Plant Reproduction, Journal Year: 2024, Volume and Issue: 38(1)
Published: Nov. 29, 2024
Language: Английский
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
Citations
2
Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 52(D1), P. D1629 - D1638
Published: Aug. 28, 2023
Abstract Recent advancements in single-cell RNA sequencing (scRNA-seq) technology have enabled the comprehensive profiling of gene expression patterns at level, offering unprecedented insights into cellular diversity and heterogeneity within plant tissues. In this study, we present a systematic approach to construct database, scPlantDB, which is publicly available https://biobigdata.nju.edu.cn/scplantdb. We integrated transcriptomic profiles from 67 high-quality datasets across 17 species, comprising approximately 2.5 million cells. The data underwent rigorous collection, manual curation, strict quality control standardized processing public databases. scPlantDB offers interactive visualization facilitating exploration both single-dataset multiple-dataset analyses. It enables comparison functional annotation markers diverse cell types species while providing tools identify compare based on these markers. summary, serves as database for investigating atlases. valuable resource research community.
Language: Английский
Citations
29
Plant Communications, Journal Year: 2024, Volume and Issue: 5(8), P. 100941 - 100941
Published: May 7, 2024
Language: Английский
Citations
12
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
Citations
11
Crop Design, Journal Year: 2023, Volume and Issue: 2(2), P. 100041 - 100041
Published: Aug. 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
Language: Английский
Citations
22
Advanced Science, Journal Year: 2024, Volume and Issue: 11(24)
Published: April 18, 2024
Abstract Cell‐specific transcriptional regulatory networks (TRNs) play vital roles in plant development and response to environmental stresses. However, traditional single‐cell mono‐omics techniques are unable directly capture the relationships dynamics between different layers of molecular information within same cells. While advanced algorithm facilitates merging scRNA‐seq scATAC‐seq datasets, accurate data integration remains a challenge, particularly when investigating cell‐type‐specific TRNs. By examining gene expression chromatin accessibility simultaneously 16,670 Arabidopsis root tip nuclei, TRNs reconstructed that govern under osmotic stress. In contrast commonly used computational at cell‐type level, 12,968 peak‐to‐gene linkage is captured bona fide level construct an unprecedented resolution. Furthermore, datasets allow more accurately reconstruct coordinated changes states during cellular state transition. During development, initial cells precedes expression, suggesting may prime for subsequent differentiation steps. Pseudo‐time trajectory analysis reveal stress can shift functional trichoblast. Candidate stress‐related gene‐linked cis‐regulatory elements (gl‐cCREs) as well potential target genes also identified, uncovered large heterogeneity
Language: Английский
Citations
7
Plant Communications, Journal Year: 2023, Volume and Issue: 5(2), P. 100717 - 100717
Published: Sept. 15, 2023
The plant genome produces an extremely large collection of long noncoding RNAs (lncRNAs) that are generally expressed in a context-specific manner and have pivotal roles regulation diverse biological processes. Here, we mapped the transcriptional heterogeneity lncRNAs their associated gene regulatory networks at single-cell resolution. We generated comprehensive cell atlas whole-organism level by integrative analysis 28 published RNA sequencing (scRNA-seq) datasets from juvenile Arabidopsis seedlings. then provided in-depth cell-type-related lncRNA signatures show expression patterns consistent with canonical protein-coding markers. further demonstrated cell-type-specific largely explains tissue specificity. In addition, predicted on basis motif enrichment co-expression mRNAs, identified putative transcription factors orchestrating lncRNAs. results available single-cell-based database (scPLAD; https://biobigdata.nju.edu.cn/scPLAD/). Overall, this work demonstrates power data applied to biology provides fundamental insights into specificity regulation.
Language: Английский
Citations
13
Advanced Science, Journal Year: 2025, Volume and Issue: unknown
Published: March 16, 2025
Abstract Drought is a critical environmental challenge affecting plant growth and productivity. Understanding the regulatory networks governing drought response at cellular level remains an open question. Here, comprehensive multi‐omics integration framework that combines transcriptomic, proteomic, epigenetic, network‐based analyses to delineate cell‐type‐specific involved in presented. By analyzing nearly 30 000 data samples across species, unique insights are revealed into conserved responses dynamics, leveraging novel integrative analytical workflows. Notably, CIPK23 emerges as protein kinase mediating tolerance through interactions with CBL4 , validated by yeast two‐hybrid BiFC assays. Experimental validation Arabidopsis thaliana Vitis vinifera confirms functional conservation of which enhances resistance overexpression lines. In addition, authors’ causal network analysis pinpoints drivers such NLP7 providing molecular mechanisms adaptation. These findings advance understanding offer potential targets for improving crop resilience diverse species.
Language: Английский
Citations
0
Journal of Sustainable Agriculture and Environment, Journal Year: 2025, Volume and Issue: 4(2)
Published: March 31, 2025
ABSTRACT To fulfil food and nutritional demand for nine billion people by the mid‐21st century, global production must increase 60% regardless of challenges such as environmental pollution, water scarcity land degradation. Climate change exacerbates frequency intensity biotic abiotic stresses, which, in turn, severely compromise crop yields, jeopardize supply, deteriorate sustainable development goals achieving safety, limit climate‐smart production. Current consumption practices negatively influence environment, posing a major threat to ecosystem human health. Addressing these critical issues achieve agriculture necessitates designing future crops employing cutting‐edge breeding strategies enhanced productivity with minimal footprints. This endeavour requires comprehensive understanding plant stress adaptation, signalling pathways mitigation mechanisms. In this review, we first explain diverse impacts ongoing climate events on Subsequently, outline various tackle change, including agronomic practices, advanced technologies physiological molecular mechanisms tolerance. We also discuss engineering superior tolerance disease resistance nurturing healthy microbial partnerships between plants soil ensure nutrition security current populations amidst mounting challenges.
Language: Английский
Citations
0
Plant Biotechnology Reports, Journal Year: 2025, Volume and Issue: unknown
Published: April 3, 2025
Language: Английский
Citations
0