Advances in the Application of Single-Cell Transcriptomics in Plant Systems and Synthetic Biology DOI Creative Commons
Md Torikul Islam, Yang Liu, Md Mahmudul Hassan

et al.

BioDesign Research, Journal Year: 2024, Volume and Issue: 6, P. 0029 - 0029

Published: Jan. 1, 2024

Plants are complex systems hierarchically organized and composed of various cell types. To understand the molecular underpinnings plant systems, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for revealing high resolution gene expression patterns at cellular level investigating cell-type heterogeneity. Furthermore, scRNA-seq analysis biosystems great potential generating new knowledge to inform design synthetic biology, which aims modify plants genetically/epigenetically through genome editing, engineering, or re-writing based on rational increasing crop yield quality, promoting bioeconomy enhancing environmental sustainability. In particular, data from studies can be utilized facilitate development high-precision Build-Design-Test-Learn capabilities maximizing targeted performance engineered while minimizing unintended side effects. date, been demonstrated in limited number species, including model (e.g., Arabidopsis thaliana), agricultural crops Oryza sativa), bioenergy Populus spp.). It is expected that future technical advancements will reduce cost consequently accelerate application this emerging technology plants. review, we summarize current scRNA-seq, sample preparation, sequencing, analysis, provide guidance how choose appropriate methods different types samples. We then highlight applications both biology research. Finally, discuss challenges opportunities

Language: Английский

Single-Cell Transcriptome Analysis in Plants: Advances and Challenges DOI Creative Commons
Rahul Shaw, Xin Tian, Jian Xu

et al.

Molecular Plant, Journal Year: 2020, Volume and Issue: 14(1), P. 115 - 126

Published: Nov. 2, 2020

Language: Английский

Citations

199
The single-cell stereo-seq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leaves DOI Creative Commons
Keke Xia, Hai‐Xi Sun, Jie Li

et al.

Developmental Cell, Journal Year: 2022, Volume and Issue: 57(10), P. 1299 - 1310.e4

Published: May 1, 2022

Understanding the complex functions of plant leaves requires a thorough characterization discrete cell features. Although single-cell gene expression profiling technologies have been developed, their application in characterizing subtypes has not achieved yet. Here, we present scStereo-seq (single-cell spatial enhanced resolution omics sequencing) that enabled us to show bona fide transcriptome profiles Arabidopsis leaves. Subtle but significant transcriptomic differences between upper and lower epidermal cells successfully distinguished. Furthermore, discovered cell-type-specific gradients from main vein leaf edge, which led finding distinct developmental trajectories vascular guard cells. Our study showcases importance physical locations individual for exerting biological plants demonstrates is powerful tool integrate location information biology study.

Language: Английский

Citations

164
Single-cell multi-omics in the medicinal plant Catharanthus roseus DOI Creative Commons
Chenxin Li, Joshua C. Wood, Hai Anh Vu

et al.

Nature Chemical Biology, Journal Year: 2023, Volume and Issue: 19(8), P. 1031 - 1041

Published: May 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.

Language: Английский

Citations

94
Single-cell technologies: From research to application DOI
Lu Wen, Guoqiang Li, Tao Huang

et al.

The Innovation, Journal Year: 2022, Volume and Issue: 3(6), P. 100342 - 100342

Published: Oct. 18, 2022

Language: Английский

Citations

84
Single‐cell RNA‐seq reveals fate determination control of an individual fibre cell initiation in cotton (Gossypium hirsutum) DOI
Yuan Qin, Mengling Sun, Weiwen Li

et al.

Plant Biotechnology Journal, Journal Year: 2022, Volume and Issue: 20(12), P. 2372 - 2388

Published: Aug. 29, 2022

Summary Cotton fibre is a unicellular seed trichome, and lint initials per as factor determines yield. However, the mechanisms controlling initiation from ovule epidermis are not understood well enough. Here, with single‐cell RNA sequencing (scRNA‐seq), total of 14 535 cells were identified cotton outer integument Xu142_LF line at four developmental stages (1.5, 1, 0.5 days before anthesis day anthesis). Three major cell types, fibre, non‐fibre pigment layer then verified by in situ hybridization. A comparative analysis on scRNA‐seq data between Xu142 its fibreless mutant fl further confirmed cluster definition. The trajectory was reconstructed, differentiated 1 anthesis. Gene regulatory networks revealed spatiotemporal pattern core transcription factors, MYB25‐like HOX3 demonstrated played key roles commanders differentiation tip‐biased diffuse growth respectively. model for early development single proposed here, which sheds light deciphering mechanism plant trichome improvement

Language: Английский

Citations

79
Single-cell profiling of Arabidopsis leaves to Pseudomonas syringae infection DOI Creative Commons
Jie Zhu, Signe Lolle,

Andrea Tang

et al.

Cell Reports, Journal Year: 2023, Volume and Issue: 42(7), P. 112676 - 112676

Published: June 20, 2023

Plant response to pathogen infection varies within a leaf, yet this heterogeneity is not well resolved. We expose Arabidopsis Pseudomonas syringae or mock treatment and profile >11,000 individual cells using single-cell RNA sequencing. Integrative analysis of cell populations from both treatments identifies distinct pathogen-responsive clusters exhibiting transcriptional responses ranging immunity susceptibility. Pseudotime analyses through reveals continuum disease progression an immune susceptible state. Confocal imaging promoter-reporter lines for transcripts enriched in shows expression surrounding substomatal cavities colonized close proximity bacterial colonies, suggesting that represent sites early invasion. Susceptibility exhibit more general localization are highly induced at later stages infection. Overall, our work cellular infected leaf provides insight into plant differential level.

Language: Английский

Citations

53
Single-cell transcriptomics unveils xylem cell development and evolution DOI Creative Commons
Chia-Chun Tung, Shang‐Che Kuo, Chia-Ling Yang

et al.

Genome biology, Journal Year: 2023, Volume and Issue: 24(1)

Published: Jan. 9, 2023

Abstract Background Xylem, the most abundant tissue on Earth, is responsible for lateral growth in plants. Typical xylem has a radial system composed of ray parenchyma cells and an axial fusiform cells. In angiosperms, comprise vessel elements water transportation libriform fibers mechanical support, while both functions are performed by tracheids other vascular plants such as gymnosperms. Little known about developmental programs evolutionary relationships these cell types. Results Through single-cell laser capture microdissection transcriptomic profiling, we determine lineages stem-differentiating across four divergent woody angiosperms. Based cross-species analyses clusters overlapping trajectories, reveal highly conserved ray, yet variable fusiform, Core eudicots Populus trichocarpa Eucalyptus grandis share nearly identical lineages, whereas more basal angiosperm Liriodendron chinense lineage distinct from that core eudicots. The eudicot Trochodendron aralioides , evolutionarily reversed trait, exhibit strong similarity to rather than fibers. Conclusions This evo-devo framework provides comprehensive understanding formation multiple plant species spanning over hundred million years history.

Language: Английский

Citations

51
Improving photosynthetic efficiency toward food security: Strategies, advances, and perspectives DOI Creative Commons
Edward Smith, Marvin van Aalst, Tiina Tosens

et al.

Molecular Plant, Journal Year: 2023, Volume and Issue: 16(10), P. 1547 - 1563

Published: Sept. 1, 2023

published or not.The documents may come from teaching and research institutions in France abroad, public private centers.L'archive ouverte pluridisciplinaire

Language: Английский

Citations

48
Asymmetric gene expression and cell-type-specific regulatory networks in the root of bread wheat revealed by single-cell multiomics analysis DOI Creative Commons
Lihua Zhang, Chao He, Yuting Lai

et al.

Genome biology, Journal Year: 2023, Volume and Issue: 24(1)

Published: April 4, 2023

Homoeologs are defined as homologous genes resulting from allopolyploidy. Bread wheat, Triticum aestivum, is an allohexaploid species with many homoeologs. Homoeolog expression bias, referring to the relative contribution of homoeologs transcriptome, critical for determining traits that influence wheat growth and development. Asymmetric transcription has been so far investigated in a tissue or organ-specific manner, which could be misleading due mixture cell types.

Language: Английский

Citations

45
Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of pigment glands in Gossypium bickii DOI Creative Commons
Yue Sun,

Yifei Han,

Kuang Sheng

et al.

Molecular Plant, Journal Year: 2023, Volume and Issue: 16(4), P. 694 - 708

Published: Feb. 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.

Language: Английский

Citations

43