snRNA-seq analysis of the moss Physcomitrium patens identifies a conserved cytokinin-ESR module promoting pluripotent stem cell identity DOI Creative Commons
Yuki Hata, Nicola A. Hetherington, Kai Battenberg

et al.

Developmental Cell, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

The shoot apical meristem (SAM), which contains pluripotent stem cells, serves as the source of entire system in land plants. To find mechanisms underlying SAM development and its origin, we employed single-nucleus RNA sequencing technology Physcomitrium patens, a single cell known gametophore cell. We identified distinct clusters representing major types P. patens gametophyte, including cells. showed dynamic gene expression changes during fate progression found upregulation cytokinin biosynthesis genes this also ENHANCER OF SHOOT REGENERATION 1 (ESR1) orthologs important regulators cells downstream cytokinin. Given that ESRs promote formation under angiosperms, propose cytokinin-ESR module represents conserved mechanism promoting identity evolved common ancestor

Language: Английский

Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap DOI Creative Commons
Tatsuya Nobori, Marina Oliva, Ryan Lister

et al.

Nature Plants, Journal Year: 2023, Volume and Issue: 9(7), P. 1026 - 1033

Published: June 12, 2023

Abstract Retrieving the complex responses of individual cells in native three-dimensional tissue context is crucial for a complete understanding functions. Here, we present PHYTOMap (plant hybridization-based targeted observation gene expression map), multiplexed fluorescence situ hybridization method that enables single-cell and spatial analysis whole-mount plant transgene-free manner at low cost. We applied to simultaneously analyse 28 cell-type marker genes Arabidopsis roots successfully identified major cell types, demonstrating our can substantially accelerate mapping defined RNA-sequencing datasets tissue.

Language: Английский

Citations

57
Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics DOI Creative Commons

Carolin Grones,

Thomas Eekhout, Dongbo Shi

et al.

The Plant Cell, Journal Year: 2024, Volume and Issue: 36(4), P. 812 - 828

Published: Jan. 17, 2024

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

Language: Английский

Citations

25
Orthologous marker groups reveal broad cell identity conservation across plant single-cell transcriptomes DOI Creative Commons
Tran N. Chau, Prakash Raj Timilsena,

Sai Pavan Bathala

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 2, 2025

Single-cell RNA sequencing (scRNA-seq) is widely used in plant biology and a powerful tool for studying cell identity differentiation. However, the scarcity of known cell-type marker genes divergence expression patterns limit accuracy identification our capacity to investigate conservation many species. To tackle this challenge, we devise novel computational strategy called Orthologous Marker Gene Groups (OMGs), which can identify types both model non-model species allows rapid comparison across published single-cell maps. Our method does not require cross-species data integration, while still accurately determining inter-species cellular similarities. We validate by analyzing from with well-annotated maps, show methods capture majority manually annotated types. The robustness further demonstrated its ability pertinently map clusters 1 million cells, 268 15 diverse reveal 14 dominant groups substantial shared markers monocots dicots. facilitate use broad research community, launch user-friendly web-based OMG browser, simplifies process datasets biologists. A Ortho-Marker (OMGs) was developed enable single data. revealed conserved accessible via browser.

Language: Английский

Citations

2
Single-nucleus transcriptomes reveal spatiotemporal symbiotic perception and early response in Medicago DOI
Zhijian Liu, Jun Yang, Yanping Long

et al.

Nature Plants, Journal Year: 2023, Volume and Issue: 9(10), P. 1734 - 1748

Published: Sept. 25, 2023

Language: Английский

Citations

28
Advances in the Application of Single-Cell Transcriptomics in Plant Systems and Synthetic Biology DOI Creative Commons
Md Torikul Islam, Yang Liu, Md Mahmudul Hassan

et al.

BioDesign Research, Journal Year: 2024, Volume and Issue: 6, P. 0029 - 0029

Published: Jan. 1, 2024

Plants are complex systems hierarchically organized and composed of various cell types. To understand the molecular underpinnings plant systems, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for revealing high resolution gene expression patterns at cellular level investigating cell-type heterogeneity. Furthermore, scRNA-seq analysis biosystems great potential generating new knowledge to inform design synthetic biology, which aims modify plants genetically/epigenetically through genome editing, engineering, or re-writing based on rational increasing crop yield quality, promoting bioeconomy enhancing environmental sustainability. In particular, data from studies can be utilized facilitate development high-precision Build-Design-Test-Learn capabilities maximizing targeted performance engineered while minimizing unintended side effects. date, been demonstrated in limited number species, including model (e.g., Arabidopsis thaliana), agricultural crops Oryza sativa), bioenergy Populus spp.). It is expected that future technical advancements will reduce cost consequently accelerate application this emerging technology plants. review, we summarize current scRNA-seq, sample preparation, sequencing, analysis, provide guidance how choose appropriate methods different types samples. We then highlight applications both biology research. Finally, discuss challenges opportunities

Language: Английский

Citations

13
Single-cell transcriptomics reveals heterogeneity in plant responses to the environment: a focus on biotic and abiotic interactions DOI
Rubén Tenorio Berrío, Marieke Dubois

Journal of Experimental Botany, Journal Year: 2024, Volume and Issue: 75(17), P. 5188 - 5203

Published: March 11, 2024

Biotic and abiotic environmental cues are major factors influencing plant growth productivity. Interactions with biotic (e.g. symbionts pathogens) changes in temperature, water, or nutrient availability) trigger signaling downstream transcriptome adjustments plants. While bulk RNA-sequencing technologies have traditionally been used to profile these transcriptional changes, tissue homogenization may mask heterogeneity of responses resulting from the cellular complexity organs. Thus, whether different cell types respond equally fluctuations, subsets cell-type specific, long-lasting questions biology. The recent breakthrough single-cell transcriptomics research offers an unprecedented view under changing conditions. In this review, we discuss contribution understanding cell-type-specific interactions. Besides biological findings, present some technical challenges coupled studies plant-environment interactions, proposing possible solutions exciting paths for future research.

Language: Английский

Citations

11
Lost in space: what single-cell RNA sequencing cannot tell you DOI Creative Commons
Kelvin Adema, Michael A. Schon, Michael D. Nodine

et al.

Trends in Plant Science, Journal Year: 2024, Volume and Issue: 29(9), P. 1018 - 1028

Published: April 2, 2024

Plant scientists are rapidly integrating single-cell RNA sequencing (scRNA-seq) into their workflows. Maximizing the potential of scRNA-seq requires a proper understanding spatiotemporal context cells. However, positional information is inherently lost during scRNA-seq, limiting its to characterize complex biological systems. In this review we highlight how current analysis pipelines cannot completely recover spatial information, which confounds interpretation. Various strategies exist identify location RNA, from classical in situ hybridization transcriptomics. Herein discuss possibility utilizing supervise analyses. An integrative approach will maximize each technology, and lead insights go beyond capability individual technology.

Language: Английский

Citations

11
Single-nucleus sequencing deciphers developmental trajectories in rice pistils DOI Creative Commons
Chengxiang Li,

Songyao Zhang,

Xingying Yan

et al.

Developmental Cell, Journal Year: 2023, Volume and Issue: 58(8), P. 694 - 708.e4

Published: April 1, 2023

Language: Английский

Citations

22
Recent progresses in plant single-cell transcriptomics DOI Creative Commons
Dihuai Zheng,

Jiwei Xu,

Yaqian Lu

et al.

Crop Design, Journal Year: 2023, Volume and Issue: 2(2), P. 100041 - 100041

Published: Aug. 1, 2023

High-throughput sequencing technologies at single-cell resolution have great potential to reveal a new landscape of plant cells. Single-cell/nucleus RNA (scRNA/snRNA), single-cell/nucleus assay for transposase accessible chromatin (scATAC/snATAC) and spatial transcriptome been applied in multiple tissues. Consequently, significant increase publications on transcriptomics was seen the recent two years. In this review, we will summarize advantages weaknesses these approaches, offer glimpse their developments cell biology, bioinformatic tools databases latest

Language: Английский

Citations

22
Opportunities and challenges in the application of single-cell and spatial transcriptomics in plants DOI Creative Commons
Ce Chen,

Yining Ge,

Lingli Lu

et al.

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: Aug. 11, 2023

Single-cell and spatial transcriptomics have diverted researchers’ attention from the multicellular level to single-cell information. transcriptomes provide insights into transcriptome at level, whereas help preserve Although these two omics technologies are helpful mature, further research is needed ensure their widespread applicability in plant studies. Reviewing recent on or transcriptomics, we compared different experimental methods used various plants. The limitations challenges clear for both transcriptomic analyses, such as lack of applicability, information, high resolution. Subsequently, put forth applications, cross-species analysis roots idea that needs be combined with other analyses achieve superiority over individual analyses. Overall, results this review suggest combining element distribution can a promising direction, particularly research.

Language: Английский

Citations

22