Single‐cell RNA sequencing technologies and applications: A brief overview

Clinical and Translational Medicine, Journal Year: 2022, Volume and Issue: 12(3)

Published: March 1, 2022

Language: Английский

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Single-cell transcriptome atlas and chromatin accessibility landscape reveal differentiation trajectories in the rice root

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: April 6, 2021

Abstract Root development relies on the establishment of meristematic tissues that give rise to distinct cell types differentiate across defined temporal and spatial gradients. Dissection developmental trajectories transcriptional networks underlie them could aid understanding function root apical meristem in both dicots monocots. Here, we present a single-cell RNA (scRNA) sequencing chromatin accessibility survey rice radicles. By profiling individual tip cells reconstruct continuous epidermal ground tissues, elucidate regulatory underlying fate determination these lineages. We further identify characteristic processes, transcriptome profiles, marker genes for reveal conserved divergent pathways between Finally, demonstrate potential platform functional genetic studies by using spatiotemporal modeling mutant from cell-specific gene cohort.

Language: Английский

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The single-cell stereo-seq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leaves

Developmental Cell, Journal Year: 2022, Volume and Issue: 57(10), P. 1299 - 1310.e4

Published: May 1, 2022

Understanding the complex functions of plant leaves requires a thorough characterization discrete cell features. Although single-cell gene expression profiling technologies have been developed, their application in characterizing subtypes has not achieved yet. Here, we present scStereo-seq (single-cell spatial enhanced resolution omics sequencing) that enabled us to show bona fide transcriptome profiles Arabidopsis leaves. Subtle but significant transcriptomic differences between upper and lower epidermal cells successfully distinguished. Furthermore, discovered cell-type-specific gradients from main vein leaf edge, which led finding distinct developmental trajectories vascular guard cells. Our study showcases importance physical locations individual for exerting biological plants demonstrates is powerful tool integrate location information biology study.

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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A rice single cell transcriptomic atlas defines the developmental trajectories of rice floret and inflorescence meristems

New Phytologist, Journal Year: 2022, Volume and Issue: 234(2), P. 494 - 512

Published: Feb. 4, 2022

Summary Rice inflorescence development determines yield and relies on the activity of axillary meristems (AMs); however, high‐resolution analysis its early is lacking. Here, we have used high‐throughput single‐cell RNA sequencing to profile 37 571 rice cells constructed a genome‐scale gene expression resource covering inflorescence‐to‐floret transition during reproductive development. The differentiation trajectories florets AMs were reconstructed, discrete cell types groups regulators in highly heterogeneous young identified then validated by situ hybridization with fluorescent marker lines. Our data demonstrate that WOX transcription factor, DWARF TILLER1, regulates flower meristem activity, provide evidence for role auxin branching exploring biological importer OsAUX1. comprehensive transcriptomic atlas development, supported genetic evidence, provides single‐cell‐level insights into AM floret

Language: Английский

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Recent advances in proteomics and metabolomics in plants

Molecular Horticulture, Journal Year: 2022, Volume and Issue: 2(1)

Published: July 23, 2022

Over the past decade, systems biology and plant-omics have increasingly become main stream in plant research. New developments mass spectrometry bioinformatics tools, methodological schema to integrate multi-omics data leveraged recent advances proteomics metabolomics. These progresses are driving a rapid evolution field of research, greatly facilitating our understanding mechanistic aspects metabolisms interactions plants with their external environment. Here, we review MS-based metabolomics tools workflows special focus on applications research using several case studies related stress response, gene/protein function characterization, metabolic signaling pathways exploration, natural product discovery. We also present projection concerning future perspectives development including challenges for system biology. This is intended provide readers an overview how advanced MS technology, integrated application can be used advance

Language: Английский

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Regulatory networks in plant responses to drought and cold stress

PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 195(1), P. 170 - 189

Published: March 21, 2024

Abstract Drought and cold represent distinct types of abiotic stress, each initiating unique primary signaling pathways in response to dehydration temperature changes, respectively. However, a convergence at the gene regulatory level is observed where common set stress-responsive genes activated mitigate impacts both stresses. In this review, we explore these intricate networks, illustrating how plants coordinate stress signals into collective transcriptional strategy. We delve molecular mechanisms perception, signaling, activation pathways, with focus on insights gained from model species. By elucidating shared aspects plant responses drought cold, provide insight adaptive strategies plants, paving way for engineering stress-resilient crop varieties that can withstand changing climate.

Language: Английский

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Asymmetric gene expression and cell-type-specific regulatory networks in the root of bread wheat revealed by single-cell multiomics analysis

Genome biology, Journal Year: 2023, Volume and Issue: 24(1)

Published: April 4, 2023

Homoeologs are defined as homologous genes resulting from allopolyploidy. Bread wheat, Triticum aestivum, is an allohexaploid species with many homoeologs. Homoeolog expression bias, referring to the relative contribution of homoeologs transcriptome, critical for determining traits that influence wheat growth and development. Asymmetric transcription has been so far investigated in a tissue or organ-specific manner, which could be misleading due mixture cell types.

Language: Английский

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Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of pigment glands in Gossypium bickii

Molecular Plant, Journal Year: 2023, Volume and Issue: 16(4), P. 694 - 708

Published: Feb. 10, 2023

Comprehensive utilization of cottonseeds is limited by the presence pigment glands and its inclusion gossypol. The ideal cotton has glandless seeds but a glanded plant, trait found in only few Australian wild species, including Gossypium bickii. Introgression this into cultivated species proved to be difficult. Understanding biological processes toward gland morphogenesis associated underlying molecular mechanisms will facilitate breeding varieties with plant. In study, single-cell RNA sequencing (scRNA-seq) was performed on 12 222 protoplasts isolated from cotyledons germinating G. bickii 48 h after imbibition. Clustered 14 distinct clusters unsupervisedly, these cells could grouped eight cell populations assistance known marker genes. were well separated others parenchyma cells, secretory apoptotic cells. By integrating developmental trajectory, transcription factor regulatory networks, core functional validation, we established model for formation. model, light gibberellin verified promote formation glands. addition, three novel genes, GbiERF114 (ETHYLENE RESPONSE FACTOR 114), GbiZAT11 (ZINC FINGER OF ARABIDOPSIS THALIANA 11), GbiNTL9 (NAC TRANSCRIPTION FACTOR-LIKE 9), affect Collectively, findings provide new insights lay cornerstone future scRNA-seq investigations.

Language: Английский

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