Physiology and Molecular Biology of Plants, Journal Year: 2025, Volume and Issue: 31(2), P. 199 - 209
Published: Feb. 1, 2025
Language: Английский
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: Jan. 8, 2024
ABSTRACT Crassulacean acid metabolism (CAM) is an evolutionary modification of the C 3 photosynthetic carbon dioxide fixation pathway used by approximately 7% terrestrial plants to live in drought-prone environments. Facultative CAM species, such as Mesembryanthemum crystallinum (common ice plant), possess unique ability switch from photosynthesis response high-salinity and water-deficit stress. Here we characterized environmentally-triggered transition plant using single nucleus RNA sequencing (snRNA-seq) identify its putative regulators, supported a novel high-quality assembled annotated genome. Analysis snRNA-seq datasets leaves transitioning between collected at dawn dusk revealed substantial transcriptional changes mesophyll cells onset induction. Notably, our findings sub-cell types engaged either or dusk. Cell trajectory inference analysis reconstructed both 24-hour cycles, enabling direct comparison gene expression profiles these pathways. This comparative study uncovered divergent patterns key circadian clock genes cell trajectories, pointing connection regulation
Language: Английский
Citations
10
Nature Plants, Journal Year: 2025, Volume and Issue: unknown
Published: Feb. 24, 2025
Abstract Co-option of gene regulatory networks leads to the acquisition new cell types and tissues. Stomata, valves formed by guard cells (GCs), are present in most land plants regulate CO 2 exchange. The transcription factor (TF) FAMA globally regulates GC differentiation. In Brassicales, also promotes development idioblast myrosin (MCs), another type specialized along vasculature essential for Brassicales-specific chemical defences. Here we show that Arabidopsis thaliana , directly induces TF WASABI MAKER ( WSB ), which triggers MC STOMATAL CARPENTER 1 SCAP1 a stomatal lineage-specific direct target), synergistically promote wsb mutants lacked MCs scap1 double mutant normal GCs. Evolutionary analyses revealed is conserved across stomatous angiosperms. We propose reduced transcriptional FAMA– module was co-opted before evolving induce
Language: Английский
Citations
1
Development, Journal Year: 2022, Volume and Issue: 149(21)
Published: Sept. 30, 2022
ABSTRACT Differentiation of stem cells in the plant apex gives rise to aerial tissues and organs. Presently, we lack a lineage map shoot woody perennials – crucial gap considering their role determining primary secondary growth. Here, used single-nuclei RNA-sequencing determine cell type-specific transcriptomes Populus vegetative apex. We identified highly heterogeneous populations clustered into seven broad groups represented by 18 transcriptionally distinct clusters. Next, established developmental trajectories epidermis, leaf mesophyll vascular tissue. Motivated high similarities between Arabidopsis population apex, applied pipeline for interspecific single-cell gene expression data integration. contrasted phloem xylem formation both species, establishing first comparison development model annual herbaceous perennial species. Our results offer valuable resource investigating principles underlying division differentiation conserved species while also allowing us examine species-specific differences at resolution.
Language: Английский
Citations
35
Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14
Published: Aug. 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.
Language: Английский
Citations
22
Current Opinion in Plant Biology, Journal Year: 2023, Volume and Issue: 74, P. 102378 - 102378
Published: May 10, 2023
Rapid development of high-throughput single-cell RNA sequencing (scRNA-seq) technologies offers exciting opportunities to reveal new and rare cell types, previously hidden states, continuous developmental trajectories. In this review, we first illustrate the ways in which scRNA-seq enables researchers distinguish between distinct plant populations, delineate cycle continuums, infer differentiation trajectories diverse types shoots, roots, floral vascular meristems with unprecedented resolution. We then highlight emerging power dissect heterogeneity regenerating tissues uncover cellular basis reprogramming stem commitment during regeneration. conclude by discussing related outstanding questions field.
Language: Английский
Citations
21
PLANT PHYSIOLOGY, Journal Year: 2023, Volume and Issue: 194(1), P. 456 - 474
Published: Sept. 14, 2023
Abstract Cassava (Manihot esculenta Crantz) is an important crop with a high photosynthetic rate and yield. It classified as C3–C4 plant based on its structural characteristics. To investigate the characteristics of cassava leaves at cellular level, we created single-cell transcriptome atlas leaves. A total 11,177 high-quality leaf cells were divided into 15 cell clusters. Based marker genes, identified 3 major tissues leaves, which mesophyll, epidermis, vascular tissue, analyzed their distinctive properties metabolic activity. supplement genes for identifying types cells, screened 120 candidate genes. We constructed development trajectory map discovered 6 related to differentiation fate. The single level provide theoretical foundation further enhancing yield nutrition.
Language: Английский
Citations
19
Plant Communications, Journal Year: 2023, Volume and Issue: 4(5), P. 100676 - 100676
Published: Aug. 28, 2023
Plant defense responses involve several biological processes that allow plants to fight against pathogenic attacks. How these different are orchestrated within organs and depend on specific cell types is poorly known. Here, using single-cell RNA sequencing (scRNA-seq) technology three independent replicates, we identified populations representing the core transcriptional of wild-type Arabidopsis leaves inoculated with bacterial pathogen Pseudomonas syringae DC3000. Among populations, retrieved major (mesophyll, guard, epidermal, companion, vascular S cells) which could associate characteristic reprogramming regulators, thereby specifying cell-type pathogen. Further analyses dynamics, basis inference trajectories, indicated types, in addition their responses, can also share similar modules gene reprogramming, uncovering a ubiquitous antagonism between immune susceptible processes. Moreover, it appears cells, epidermal mesophyll cells evolve along two separate paths, one converging toward an identical fate, characterized mostly by lignification detoxification functions. As this divergence does not correspond differentiation speculate might reflect discrimination cell-autonomous non-cell-autonomous responses. Altogether our data provide upgraded framework describe, explore, explain specialization coordination plant upon challenge.
Language: Английский
Citations
15
Crop Design, Journal Year: 2024, Volume and Issue: 3(2), P. 100057 - 100057
Published: Feb. 24, 2024
Over the past decade, bulk RNA sequencing (RNA-seq) has become an indispensable tool in molecular biology, and have made novel development, with two innovative methodologies being developed, single-cell (scRNA-seq) technology spatial transcriptome (ST) technology. The scRNA-seq allows researchers to analyze gene expression individual cells, providing more detailed information relative technologies. Meanwhile, ST overcomes limitations of terms loss information, enabling scientists better understand distribution within tissues. These advancements transcriptomics technologies revolutionize field genomics been widely used disease diagnosis medicine. However, they are less utilized plant research. This review describes advantage three technologies, presents their applications sciences.
Language: Английский
Citations
6
Genome biology, Journal Year: 2024, Volume and Issue: 25(1)
Published: July 24, 2024
Abstract Background Plant meristems are structured organs consisting of distinct layers stem cells, which differentiate into new plant tissue. Mutations in meristematic can propagate large sectors the plant. However, characteristics mutations remain unclear, limiting our understanding genetic basis somaclonal phenotypic variation. Results Here, we analyse frequency and distribution somatic an apricot tree. We separately sequence epidermis (developing from meristem layer 1) flesh 2) several fruits sampled across entire find that most (> 90%) specific to individual layers. Interestingly, 1 shows a higher mutation load than 2, implying different mutational dynamics between The follows branching This suggests propagated developing branches through axillary meristems. In turn, this leads us unexpected observation genomes distant more similar each other 2 same branches. Finally, using single-cell RNA sequencing, demonstrate layer-specific were only transcribed cells respective form Conclusions with origin. Our observations on specificity outline how they distributed, propagate, impact clonally crops.
Language: Английский
Citations
6
PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 195(3), P. 1941 - 1953
Published: March 1, 2024
Abstract Mature plant leaves are a composite of distinct cell types, including epidermal, mesophyll, and vascular cells. Notably, the proportion these cells relative transcript concentrations within different types may change over time. While gene expression data at single-cell level can provide cell-type-specific values, it is often too expensive to obtain for high-resolution time series. Although bulk RNA-seq be performed in series, using whole measures average values across all each sample. In this study, we combined with time-series from assemble an atlas changes Arabidopsis (Arabidopsis thaliana). We inferred how vary diurnal developmental timescales. Importantly, analysis revealed 3 subgroups mesophyll temporal profiles expression. Finally, developed tissue-specific networks that form community resource: Leaf Time-dependent Atlas (AraLeTa). This allows users extract confirmed by transcription factor–binding specific certain times day stages. AraLeTa available https://regulatorynet.shinyapps.io/araleta/.
Language: Английский
Citations
5