Publications

29.03.2024

Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics.

Single-cell and single-nucleus RNA-sequencing technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these technologies are gaining traction in plant molecular and developmental biology for elucidating the transcriptional changes across cell types in a specific tissue or organ, upon treatments, in response to biotic and abiotic stresses, or between genotypes. Despite the rapidly accelerating use of these technologies, collective and standardized experimental and analytical procedures to support the acquisition of high-quality data sets are still missing. In this commentary, we discuss common challenges associated with the use of single-cell transcriptomics in plants and propose general guidelines to improve reproducibility, quality, comparability, and interpretation and to make the data readily available to the community in this fast-developing field of research.

Grones C, Eekhout T, Shi D, Neumann M, Berg LS, Ke Y, Shahan R, Cox KL Jr, Gomez-Cano F, Nelissen H, Lohmann JU, Giacomello S, Martin OC, Cole B, Wang JW, Kaufmann K, Raissig MT, Palfalvi G, Greb T, Libault M, De Rybel B. Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics. Plant Cell. 2024 Mar 29;36(4):812-828.  https://doi.org/10.1093/plcell/koae003

Image:

Overview of plant single-cell and single-nucleus experiments. A) Number of publications describing sc/snRNA-seq data in the plant field
per year from 2019 until 2022. B) Distribution of species used in these papers (n: 46). C) Overview of the different sc/sn technologies and their usage
in the plant field. Example references used: a. (Farmer et al. 2021; Cervantes-Pérez et al. 2022; Conde et al. 2022; Neumann et al. 2022; Sun et al. 2022;
Guillotin et al. 2023; Li et al. 2023; Liu et al. 2023); b. (Tian et al. 2020; Marand et al. 2021); c. (Wendrich et al. 2020; Graeff et al. 2021; Lopez-Anido et al.
2021; Ortiz-Ramírez et al. 2021; Wang , Huan, et al. 2021; Apelt et al. 2022; Otero et al. 2022; Kim et al. 2023); d. (Denyer et al. 2019; Jean-Baptiste et al.
2019; Ryu et al. 2019; Shulse et al. 2019; Turco et al. 2019; Zhang et al. 2019; Satterlee et al. 2020; Bezrutczyk et al. 2021; Chen et al. 2021; Gala et al.
2021; Kim et al. 2021; Liu et al. 2021; Ma et al. 2021; Yang et al. 2021; Zhang , Chen, et al. 2021; Zhang, Chen, and Wang 2021; Li et al. 2022; Shahan et al.
2022; Tao et al. 2022); e. (Kao et al. 2021; Picard et al. 2021; Sunaga-Franze et al. 2021; Abramson et al. 2022; Li et al. 2023); f. none; g. (Efroni et al. 2016;
Lopez-Anido et al. 2021; Roszak et al. 2021; Serrano-Ron et al. 2021; Omary et al. 2022); h. (Zong et al. 2022); and i. (Nelms and Walbot 2019; Song
et al. 2020; Xie et al. 2022).

Credit:

© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists.