Single-cell multi-omics in the medicinal plant Catharanthus roseus

Nature Chemical Biology, Journal Year: 2023, Volume and Issue: 19(8), P. 1031 - 1041

Published: May 15, 2023

Advances in omics technologies now permit the generation of highly contiguous genome assemblies, detection transcripts and metabolites at level single cells high-resolution determination gene regulatory features. Here, using a complementary, multi-omics approach, we interrogated monoterpene indole alkaloid (MIA) biosynthetic pathway Catharanthus roseus, source leading anticancer drugs. We identified clusters genes involved MIA biosynthesis on eight C. roseus chromosomes extensive duplication genes. Clustering was not limited to linear genome, through chromatin interaction data, were present within same topologically associated domain, permitting identification secologanin transporter. Single-cell RNA-sequencing revealed sequential cell-type-specific partitioning leaf that, when coupled with single-cell metabolomics permitted reductase that yields bis-indole anhydrovinblastine. also expression root pathway.

Language: Английский

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Single‐cell RNA‐seq reveals fate determination control of an individual fibre cell initiation in cotton (Gossypium hirsutum)

Plant Biotechnology Journal, Journal Year: 2022, Volume and Issue: 20(12), P. 2372 - 2388

Published: Aug. 29, 2022

Summary Cotton fibre is a unicellular seed trichome, and lint initials per as factor determines yield. However, the mechanisms controlling initiation from ovule epidermis are not understood well enough. Here, with single‐cell RNA sequencing (scRNA‐seq), total of 14 535 cells were identified cotton outer integument Xu142_LF line at four developmental stages (1.5, 1, 0.5 days before anthesis day anthesis). Three major cell types, fibre, non‐fibre pigment layer then verified by in situ hybridization. A comparative analysis on scRNA‐seq data between Xu142 its fibreless mutant fl further confirmed cluster definition. The trajectory was reconstructed, differentiated 1 anthesis. Gene regulatory networks revealed spatiotemporal pattern core transcription factors, MYB25‐like HOX3 demonstrated played key roles commanders differentiation tip‐biased diffuse growth respectively. model for early development single proposed here, which sheds light deciphering mechanism plant trichome improvement

Language: Английский

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Single-cell RNA sequencing provides a high-resolution roadmap for understanding the multicellular compartmentation of specialized metabolism

Nature Plants, Journal Year: 2022, Volume and Issue: 9(1), P. 179 - 190

Published: Dec. 15, 2022

Language: Английский

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Improving photosynthetic efficiency toward food security: Strategies, advances, and perspectives

Molecular Plant, Journal Year: 2023, Volume and Issue: 16(10), P. 1547 - 1563

Published: Sept. 1, 2023

published or not.The documents may come from teaching and research institutions in France abroad, public private centers.L'archive ouverte pluridisciplinaire

Language: Английский

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Orthologous marker groups reveal broad cell identity conservation across plant single-cell transcriptomes

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

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Diffusion and bulk flow of amino acids mediate calcium waves in plants

Science Advances, Journal Year: 2022, Volume and Issue: 8(42)

Published: Oct. 21, 2022

In plants, a variety of stimuli trigger long-range calcium signals that travel rapidly along the vasculature to distal tissues via poorly understood mechanisms. Here, we use quantitative imaging and analysis demonstrate traveling waves are mediated by diffusion bulk flow amino acid chemical messengers. We propose wounding triggers release acids diffuse locally through apoplast, activating calcium-permeable channel GLUTAMATE RECEPTOR-LIKE 3.3 as they pass. Over long distances vasculature, wound-triggered dynamics fluorescent tracer show likely driven channel-activating chemical. observed multiple with similar dynamics, but alone cannot initiate all systemic defense responses, suggesting mobile messengers core component complex signaling in plants.

Language: Английский

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Single-cell RNA sequencing reveals a hierarchical transcriptional regulatory network of terpenoid biosynthesis in cotton secretory glandular cells

Molecular Plant, Journal Year: 2023, Volume and Issue: 16(12), P. 1990 - 2003

Published: Oct. 17, 2023

Plants can synthesize a wide range of terpenoids in response to various environmental cues. However, the specific regulatory mechanisms governing terpenoid biosynthesis at cellular level remain largely elusive. In this study, we employed single-cell RNA sequencing comprehensively characterize transcriptome profile cotton leaves and established hierarchical transcriptional network regulating cell-specific production. We observed substantial expression levels genes associated with both volatile terpenes (such as β-caryophyllene β-myrcene) non-volatile gossypol-type secretory glandular cells. Moreover, two novel transcription factors, namely GoHSFA4a GoNAC42, are identified function downstream Gossypium PIGMENT GLAND FORMATION genes. Both factors could directly regulate biosynthetic cells developmental stimuli. For convenient retrieval data generated developed user-friendly web server . Our findings not only offer valuable insights into precise regulation but also provide potential targets for breeding endeavors.

Language: Английский

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Spatially resolved transcriptomic analysis of the germinating barley grain

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 51(15), P. 7798 - 7819

Published: June 23, 2023

Seeds are a vital source of calories for humans and unique stage in the life cycle flowering plants. During seed germination, embryo undergoes major developmental transitions to become seedling. Studying gene expression individual cell types has been challenging due lack spatial information or low throughput existing methods. To overcome these limitations, transcriptomics workflow was developed germinating barley grain. This approach enabled high-throughput analysis expression, revealing specific patterns various functional categories at sub-tissue level. study revealed over 14 000 genes differentially regulated during first 24 h after imbibition. Individual genes, such as aquaporin family, starch degradation, wall modification, transport processes, ribosomal proteins transcription factors, were found have time. Using autocorrelation algorithms, we identified auxin that had increasingly focused within subdomains time, suggesting their role establishing axis. Overall, our provides an unprecedented spatially resolved cellular map germination identifies genomics targets better understand restricted processes germination. The data can be viewed https://spatial.latrobe.edu.au/.

Language: Английский

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Understanding plant pathogen interactions using spatial and single-cell technologies

Communications Biology, Journal Year: 2023, Volume and Issue: 6(1)

Published: Aug. 4, 2023

Plants are in contact with diverse pathogens and microorganisms. Intense investigation over the last 30 years has resulted identification of multiple immune receptors model crop species as well signaling overlap surface-localized intracellular receptors. However, scientists still have a limited understanding how plants respond to spatial cellular resolution. Recent advancements single-cell, single-nucleus technologies can now be applied plant-pathogen interactions. Here, we outline current state these highlight outstanding biological questions that addressed future.

Language: Английский

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

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

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