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

Plant Biotechnology Journal, Год журнала: 2022, Номер 20(12), С. 2372 - 2388

Опубликована: Авг. 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

Язык: Английский

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Transcriptomics, proteomics, and metabolomics interventions prompt crop improvement against metal(loid) toxicity

Plant Cell Reports, Год журнала: 2024, Номер 43(3)

Опубликована: Фев. 27, 2024

The escalating challenges posed by metal(loid) toxicity in agricultural ecosystems, exacerbated rapid climate change and anthropogenic pressures, demand urgent attention. Soil contamination is a critical issue because it significantly impacts crop productivity. widespread threat of can jeopardize global food security due to contaminated supplies pose environmental risks, contributing soil water pollution thus impacting the whole ecosystem. In this context, plants have evolved complex mechanisms combat stress. Amid array innovative approaches, omics, notably transcriptomics, proteomics, metabolomics, emerged as transformative tools, shedding light on genes, proteins, key metabolites involved stress responses tolerance mechanisms. These identified candidates hold promise for developing high-yielding crops with desirable agronomic traits. Computational biology tools like bioinformatics, biological databases, analytical pipelines support these omics approaches harnessing diverse information facilitating mapping genotype-to-phenotype relationships under conditions. This review explores: (1) multifaceted strategies that use adapt their environment; (2) latest findings metal(loid)-mediated metabolomics studies across various plant species; (3) integration data artificial intelligence high-throughput phenotyping; (4) bioinformatics single and/or multi-omics integration; (5) insights into adaptations future outlooks; (6) capacity advances creating sustainable resilient thrive metal(loid)-contaminated environments.

Язык: Английский

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Effective multi-modal clustering method via skip aggregation network for parallel scRNA-seq and scATAC-seq data

Briefings in Bioinformatics, Год журнала: 2024, Номер 25(2)

Опубликована: Янв. 22, 2024

Abstract In recent years, there has been a growing trend in the realm of parallel clustering analysis for single-cell RNA-seq (scRNA) and Assay Transposase Accessible Chromatin (scATAC) data. However, prevailing methods often treat these two data modalities as equals, neglecting fact that scRNA mode holds significantly richer information compared to scATAC. This disregard hinders model benefits from insights derived multiple modalities, compromising overall performance. To this end, we propose an effective multi-modal scEMC Concretely, have devised skip aggregation network simultaneously learn global structural among cells integrate diverse modalities. safeguard quality integrated cell representation against influence stemming sparse scATAC data, connect with aggregated via connection. Moreover, effectively fit real distribution cells, introduced Zero Inflated Negative Binomial-based denoising autoencoder accommodates corrupted containing synthetic noise, concurrently integrating joint optimization module employs losses. Extensive experiments serve underscore effectiveness our model. work contributes ongoing exploration subpopulations tumor microenvironments, code will be public at https://github.com/DayuHuu/scEMC.

Язык: Английский

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Integrative Multi-Omics Approaches for Identifying and Characterizing Biological Elements in Crop Traits: Current Progress and Future Prospects

International Journal of Molecular Sciences, Год журнала: 2025, Номер 26(4), С. 1466 - 1466

Опубликована: Фев. 10, 2025

The advancement of multi-omics tools has revolutionized the study complex biological systems, providing comprehensive insights into molecular mechanisms underlying critical traits across various organisms. By integrating data from genomics, transcriptomics, metabolomics, and other omics platforms, researchers can systematically identify characterize elements that contribute to phenotypic traits. This review delves recent progress in applying approaches elucidate genetic, epigenetic, metabolic networks associated with key plants. We emphasize potential these integrative strategies enhance crop improvement, optimize agricultural practices, promote sustainable environmental management. Furthermore, we explore future prospects field, underscoring importance cutting-edge technological advancements need for interdisciplinary collaboration address ongoing challenges. bridging this aims provide a holistic framework advancing research plant biology agriculture.

Язык: Английский

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Spatial transcriptomics drives a new era in plant research

The Plant Journal, Год журнала: 2023, Номер 116(6), С. 1571 - 1581

Опубликована: Авг. 31, 2023

SUMMARY The plant community lags far behind the animal and human fields concerning application of single‐cell methodologies. This is primarily due to challenges associated with tissue dissection limitations available technologies. However, recent advances in spatial transcriptomics enable study single‐cells derived from tissues a perspective. technology already successfully used identify cell types, reconstruct cell‐fate lineages, reveal cell‐to‐cell interactions. Future technological advancements will overcome sample processing, data analysis, integration multiple‐omics Thanks transcriptomics, we anticipate several research projects significantly advance our understanding critical aspects biology.

Язык: Английский

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Current views of drought research: experimental methods, adaptation mechanisms and regulatory strategies

Frontiers in Plant Science, Год журнала: 2024, Номер 15

Опубликована: Апрель 4, 2024

Drought stress is one of the most important abiotic stresses which causes many yield losses every year. This paper presents a comprehensive review recent advances in international drought research. First, main types and commonly used methods current experiment were introduced, advantages disadvantages each method evaluated. Second, response plants to was reviewed from aspects morphology, physiology, biochemistry molecular progression. Then, potential improve resistance emerging technologies introduced. Finally, research dilemma future development direction summarized. In summary, this provides insights into different perspectives theoretical reference for scholars engaged about engage

Язык: Английский

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Role of OMICS ‐Based Technologies in Plant Sciences

Опубликована: Март 29, 2024

Research into the complex molecular and genetic pathways driving plant growth, development, adaptation, interactions has been made possible because of development integration OMICS-based technologies. This chapter gives a general view critical role that techniques play in expanding our knowledge biology encouraging advancements sciences. Researchers can now decode make-up, gene expression profiles, protein dynamics, metabolite profiles plants with an unparalleled level precision thanks to genomics, transcriptomics, proteomics, metabolomics, other OMICS fields. With aid these technologies, genomes may be thoroughly characterized, enabling discovery crucial genes involved multiple physiological processes, stress responses, manufacture bioactive substances. Through quantitative trait locus mapping, marker-assisted selection, genome-wide association analyses, approaches have sped up creation innovative, high-yielding, stress-resistant varieties context breeding agricultural improvement. speed process by revealing underpinnings desirable traits, addressing global concerns such as food security climate resistance. Furthermore, metabolic pathways, signaling networks, regulatory mechanisms control responses biotic abiotic challenges revealed using The gained from studies it create creative methods for improving resource efficiency, reducing environmental impact, increasing tolerance agriculture. Handling enormous datasets produced technology bioinformatics computational tools. Advanced data analysis methods, network modeling machine learning, make easier extract significant insights large-scale multiomics datasets, allowing researchers understand complicated biological relationships. technologies sparked revolution sciences, understanding genetics, biology, plants. are well positioned address urgent issues agriculture, sustainability, stewardship through their application. advancing fostering innovation, furthering efforts resilient nourished future is emphasized this abstract.

Язык: Английский

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A single-cell transcriptome atlas reveals the trajectory of early cell fate transition during callus induction in Arabidopsis

Plant Communications, Год журнала: 2024, Номер 5(8), С. 100941 - 100941

Опубликована: Май 7, 2024

Язык: Английский

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Recent progresses in plant single-cell transcriptomics

Crop Design, Год журнала: 2023, Номер 2(2), С. 100041 - 100041

Опубликована: Авг. 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

Язык: Английский

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Opportunities and challenges in the application of single-cell and spatial transcriptomics in plants

Frontiers in Plant Science, Год журнала: 2023, Номер 14

Опубликована: Авг. 11, 2023

Single-cell and spatial transcriptomics have diverted researchers’ attention from the multicellular level to single-cell information. transcriptomes provide insights into transcriptome at level, whereas help preserve Although these two omics technologies are helpful mature, further research is needed ensure their widespread applicability in plant studies. Reviewing recent on or transcriptomics, we compared different experimental methods used various plants. The limitations challenges clear for both transcriptomic analyses, such as lack of applicability, information, high resolution. Subsequently, put forth applications, cross-species analysis roots idea that needs be combined with other analyses achieve superiority over individual analyses. Overall, results this review suggest combining element distribution can a promising direction, particularly research.

Язык: Английский

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