Single-cell genomics revolutionizes plant development studies across scales DOI Open Access
Mingyuan Zhu, Isaiah Taylor, Philip N. Benfey

et al.

Development, Journal Year: 2022, Volume and Issue: 149(6)

Published: March 14, 2022

ABSTRACT Understanding the development of tissues, organs and entire organisms through lens single-cell genomics has revolutionized developmental biology. Although transcriptomics been pioneered in animal systems, from an experimental perspective, plant holds some distinct advantages: cells do not migrate relation to one another, new organ formation (of leaves, roots, flowers, etc.) continues post-embryonically persistent stem cell populations known as meristems. For a time, studies lagged behind or culture-based, approaches, largely owing difficulty dissociating their rigid walls. Recent intensive single-nucleus isolation techniques across species opened up wide range approaches. This produced rapidly expanding diversity information tissue types species, concomitant with creative methods. In this brief Spotlight, we highlight technical developments how they have led profiling various organs. We also emphasize contribution revealing trajectories among different within Furthermore, present efforts toward comparative analysis tissues at level. Single-cell is beginning generate comprehensive relating emerge populations.

Language: Английский

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

26
Single‐cell RNA‐seq describes the transcriptome landscape and identifies critical transcription factors in the leaf blade of the allotetraploid peanut (Arachis hypogaea L.) DOI Creative Commons
Hao Liu,

Dongxiu Hu,

Puxuan Du

et al.

Plant Biotechnology Journal, Journal Year: 2021, Volume and Issue: 19(11), P. 2261 - 2276

Published: June 26, 2021

Summary Single‐cell RNA‐seq (scRNA‐seq) has been highlighted as a powerful tool for the description of human cell transcriptome, but technology not broadly applied in plant cells. Herein, we describe successful development robust protoplast isolation system peanut leaf. A total 6,815 single cells were divided into eight clusters based on reported marker genes by applying scRNA‐seq. Further, pseudo‐time analysis was used to developmental trajectory and interaction network transcription factors (TFs) distinct types during leaf growth. The enabled re‐investigation primordium‐driven processes mesophyll epidermis. These results suggest that palisade likely differentiate spongy cells, while epidermal originated earlier than primordium. Subsequently, developed method integrated multiple technologies efficiently validate scRNA‐seq result homogenous population. expression levels several TFs strongly correlated with ontogeny accordance obtained values. Additionally, AHL23 ( AT‐HOOK MOTIF NUCLEAR LOCALIZED PROTEIN 23 ), which is localized nucleus, promoted growth when ectopically expressed Arabidopsis modulating phytohormone pathway. Together, our study displays application can provide new hypotheses regarding differentiation blade Arachis hypogaea . We believe this approach will enable significant advances functional allotetraploid other species.

Language: Английский

Citations

80
A Single-Nucleus Atlas of Seed-to-Seed Development in Arabidopsis DOI Creative Commons
Travis Lee, Tatsuya Nobori, Natanella Illouz‐Eliaz

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: March 24, 2023

SUMMARY Extensive studies of the reference plant Arabidopsis have enabled a deep understanding tissues throughout development, yet census cell types and states development is lacking. Here, we present single-nucleus transcriptome atlas seed-to-seed employing over 800,000 nuclei, encompassing diverse set across ten developmental stages, with spatial transcriptomic validation dynamic seed silique. Cross-organ analyses revealed transcriptional conservation heterogeneity within individual influenced by organ-of-origin timing, including groups transcription factors, suggesting gatekeeping factor activation. This provides resource for study type specification continuum stimulus-response genetic perturbations at single-cell resolution.

Language: Английский

Citations

36
Epigenetic Regulation During Plant Development and the Capacity for Epigenetic Memory DOI Creative Commons

Elizabeth A. Hemenway,

Mary Gehring

Annual Review of Plant Biology, Journal Year: 2023, Volume and Issue: 74(1), P. 87 - 109

Published: March 1, 2023

The establishment, maintenance, and removal of epigenetic modifications provide an additional layer regulation, beyond genetically encoded factors, by which plants can control developmental processes adapt to the environment. Epigenetic inheritance, while historically referring information not in DNA sequence that is inherited between generations, also refer are maintained within individual but reset generations. Both types inheritance occur plants, functions mechanisms distinguishing two great interest field. Here, we discuss examples dynamics maintenance during selected stages growth development their functional consequences. states dynamic response stress, with consequences for transposable element regulation. How resetting generations occurs normal stress emerging area research.

Language: Английский

Citations

32
Decoding the gene regulatory network of endosperm differentiation in maize DOI Creative Commons
Yue Yuan, Qiang Huo, Ziru Zhang

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Jan. 2, 2024

The persistent cereal endosperm constitutes the majority of grain volume. Dissecting gene regulatory network underlying development will facilitate yield and quality improvement crops. Here, we use single-cell transcriptomics to analyze developing maize (Zea mays) during cell differentiation. After obtaining transcriptomic data from 17,022 single cells, identify 12 clusters corresponding five types revealing complex transcriptional heterogeneity. We delineate temporal gene-expression pattern 6 7 days after pollination. profile genomic DNA-binding sites 161 transcription factors differentially expressed between constructed a by combining with direct profiles, identifying 181 regulons containing genes encoding along their high-confidence targets, Furthermore, map clusters, cell-cluster-specific essential regulators, experimentally validated three predicted key regulators. This study provides framework for understanding function at resolution.

Language: Английский

Citations

16
A spatially resolved multi-omic single-cell atlas of soybean development DOI
Xuan Zhang, Ziliang Luo, Alexandre P. Marand

et al.

Cell, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 1, 2024

Language: Английский

Citations

11
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
HD-Zip IV transcription factors: Drivers of epidermal cell fate integrate metabolic signals DOI Creative Commons
Kathrin Schrick, Usama Ahmad, Hieu V. Nguyen

et al.

Current Opinion in Plant Biology, Journal Year: 2023, Volume and Issue: 75, P. 102417 - 102417

Published: July 11, 2023

Language: Английский

Citations

19
Development and application of transcriptomics technologies in plant science DOI Creative Commons
H.W. Wang, Yueting Xu, Zhizhong Zhang

et al.

Crop Design, Journal Year: 2024, Volume and Issue: 3(2), P. 100057 - 100057

Published: Feb. 24, 2024

Over the past decade, bulk RNA sequencing (RNA-seq) has become an indispensable tool in molecular biology, and have made novel development, with two innovative methodologies being developed, single-cell (scRNA-seq) technology spatial transcriptome (ST) technology. The scRNA-seq allows researchers to analyze gene expression individual cells, providing more detailed information relative technologies. Meanwhile, ST overcomes limitations of terms loss information, enabling scientists better understand distribution within tissues. These advancements transcriptomics technologies revolutionize field genomics been widely used disease diagnosis medicine. However, they are less utilized plant research. This review describes advantage three technologies, presents their applications sciences.

Language: Английский

Citations

8
Parental conflict driven regulation of endosperm cellularization by a family of Auxin Response Factors DOI Creative Commons
Nicolas Butel, Yichun Qiu, Weijie Xu

et al.

Nature Plants, Journal Year: 2024, Volume and Issue: 10(6), P. 1018 - 1026

Published: May 28, 2024

Abstract The endosperm is a reproductive tissue supporting embryo development. In most flowering plants, the initial divisions of nuclei are not succeeded by cellularization; this process occurs only after specific number mitotic cycles have taken place. timing cellularization significantly influences seed viability and size. Previous research implicated auxin as key factor in initiating nuclear determining cellularization. Here we uncover involvement family clustered response factors (cARFs) dosage-sensitive regulators cARFs , maternally expressed paternally silenced, shown to induce cellularization, thereby restricting growth. Our findings align with predictions parental conflict theory, suggesting that represent major molecular targets conflict. We further demonstrate recurring amplification Brassicaceae, an evolutionary reinforcing maternal control over study highlights antagonistic on converges biosynthesis signalling.

Language: Английский

Citations

8