Single-cell and spatial multi-omics in the plant sciences: Technical advances, applications, and perspectives

Plant Communications, Journal Year: 2022, Volume and Issue: 4(3), P. 100508 - 100508

Published: Dec. 20, 2022

Plants contain a large number of cell types and exhibit complex regulatory mechanisms. Studies at the single-cell level have gradually become more common in plant science. Single-cell transcriptomics, spatial metabolomics techniques been combined to analyze development. These used study transcriptomes metabolomes tissues level, enabling systematic investigation gene expression metabolism specific during defined developmental stages. In this review, we present an overview significant breakthroughs multi-omics plants, discuss how these approaches may soon play essential roles research.

Language: Английский

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Single-Cell RNA Sequencing for Plant Research: Insights and Possible Benefits

International Journal of Molecular Sciences, Journal Year: 2022, Volume and Issue: 23(9), P. 4497 - 4497

Published: April 19, 2022

In recent years, advances in single-cell RNA sequencing (scRNA-seq) technologies have continued to change our views on biological systems by increasing the spatiotemporal resolution of analysis resolution. Application scRNA-seq plants enables comprehensive characterization both common and rare cell types states, uncovering new revealing how relate each other spatially developmentally. This review provides an overview methodologies, highlights application plant science, justifies why is a master player sequencing, explains role transcriptomics environmental stress adaptation, alongside challenges prospects transcriptomics. Collectively, we put forward central research.

Language: Английский

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Advances and applications of single‐cell omics technologies in plant research

The Plant Journal, Journal Year: 2022, Volume and Issue: 110(6), P. 1551 - 1563

Published: April 15, 2022

SUMMARY Single‐cell sequencing approaches reveal the intracellular dynamics of individual cells and answer biological questions with high‐dimensional catalogs millions cells, including genomics, transcriptomics, chromatin accessibility, epigenomics, proteomics data across species. These emerging yet thriving technologies have been fully embraced by field plant biology, a constantly expanding portfolio applications. Here, we introduce current technical advances used for single‐cell omics, especially genome transcriptome sequencing. Firstly, overview methods protoplast nucleus isolation amplification. Subsequently, use well‐executed benchmarking studies to highlight made through application omics techniques. Looking forward, offer glimpse additional hurdles future opportunities that will broad adoption revolutionary perspectives in biology.

Language: Английский

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Development of a single-cell atlas for woodland strawberry (Fragaria vesca) leaves during early Botrytis cinerea infection using single-cell RNA-seq

Horticulture Research, Journal Year: 2022, Volume and Issue: 9

Published: Jan. 1, 2022

Abstract Pathogen invasion leads to fast, local-to-systemic signal transduction that initiates plant defense responses. Despite tremendous progress in past decades, aspects of this process remain unknown, such as which cell types respond first and how signals are transferred among types. Here, we used single-cell RNA-seq >50 000 single cells document the gene expression landscape leaves woodland strawberry during infection by Botrytis cinerea identify major We constructed a atlas characterized distinct patterns hydathode, epidermal, mesophyll incubation period B. infection. Pseudotime trajectory analysis revealed transition from normal functioning response epidermal upon Genes related disease resistance showed different types: resistance-related genes encoding transcription factors were highly expressed individual interacted trigger systemic immunity cinerea. This is report transcriptional pathogenic process; it provides new insights into holistic dynamics host–pathogen interactions can guide identification formulation strategies for resistant cultivar development.

Language: Английский

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Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice

Developmental Cell, Journal Year: 2022, Volume and Issue: 57(9), P. 1177 - 1192.e6

Published: May 1, 2022

Understanding how roots modulate development under varied irrigation or rainfall is crucial for of climate-resilient crops. We established a toolbox tagged rice lines to profile translating mRNAs and chromatin accessibility within specific cell populations. used these study in range environments: plates the lab, controlled greenhouse stress recovery conditions, outdoors paddy. Integration mRNA data resolves regulatory networks following: cycle genes proliferating cells that attenuate DNA synthesis submergence; involved auxin signaling, circadian clock, small RNA regulation ground tissue; suberin biosynthesis, iron transporters, nitrogen assimilation endodermal/exodermal modulated with water availability. By applying systems approach, we identify known candidate driver transcription factors water-deficit responses xylem plasticity. Collectively, this resource will facilitate genetic improvements root optimal climate resilience.

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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Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants

Plant Communications, Journal Year: 2023, Volume and Issue: 4(4), P. 100558 - 100558

Published: Feb. 9, 2023

With the development of high-throughput biology techniques and artificial intelligence, it has become increasingly feasible to design construct biological parts, modules, circuits, even whole systems. To overcome limitations native promoters in controlling gene expression, promoter aims synthesize short, inducible, conditionally controlled coordinate expression multiple genes diverse plant metabolic signaling pathways. Synthetic are versatile can drive accurately with smart responses; they show potential for enhancing desirable traits crops, thereby improving crop yield, nutritional quality, food security. This review first illustrates importance synthetic promoters, then introduces architecture thoroughly summarizes advances construction. Restrictions future applications such improvement also discussed.

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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Nitrogen sensing and regulatory networks: it's about time and space

The Plant Cell, Journal Year: 2024, Volume and Issue: 36(5), P. 1482 - 1503

Published: Feb. 14, 2024

A plant's response to external and internal nitrogen signals/status relies on sensing signaling mechanisms that operate across spatial temporal dimensions. From a comprehensive systems biology perspective, this involves integrating responses in different cell types over long distances ensure organ coordination real time yield practical applications. In prospective review, we focus novel aspects of (N) sensing/signaling uncovered using approaches, largely the model Arabidopsis. The span: transcriptional N-dose mediated by Michaelis-Menten kinetics, role master NLP7 transcription factor as nitrate sensor, its nitrate-dependent TF nuclear retention, "hit-and-run" mode target gene regulation, cascade identified "network walking." Spatial N-sensing/signaling have been type-specific studies roots root-to-shoot communication. We explore new approaches single-cell sequencing data, trajectory inference, pseudotime analysis well machine learning artificial intelligence approaches. Finally, unveiling underlying dynamics networks species from crop could pave way for translational improve nitrogen-use efficiency crops. Such outcomes potentially reduce detrimental effects excessive fertilizer usage groundwater pollution greenhouse gas emissions.

Language: Английский

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A foundational large language model for edible plant genomes

Communications Biology, Journal Year: 2024, Volume and Issue: 7(1)

Published: July 9, 2024

Abstract Significant progress has been made in the field of plant genomics, as demonstrated by increased use high-throughput methodologies that enable characterization multiple genome-wide molecular phenotypes. These findings have provided valuable insights into traits and their underlying genetic mechanisms, particularly model species. Nonetheless, effectively leveraging them to make accurate predictions represents a critical step crop genomic improvement. We present AgroNT, foundational large language trained on genomes from 48 species with predominant focus show AgroNT can obtain state-of-the-art for regulatory annotations, promoter/terminator strength, tissue-specific gene expression, prioritize functional variants. conduct large-scale silico saturation mutagenesis analysis cassava evaluate impact over 10 million mutations provide predicted effects resource variant characterization. Finally, we propose diverse datasets compiled here Plants Genomic Benchmark (PGB), providing comprehensive benchmark deep learning-based methods research. The pre-trained is publicly available HuggingFace at https://huggingface.co/InstaDeepAI/agro-nucleotide-transformer-1b future research purposes.

Language: Английский

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