Nature Plants, Год журнала: 2024, Номер 10(5), С. 815 - 827
Опубликована: Май 14, 2024
Язык: Английский
Proceedings of the National Academy of Sciences, Год журнала: 2023, Номер 120(38)
Опубликована: Сен. 13, 2023
Callus is a reprogrammed cell mass involved in plant regeneration and gene transformation crop engineering. Pluripotent callus cells develop into fertile shoots through shoot regeneration. The molecular basis of the process remains largely elusive. This study pioneers exploration spatial transcriptome tomato during findings reveal presence highly heterogeneous populations within callus, including epidermis, vascular tissue, primordia, inner outgrowth shoots. By characterizing spatially resolved features primordia surrounding cells, specific factors essential for formation are identified. Notably, chlorenchyma enriched photosynthesis-related processes, play crucial role promoting subsequent Light shown to promote by inducing development coordinating sugar signaling. These significantly advance our understanding cellular aspects demonstrate immense potential transcriptomics biology.
Язык: Английский
Процитировано
48
Cell, Год журнала: 2024, Номер 187(17), С. 4488 - 4519
Опубликована: Авг. 1, 2024
Язык: Английский
Процитировано
27
The Plant Cell, Год журнала: 2024, Номер 36(4), С. 812 - 828
Опубликована: Янв. 17, 2024
Abstract Single-cell and single-nucleus RNA-sequencing technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these are gaining traction in molecular developmental biology for elucidating transcriptional changes across cell types a specific tissue or organ, upon treatments, response to biotic abiotic stresses, between genotypes. Despite rapidly accelerating use technologies, collective standardized experimental analytical procedures support acquisition high-quality data sets still missing. In this commentary, we discuss common challenges associated with single-cell transcriptomics plants propose general guidelines improve reproducibility, quality, comparability, interpretation make readily available community fast-developing field research.
Язык: Английский
Процитировано
25
Nature, Год журнала: 2025, Номер unknown
Опубликована: Янв. 22, 2025
Abstract Single-cell genomic technologies enable the multimodal profiling of millions cells across temporal and spatial dimensions. However, experimental limitations hinder comprehensive measurement under native dynamics in their tissue niche. Optimal transport has emerged as a powerful tool to address these constraints facilitated recovery original cellular context 1–4 . Yet, most optimal applications are unable incorporate information or scale single-cell atlases. Here we introduce multi-omics (moscot), scalable framework for genomics that supports multimodality all applications. We demonstrate capability moscot efficiently reconstruct developmental trajectories 1.7 million from mouse embryos 20 time points. To illustrate space, enrich transcriptomic datasets by mapping profiles liver sample align multiple coronal sections brain. present moscot.spatiotemporal, an approach leverages gene-expression data both dimensions uncover spatiotemporal embryogenesis. also resolve endocrine-lineage relationships delta epsilon previously unpublished mouse, time-resolved pancreas development dataset using paired measurements gene expression chromatin accessibility. Our findings confirmed through validation NEUROD2 regulator progenitor model human induced pluripotent stem cell islet differentiation. Moscot is available open-source software, accompanied extensive documentation.
Язык: Английский
Процитировано
5
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
Процитировано
2
Plant Communications, Год журнала: 2022, Номер 4(3), С. 100508 - 100508
Опубликована: Дек. 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.
Язык: Английский
Процитировано
58
Cells, Год журнала: 2023, Номер 12(16), С. 2042 - 2042
Опубликована: Авг. 10, 2023
Spatial transcriptomic technologies enable measurement of expression levels genes systematically throughout tissue space, deepening our understanding cellular organizations and interactions within tissues as well illuminating biological insights in neuroscience, developmental biology a range diseases, including cancer. A variety spatial have been developed and/or commercialized, differing resolution, sensitivity, multiplexing capability, throughput coverage. In this paper, we review key enabling their applications the perspective techniques new emerging that are to address current limitations methodologies. addition, describe how transcriptomics data can be integrated with other omics modalities, complementing methods deciphering cellar phenotypes providing novel insight into organization.
Язык: Английский
Процитировано
34
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
Процитировано
31
Plant Communications, Год журнала: 2023, Номер 4(5), С. 100665 - 100665
Опубликована: Июль 24, 2023
The primary and secondary growth of a tree stem is responsible for the corresponding increases in height diameter trunk. However, our molecular understanding biological processes underlying two events not yet complete. In this study, we used single-cell RNA sequencing (scRNA-seq) spatial transcriptome (ST-seq) to get transcription landscapes tissues Populus tree. results comparison between cell atlas differentiation trajectory revealed different regulatory networks from cambium xylem precursors phloem precursors. These may be controlled through accumulation distribution auxin. analysis suggests that vessel fiber development followed sequential pattern progressive transcriptional regulation. research gives new insights into identity occur throughout stems, which would help cellular dynamics during perennial trees.
Язык: Английский
Процитировано
30
Molecular Biomedicine, Год журнала: 2023, Номер 4(1)
Опубликована: Окт. 9, 2023
Abstract The proper functioning of diverse biological systems depends on the spatial organization their cells, a critical factor for processes like shaping intricate tissue functions and precisely determining cell fate. Nonetheless, conventional bulk or single-cell RNA sequencing methods were incapable simultaneously capturing both gene expression profiles locations cells. Hence, multitude spatially resolved technologies have emerged, offering novel dimension investigating regional expression, domains, interactions between Spatial transcriptomics (ST) is method that maps in while preserving information. It can reveal cellular heterogeneity, functional complex systems. ST also complement integrate with other omics to provide more comprehensive holistic view at multiple levels resolution. Since advent ST, new higher throughput resolution become available, holding significant potential expedite fresh insights into comprehending complexity. Consequently, rapid increase associated research has occurred, using these unravel complexity during developmental disease conditions. In this review, we summarize recent advancement historical, technical, application contexts. We compare different types based principles workflows, present bioinformatics tools analyzing integrating data modalities. highlight applications various domains biomedical research, especially development diseases. Finally, discuss current limitations challenges field, propose future directions ST.
Язык: Английский
Процитировано
27