Recent progresses in plant single-cell transcriptomics

Zheng, Dihuai; Xu, Jiwei; Lu, Yaqian; Chen, Hongyu; Chu, Qinjie; Fan, Longjiang

doi:10.1016/j.cropd.2023.100041

Cited by 9 publications

(2 citation statements)

References 92 publications

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“…Another initiative is the JGI Plant Gene Atlas, which contains almost 2100 RNA-Seq data sets collected from 18 plant species, with the aim to improve functional gene descriptions across the plant kingdom (Sreedasyam et al 2023 ). Recently, a great number of specialized single cell and single nuclei transcriptome data sets are emerging (reviewed in: Seyfferth et al 2021 ; Cervantes-Perez et al 2022 ; Denyer and Timmermans 2022 ; Nolan and Shahan 2023 ; Zheng et al 2023 ) and databases holding single cell transcriptome data (e.g., Ma et al 2020 ; Wendrich et al 2020 ; Chen et al 2021a ; He et al 2023 ).…”

Section: How Plant Genomes Facilitate Plant Functional Genomicsmentioning

confidence: 99%

Plant genome information facilitates plant functional genomics

Bernal-Gallardo,

de Folter

2024

Planta

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Main conclusion In this review, we give an overview of plant sequencing efforts and how this impacts plant functional genomics research. Abstract Plant genome sequence information greatly facilitates the studies of plant biology, functional genomics, evolution of genomes and genes, domestication processes, phylogenetic relationships, among many others. More than two decades of sequencing efforts have boosted the number of available sequenced plant genomes. The first plant genome, of Arabidopsis, was published in the year 2000 and currently, 4604 plant genomes from 1482 plant species have been published. Various large sequence initiatives are running, which are planning to produce tens of thousands of sequenced plant genomes in the near future. In this review, we give an overview on the status of sequenced plant genomes and on the use of genome information in different research areas.

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Section: How Plant Genomes Facilitate Plant Functional Genomicsmentioning

confidence: 99%

Plant genome information facilitates plant functional genomics

Bernal-Gallardo,

de Folter

2024

Planta

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“…Transkryptomika pojedynczych komórek dostarczyła również cennych informacji na temat szlaków biosyntezy metabolitów u roślin. Na przykład, scRNA-Seq umożliwiło powiązanie określonego typu komórek korony kwiatów dzikiego tytoniu z syntezą substancji zapachowej -benzylacetonu [42]. Dodatkowo, analiza koekspresji doprowadziła do wytypowania potencjalnych genów zaangażowanych w szlak biosyntezy tego związku.…”

Section: Biologia Roślinunclassified

Sekwencjonowanie transkryptomu pojedynczych komórek: droga do odkrywania bioróżnorodności komórkowej

Samelak-Czajka,

Marszałek-Zeńczak,

Jackowiak

2024

Postepy Biochem

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Single-cell transcriptomics (scRNA-Seq) is a breakthrough technology that has opened the way to characterizing gene expression with unprecedented resolution. It has enabled the discovery of the cellular diversity of organisms and tracing their developmental processes. A range of technological solutions have been developed to allow analysis of tens of thousands to even a million cells in a single experiment, as well as an extensive set of tools for bioinformatics analysis of the generated data. The wealth of information provided by scRNA-Seq and the possibility of using this method to study cells, organoids, tissues and even entire organisms determine its wide range of applications. In this paper, we present the experimental and computational parts of the scRNA-Seq procedure, as well as the most important applications of this technology in biomedicine, developmental biology and plant biology.

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