Single-cell multi-omics in the medicinal plant Catharanthus roseus

Nature Chemical Biology, Год журнала: 2023, Номер 19(8), С. 1031 - 1041

Опубликована: Май 15, 2023

Advances in omics technologies now permit the generation of highly contiguous genome assemblies, detection transcripts and metabolites at level single cells high-resolution determination gene regulatory features. Here, using a complementary, multi-omics approach, we interrogated monoterpene indole alkaloid (MIA) biosynthetic pathway Catharanthus roseus, source leading anticancer drugs. We identified clusters genes involved MIA biosynthesis on eight C. roseus chromosomes extensive duplication genes. Clustering was not limited to linear genome, through chromatin interaction data, were present within same topologically associated domain, permitting identification secologanin transporter. Single-cell RNA-sequencing revealed sequential cell-type-specific partitioning leaf that, when coupled with single-cell metabolomics permitted reductase that yields bis-indole anhydrovinblastine. also expression root pathway.

Язык: Английский

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Chemistry, biosynthesis and biology of floral volatiles: roles in pollination and other functions

Natural Product Reports, Год журнала: 2023, Номер 40(12), С. 1901 - 1937

Опубликована: Янв. 1, 2023

Major advances have recently been made in understanding the biosynthesis and emission of floral volatiles, how their is shaped by abiotic biotic factors, which volatiles are involved communicating with mutualists parasites.

Язык: Английский

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Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of pigment glands in Gossypium bickii

Molecular Plant, Год журнала: 2023, Номер 16(4), С. 694 - 708

Опубликована: Фев. 10, 2023

Comprehensive utilization of cottonseeds is limited by the presence pigment glands and its inclusion gossypol. The ideal cotton has glandless seeds but a glanded plant, trait found in only few Australian wild species, including Gossypium bickii. Introgression this into cultivated species proved to be difficult. Understanding biological processes toward gland morphogenesis associated underlying molecular mechanisms will facilitate breeding varieties with plant. In study, single-cell RNA sequencing (scRNA-seq) was performed on 12 222 protoplasts isolated from cotyledons germinating G. bickii 48 h after imbibition. Clustered 14 distinct clusters unsupervisedly, these cells could grouped eight cell populations assistance known marker genes. were well separated others parenchyma cells, secretory apoptotic cells. By integrating developmental trajectory, transcription factor regulatory networks, core functional validation, we established model for formation. model, light gibberellin verified promote formation glands. addition, three novel genes, GbiERF114 (ETHYLENE RESPONSE FACTOR 114), GbiZAT11 (ZINC FINGER OF ARABIDOPSIS THALIANA 11), GbiNTL9 (NAC TRANSCRIPTION FACTOR-LIKE 9), affect Collectively, findings provide new insights lay cornerstone future scRNA-seq investigations.

Язык: Английский

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

Nature Communications, Год журнала: 2025, Номер 16(1)

Опубликована: Янв. 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.

Язык: Английский

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Single-Cell RNA Sequencing for Plant Research: Insights and Possible Benefits

International Journal of Molecular Sciences, Год журнала: 2022, Номер 23(9), С. 4497 - 4497

Опубликована: Апрель 19, 2022

In recent years, advances in single-cell RNA sequencing (scRNA-seq) technologies have continued to change our views on biological systems by increasing the spatiotemporal resolution of analysis resolution. Application scRNA-seq plants enables comprehensive characterization both common and rare cell types states, uncovering new revealing how relate each other spatially developmentally. This review provides an overview methodologies, highlights application plant science, justifies why is a master player sequencing, explains role transcriptomics environmental stress adaptation, alongside challenges prospects transcriptomics. Collectively, we put forward central research.

Язык: Английский

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Mass spectrometry imaging and single-cell transcriptional profiling reveal the tissue-specific regulation of bioactive ingredient biosynthesis in Taxus leaves

Plant Communications, Год журнала: 2023, Номер 4(5), С. 100630 - 100630

Опубликована: Май 25, 2023

Taxus leaves provide the raw industrial materials for taxol, a natural antineoplastic drug widely used in treatment of various cancers. However, precise distribution, biosynthesis, and transcriptional regulation taxoids other active components remain unknown. Matrix-assisted laser desorption/ionization-mass spectrometry imaging analysis was to visualize secondary metabolites leaf sections mairei, confirming tissue-specific accumulation different metabolites. Single-cell sequencing produce expression profiles 8846 cells, with median 2352 genes per cell. Based on series cluster-specific markers, cells were grouped into 15 clusters, suggesting high degree cell heterogeneity T. mairei leaves. Our data create first metabolic single-cell atlas reveal spatial temporal patterns several pathways. According cell-type annotation, most taxol biosynthesis are expressed mainly mesophyll cells; phenolic acid flavonoid highly epidermal (including stomatal complex guard cells); terpenoid steroid specifically cells. A number novel cell-specific transcription factors involved metabolite identified, including MYB17, WRKY12, WRKY31, ERF13, GT_2, bHLH46. research establishes landscape major types at resolution provides valuable resources studying basic principles cell-type-specific metabolism.

Язык: Английский

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Single-cell RNA sequencing reveals a hierarchical transcriptional regulatory network of terpenoid biosynthesis in cotton secretory glandular cells

Molecular Plant, Год журнала: 2023, Номер 16(12), С. 1990 - 2003

Опубликована: Окт. 17, 2023

Plants can synthesize a wide range of terpenoids in response to various environmental cues. However, the specific regulatory mechanisms governing terpenoid biosynthesis at cellular level remain largely elusive. In this study, we employed single-cell RNA sequencing comprehensively characterize transcriptome profile cotton leaves and established hierarchical transcriptional network regulating cell-specific production. We observed substantial expression levels genes associated with both volatile terpenes (such as β-caryophyllene β-myrcene) non-volatile gossypol-type secretory glandular cells. Moreover, two novel transcription factors, namely GoHSFA4a GoNAC42, are identified function downstream Gossypium PIGMENT GLAND FORMATION genes. Both factors could directly regulate biosynthetic cells developmental stimuli. For convenient retrieval data generated developed user-friendly web server . Our findings not only offer valuable insights into precise regulation but also provide potential targets for breeding endeavors.

Язык: Английский

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

Molecular Plant, Год журнала: 2024, Номер 17(9), С. 1439 - 1457

Опубликована: Авг. 12, 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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Introducing single cell stereo-sequencing technology to transform the plant transcriptome landscape

Trends in Plant Science, Год журнала: 2023, Номер 29(2), С. 249 - 265

Опубликована: Окт. 31, 2023

Язык: Английский

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