Advances and applications of single‐cell omics technologies in plant research

The Plant Journal, Journal Year: 2022, Volume and Issue: 110(6), P. 1551 - 1563

Published: April 15, 2022

SUMMARY Single‐cell sequencing approaches reveal the intracellular dynamics of individual cells and answer biological questions with high‐dimensional catalogs millions cells, including genomics, transcriptomics, chromatin accessibility, epigenomics, proteomics data across species. These emerging yet thriving technologies have been fully embraced by field plant biology, a constantly expanding portfolio applications. Here, we introduce current technical advances used for single‐cell omics, especially genome transcriptome sequencing. Firstly, overview methods protoplast nucleus isolation amplification. Subsequently, use well‐executed benchmarking studies to highlight made through application omics techniques. Looking forward, offer glimpse additional hurdles future opportunities that will broad adoption revolutionary perspectives in biology.

Language: Английский

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The maize single-nucleus transcriptome comprehensively describes signaling networks governing movement and development of grass stomata

The Plant Cell, Journal Year: 2022, Volume and Issue: unknown

Published: Feb. 9, 2022

The unique morphology of grass stomata enables rapid responses to environmental changes. Deciphering the basis for these is critical improving food security. We have developed a planta platform single-nucleus RNA-sequencing by combined fluorescence-activated nuclei flow sorting, and used it identify cell types in mature developing from 33,098 maize epidermis-enriched tissues. Guard cells (GCs) subsidiary (SCs) displayed differential expression genes, besides those encoding transporters, involved abscisic acid, CO2, Ca2+, starch metabolism, blue light signaling pathways, implicating coordinated signal integration speedy stomatal responses, genes affecting wall plasticity, implying more sophisticated relationship between GCs SCs development dumbbell-shaped guard formation. trajectory identified young tissues, comparison bulk RNA-seq data MUTE defective mutant development, confirmed known features, shed on key participants development. Our study provides valuable, comprehensive, fundamental foundation further insights into function.

Language: Английский

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Bibliometric review of ATAC-Seq and its application in gene expression

Briefings in Bioinformatics, Journal Year: 2022, Volume and Issue: 23(3)

Published: Feb. 9, 2022

Abstract With recent advances in high-throughput next-generation sequencing, it is possible to describe the regulation and expression of genes at multiple levels. An assay for transposase-accessible chromatin using sequencing (ATAC-seq), which uses Tn5 transposase sequence protein-free binding regions genome, can be combined with immunoprecipitation coupled deep (ChIP-seq) ribonucleic acid (RNA-seq) provide a detailed description gene expression. Here, we reviewed literature on ATAC-seq described characteristics publications. We then briefly introduced principles RNA-seq, ChIP-seq ATAC-seq, focusing main features techniques. built phylogenetic tree from species that had been previously studied by ATAC-seq. Studies Mus musculus Homo sapiens account approximately 90% total data, while other are still process accumulating data. summarized findings human diseases species, illustrating cutting-edge discoveries role multi-omics data analysis current research. Moreover, collected compared pipelines, allowed biological researchers who lack programming skills better analyze explore Through this review, clear single-cell technology will become mainstream approach future

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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Current status and trends in forest genomics

Forestry Research, Journal Year: 2022, Volume and Issue: 2(1), P. 0 - 0

Published: Jan. 1, 2022

Forests are not only the most predominant of Earth's terrestrial ecosystems, but also core supply for essential products human use. However, global climate change and ongoing population explosion severely threatens health forest ecosystem aggravtes deforestation degradation. Forest genomics has great potential increasing productivity adaptation to changing climate. In last two decades, field advanced quickly owing advent multiple high-throughput sequencing technologies, single cell RNA-seq, clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genome editing, spatial transcriptomes, as well bioinformatics analysis which have led generation multidimensional, multilayered, spatiotemporal gene expression data. These together with basic technologies routinely used in plant biotechnology, enable us tackle many important or unique issues biology, provide a panoramic view an integrative elucidation molecular regulatory mechanisms underlying phenotypic changes variations. this review, we recapitulated advancement current status 12 research branches genomics, then provided future directions focuses each area. Evidently, shift from simple biotechnology-based research, setup investigation interpretation development differentiation just begun emerge.

Language: Английский

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