Single-cell transcriptomics reveals heterogeneity in plant responses to the environment: a focus on biotic and abiotic interactions

Journal of Experimental Botany, Год журнала: 2024, Номер 75(17), С. 5188 - 5203

Опубликована: Март 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.

Язык: Английский

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The power of small signaling peptides in crop and horticultural plants

The Crop Journal, Год журнала: 2025, Номер unknown

Опубликована: Янв. 1, 2025

Язык: Английский

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Polarity-guided uneven mitotic divisions control brassinosteroid activity in proliferating plant root cells

Cell, Год журнала: 2025, Номер unknown

Опубликована: Март 1, 2025

Brassinosteroid hormones are positive regulators of plant organ growth, yet their function in proliferating tissues remains unclear. Here, through integrating single-cell RNA sequencing with long-term live-cell imaging the Arabidopsis root, we reveal that brassinosteroid activity fluctuates throughout cell cycle, decreasing during mitotic divisions and increasing G1 phase. The post-mitotic recovery is driven by intrinsic polarity mother cell, resulting one daughter enhanced signaling, while other supports biosynthesis. coexistence these distinct states phase circumvents a negative feedback loop to facilitate production signaling increases. Our findings uncover polarity-guided, uneven meristem, which control hormone ensure optimal root growth.

Язык: Английский

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Plant genome information facilitates plant functional genomics

Planta, Год журнала: 2024, Номер 259(5)

Опубликована: Апрель 9, 2024

Abstract Main conclusion In this review, we give an overview of plant sequencing efforts and how impacts functional genomics research. Plant genome sequence information greatly facilitates the studies biology, genomics, evolution genomes genes, domestication processes, phylogenetic relationships, among many others. More than two decades have boosted number available sequenced genomes. The first genome, Arabidopsis, was published in year 2000 currently, 4604 from 1482 species been published. Various large initiatives are running, which planning to produce tens thousands near future. on status use different research areas.

Язык: Английский

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Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll revealed by single‐cell transcriptomics

New Phytologist, Год журнала: 2025, Номер unknown

Опубликована: Март 3, 2025

Summary Drought stress imposes severe challenges on agriculture by impacting crop performance. Understanding drought responses in plants at a cellular level is crucial first step toward engineering improved resilience. However, the molecular to are complex as they depend multiple factors, including severity of drought, profiled organ, its developmental stage or even cell types therein. Thus, deciphering transcriptional especially challenging. In this study, we investigated tissue‐specific mild (MD) young Arabidopsis thaliana (Arabidopsis) leaves using single‐cell RNA sequencing (scRNA‐seq). To preserve integrity during isolation, inhibited synthesis transcription inhibitor actinomycin D, and demonstrated benefits transcriptome fixation for studying level. We present curated validated atlas, comprising 50 797 high‐quality cells from almost all known leaf. All type annotations were with new library reporter lines. The data available broad community an intuitive tool browsable atlas ( http://www.single‐cell.be/plant/leaf‐drought ). show that mesophyll contains two spatially separated populations distinct drought: one enriched canonical abscisic acid‐related drought‐responsive genes, another genes involved iron starvation responses. Our study thus reveals dual adaptive mechanism leaf response MD provides valuable resource future research

Язык: Английский

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A space for time. Exploring temporal regulation of plant development across spatial scales

The Plant Journal, Год журнала: 2025, Номер 122(1)

Опубликована: Март 31, 2025

SUMMARY Plants continuously undergo change during their life cycle, experiencing dramatic phase transitions altering plant form, and regulating the assignment progression of cell fates. The relative timing developmental events is tightly controlled involves integration environmental, spatial, age‐related signals actors. While have been studied extensively many regulators described, less known about temporal regulation on a smaller, cell‐level scale. Here, using examples from both animal systems, we outline time‐dependent changes. Looking at systemic scale changes, discuss germination, juvenile‐to‐adult transition, flowering, senescence, together with regeneration timing. Switching to cellular level, several instances field in which control has examined this Then, switch back plants summarize where changes are temporally regulated. As time cannot easily be separated signaling derived environment tissue context, next factors that implicated controlling events, reviewing temperature, photoperiod, nutrient availability, as well context mechanical cues Afterwards, provide an overview mechanisms shown or development, considering metabolism, division control, mobile signals, epigenetic regulation, action transcription factors. Lastly, look remaining questions for future study how recent technical advancement can enable these efforts.

Язык: Английский

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Novel Strategies for Designing Climate‐Smart Crops to Ensure Sustainable Agriculture and Future Food Security

Journal of Sustainable Agriculture and Environment, Год журнала: 2025, Номер 4(2)

Опубликована: Март 31, 2025

ABSTRACT To fulfil food and nutritional demand for nine billion people by the mid‐21st century, global production must increase 60% regardless of challenges such as environmental pollution, water scarcity land degradation. Climate change exacerbates frequency intensity biotic abiotic stresses, which, in turn, severely compromise crop yields, jeopardize supply, deteriorate sustainable development goals achieving safety, limit climate‐smart production. Current consumption practices negatively influence environment, posing a major threat to ecosystem human health. Addressing these critical issues achieve agriculture necessitates designing future crops employing cutting‐edge breeding strategies enhanced productivity with minimal footprints. This endeavour requires comprehensive understanding plant stress adaptation, signalling pathways mitigation mechanisms. In this review, we first explain diverse impacts ongoing climate events on Subsequently, outline various tackle change, including agronomic practices, advanced technologies physiological molecular mechanisms tolerance. We also discuss engineering superior tolerance disease resistance nurturing healthy microbial partnerships between plants soil ensure nutrition security current populations amidst mounting challenges.

Язык: Английский

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Single-cell transcriptomics reveal how root tissues adapt to soil stress

Nature, Год журнала: 2025, Номер unknown

Опубликована: Апрель 30, 2025

Язык: Английский

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Rewiring gene circuitry for plant improvement

Nature Genetics, Год журнала: 2024, Номер 56(8), С. 1574 - 1582

Опубликована: Июль 29, 2024

Язык: Английский

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MINI-EX version 2: cell-type-specific gene regulatory network inference using an integrative single-cell transcriptomics approach

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Дек. 24, 2023

Abstract Understanding and predicting cell-type-specific gene regulatory networks (GRNs) is essential for unraveling the complex interactions between transcription factors (TFs) that modulate expression of target genes control diverse biological processes in multicellular organisms. MINI-EX (Motif-Informed Network Inference based on single-cell EXpression data) an integrative tool tailored identifying GRNs plants. Leveraging transcriptomics data, constructs expression-based integrates TF motif information to produce with increased accuracy. Furthermore, it assigns modules distinct cell types prioritizes candidate regulators by employing a strategy encompasses network centrality measures, functional annotations, specificity. Taken together, offers powerful approach identify transcriptional cascades enhance our understanding functions plant biology. Here, we discuss recent advancements tool’s latest version explain how can be identified non-model species lacking information. Additionally, provide comprehensive guide use MINI-EX, covering entire pipeline from preparing input files starting experiment, over configuring parameters, interpreting output data.

Язык: Английский

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