURE COMMUNICATIONS, 2020, 11 (01)
[4]   Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity [J].
Angermueller, Christof ;
Clark, Stephen J. ;
Lee, Heather J. ;
Macaulay, Iain C. ;
Teng, Mabel J. ;
Hu, Tim Xiaoming ;
Krueger, Felix ;
Smallwood, Sebastien A. ;
Ponting, Chris P. ;
Voet, Thierry ;
Kelsey, Gavin ;
Stegle, Oliver ;
Reik, Wolf .
NATURE METHODS, 2016, 13 (03) :229-+
[5]   Shoot and root single cell sequencing reveals tissue- and daytime-specific transcriptome profiles [J].
Apelt, Federico ;
Mavrothalassiti, Eleni ;
Gupta, Saurabh ;
Machin, Frank ;
Olas, Justyna Jadwiga ;
Annunziata, Maria Grazia ;
Schindelasch, Dana ;
Kragler, Friedrich .
PLANT PHYSIOLOGY, 2022, 188 (02) :861-878
[6]   Analysis of the genome sequence of the flowering plant Arabidopsis thaliana [J].
Kaul, S ;
Koo, HL ;
Jenkins, J ;
Rizzo, M ;
Rooney, T ;
Tallon, LJ ;
Feldblyum, T ;
Nierman, W ;
Benito, MI ;
Lin, XY ;
Town, CD ;
Venter, JC ;
Fraser, CM ;
Tabata, S ;
Nakamura, Y ;
Kaneko, T ;
Sato, S ;
Asamizu, E ;
Kato, T ;
Kotani, H ;
Sasamoto, S ;
Ecker, JR ;
Theologis, A ;
Federspiel, NA ;
Palm, CJ ;
Osborne, BI ;
Shinn, P ;
Conway, AB ;
Vysotskaia, VS ;
Dewar, K ;
Conn, L ;
Lenz, CA ;
Kim, CJ ;
Hansen, NF ;
Liu, SX ;
Buehler, E ;
Altafi, H ;
Sakano, H ;
Dunn, P ;
Lam, B ;
Pham, PK ;
Chao, Q ;
Nguyen, M ;
Yu, GX ;
Chen, HM ;
Southwick, A ;
Lee, JM ;
Miranda, M ;
Toriumi, MJ ;
Davis, RW .
NATURE, 2000, 408 (6814) :796-815
[7]   A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart [J].
Asp, Michaela ;
Giacomello, Stefania ;
Larsson, Ludvig ;
Wu, Chenglin ;
Furth, Daniel ;
Qian, Xiaoyan ;
Wardell, Eva ;
Custodio, Joaquin ;
Reimegard, Johan ;
Salmen, Fredrik ;
Osterholm, Cecilia ;
Stahl, Patrik L. ;
Sundstrom, Erik ;
Akesson, Elisabet ;
Bergmann, Olaf ;
Bienko, Magda ;
Mansson-Broberg, Agneta ;
Nilsson, Mats ;
Sylven, Christer ;
Lundeberg, Joakim .
CELL, 2019, 179 (07) :1647-+
[8]   Dimensionality reduction for visualizing single-cell data using UMAP [J].
Becht, Etienne ;
McInnes, Leland ;
Healy, John ;
Dutertre, Charles-Antoine ;
Kwok, Immanuel W. H. ;
Ng, Lai Guan ;
Ginhoux, Florent ;
Newell, Evan W. .
NATURE BIOTECHNOLOGY, 2019, 37 (01) :38-+
[9]   Generalizing RNA velocity to transient cell states through dynamical modeling [J].
Bergen, Volker ;
Lange, Marius ;
Peidli, Stefan ;
Wolf, F. Alexander ;
Theis, Fabian J. .
NATURE BIOTECHNOLOGY, 2020, 38 (12) :1408-1414
[10]   SpatialCPie: an R/Bioconductor package for spatial transcriptomics cluster evaluation [J].
Bergenstrahle, Joseph ;
Bergenstrahle, Ludvig ;
Lundeberg, Joakim .
BMC BIOINFORMATICS, 2020, 21 (01)