Single-cell transcriptome atlas of the leaf and root of rice seedlings

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2021, Volume and Issue: 48(10), P. 881 - 898

Published: June 18, 2021

As a multicellular organism, rice flourishes relying on gene expression diversity among cells of various functions. However, cellular-resolution transcriptome features are yet to be fully recognized, let alone cell-specific transcriptional responses environmental stimuli. In this study, we apply single-cell RNA sequencing both shoot and root seedlings growing in Kimura B nutrient solution or exposed abiotic stresses characterize transcriptomes for total 237,431 individual cells. We identify 15 9 cell types the leaf root, respectively, observe that common often shared between leaves roots same tissue layer, except endodermis epidermis. Abiotic stress stimuli alter largely type-specific manner, but given type, different trigger regulation roughly set genes. Besides, detect proportional changes populations response investigate underlying molecular mechanisms through reconstruction developmental trajectory. Collectively, our study represents benchmark-setting data resource atlas an illustration exploiting such resources drive discoveries plant biology.

Language: Английский

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Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters

Nature Plants, Journal Year: 2021, Volume and Issue: 7(6), P. 842 - 855

Published: June 3, 2021

Language: Английский

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The regulatory landscape of Arabidopsis thaliana roots at single-cell resolution

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: June 7, 2021

Abstract The scarcity of accessible sites that are dynamic or cell type-specific in plants may be due part to tissue heterogeneity bulk studies. To assess the effects heterogeneity, we apply single-cell ATAC-seq Arabidopsis thaliana roots and identify thousands differentially sites, sufficient resolve all major types root. We find entirety a cell’s regulatory landscape its transcriptome independently capture type identity. leverage this shared information on identity integrate accessibility data characterize developmental progression, endoreduplication division. further use combined motif enrichments transcription factor families link expression family members changing at specific loci, resolving direct indirect shape expression. Our approach provides an analytical framework infer gene networks execute plant development.

Language: Английский

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Single-cell technologies: From research to application

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

Published: Oct. 18, 2022

Language: Английский

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Single‐cell RNA‐seq reveals fate determination control of an individual fibre cell initiation in cotton (Gossypium hirsutum)

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

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A rice single cell transcriptomic atlas defines the developmental trajectories of rice floret and inflorescence meristems

New Phytologist, Journal Year: 2022, Volume and Issue: 234(2), P. 494 - 512

Published: Feb. 4, 2022

Summary Rice inflorescence development determines yield and relies on the activity of axillary meristems (AMs); however, high‐resolution analysis its early is lacking. Here, we have used high‐throughput single‐cell RNA sequencing to profile 37 571 rice cells constructed a genome‐scale gene expression resource covering inflorescence‐to‐floret transition during reproductive development. The differentiation trajectories florets AMs were reconstructed, discrete cell types groups regulators in highly heterogeneous young identified then validated by situ hybridization with fluorescent marker lines. Our data demonstrate that WOX transcription factor, DWARF TILLER1, regulates flower meristem activity, provide evidence for role auxin branching exploring biological importer OsAUX1. comprehensive transcriptomic atlas development, supported genetic evidence, provides single‐cell‐level insights into AM floret

Language: Английский

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Upcoming progress of transcriptomics studies on plants: An overview

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: Dec. 15, 2022

Transcriptome sequencing or RNA-Sequencing is a high-resolution, sensitive and high-throughput next-generation (NGS) approach used to study non-model plants other organisms. In words, it an assembly of RNA transcripts from individual whole samples functional developmental stages. RNA- Seq significant technique for identifying gene predictions mining analysis that improves ontology understanding mechanisms biological processes, molecular functions, cellular components, but there limited information available on this topic. Transcriptomics research different types can assist researchers understand genes in better ways regulatory processes improve breeding selection cultivation practices. recent years, several advancements technology have been made the characterization transcriptomes distinct cell tissues efficient manner. RNA-Seq technologies are briefly introduced examined terms their scientific applications. nutshell, introduces all transcriptome techniques, as well applications plant biology research. This review will focus numerous existing forthcoming strategies improving various using technology, based principles, development,

Language: Английский

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Single-cell transcriptomics unveils xylem cell development and evolution

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

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Asymmetric gene expression and cell-type-specific regulatory networks in the root of bread wheat revealed by single-cell multiomics analysis

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

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

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

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