Orthologous marker groups reveal broad cell identity conservation across plant single-cell transcriptomes

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

---

Single-cell transcriptomics reveals heterogeneity in plant responses to the environment: a focus on biotic and abiotic interactions

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

---

Single-cell RNA sequencing facilitates the elucidation of the complete biosynthesis of the antidepressant hyperforin in St. John’s wort

Molecular Plant, Journal Year: 2024, Volume and Issue: 17(9), P. 1439 - 1457

Published: Aug. 12, 2024

Language: Английский

---

Single-cell technology for plant systems biology

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 133 - 156

Published: Jan. 1, 2025

Language: Английский

---

Single-cell technology for crop breeding

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 189 - 219

Published: Jan. 1, 2025

Language: Английский

---

A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators

Cell Reports, Journal Year: 2025, Volume and Issue: 44(2), P. 115240 - 115240

Published: Feb. 1, 2025

Despite the broad use of single-cell/nucleus RNA sequencing in plant research, accurate cluster annotation less-studied species remains a major challenge due to lack validated marker genes. Here, we generated single-cell atlas soil-grown wheat roots and annotated identities by transferring annotations from publicly available datasets wheat, rice, maize, Arabidopsis. The predictions our orthology-based approach were next using untargeted spatial transcriptomics. These results allowed us predict evolutionarily conserved tissue-specific markers generate cell type-specific gene regulatory networks for root tissues other used analysis. In summary, transcriptomics resource apical meristems, including numerous known uncharacterized genes developmental regulators. data analyses will facilitate future type non-model species.

Language: Английский

---

Deciphering seed development and germination in the single-cell era

Seed Science Research, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 10

Published: March 3, 2025

Abstract Seeds are complex structures that serve as dispersal units in angiosperms. consist of three specialized tissues with distinct roles and molecular compositions. Hence, the characterization genetic regulators act within individual seed tissues, how their activity changes during development germination, has been a primary focus research. However, our knowledge spatiotemporal modulation seeds, across different cell types, limited by resolution available techniques. In last few years, application single-cell technologies plants have enabled elucidation gene networks involved various developmental processes at cellular level. Some studies applied these to enabling further germination Here, we review current status seeds present workflow for conducting transcriptomics. Additionally, discuss integration multi-omics, aiming demonstrate potential enhancing comprehension regulations governing germination.

Language: Английский

---

Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll revealed by single‐cell transcriptomics

New Phytologist, Journal Year: 2025, Volume and Issue: unknown

Published: March 3, 2025

Summary Drought stress imposes severe challenges on agriculture by impacting crop performance. Understanding drought responses in plants at a cellular level is crucial first step toward engineering improved resilience. However, the molecular to are complex as they depend multiple factors, including severity of drought, profiled organ, its developmental stage or even cell types therein. Thus, deciphering transcriptional especially challenging. In this study, we investigated tissue‐specific mild (MD) young Arabidopsis thaliana (Arabidopsis) leaves using single‐cell RNA sequencing (scRNA‐seq). To preserve integrity during isolation, inhibited synthesis transcription inhibitor actinomycin D, and demonstrated benefits transcriptome fixation for studying level. We present curated validated atlas, comprising 50 797 high‐quality cells from almost all known leaf. All type annotations were with new library reporter lines. The data available broad community an intuitive tool browsable atlas ( http://www.single‐cell.be/plant/leaf‐drought ). show that mesophyll contains two spatially separated populations distinct drought: one enriched canonical abscisic acid‐related drought‐responsive genes, another genes involved iron starvation responses. Our study thus reveals dual adaptive mechanism leaf response MD provides valuable resource future research

Language: Английский

---

The dynamic and diverse nature of parenchyma cells in the Arabidopsis root during secondary growth

Nature Plants, Journal Year: 2025, Volume and Issue: unknown

Published: March 26, 2025

Abstract During secondary growth, the vascular cambium produces conductive xylem and phloem cells, while phellogen (cork cambium) deposits phellem (cork) as outermost protective barrier. Although most of tissues are made up parenchyma which also produced by both cambia, their diversity function poorly understood. Here we combined single-cell RNA sequencing analysis with lineage tracing to recreate developmental trajectories cell types in Arabidopsis root undergoing growth. By analysing 93 reporter lines, were able identify 20 different or states, many have not been described before. We additionally observed distinct transcriptome signatures cells depending on maturation state proximity types. Our data show that required for normal formation tissue Furthermore, mature gradually obtains periderm identity, this transformation can be accelerated jasmonate treatment wounding. study thus reveals capacity undergo considerable identity changes during

Language: Английский

---

Recent progress in single-cell transcriptomic studies in plants

Plant Biotechnology Reports, Journal Year: 2025, Volume and Issue: unknown

Published: April 3, 2025

Language: Английский

---