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

Bawa, George; Liu, Zhixin; Yu, Xiaole; Qin, Aizhi; Sun, Xuwu

doi:10.3390/ijms23094497

Cited by 27 publications

(20 citation statements)

References 89 publications

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“…The scRNA‐seq workflow includes dissociation of target cells from the tissue, cell isolation, RNA extraction, cDNA synthesis by reverse transcription, and single‐cell sequencing, followed by bioinformatics analyses, including expression matrix construction, cell type identification, and cell cluster annotation (Bawa et al., 2022). Early attempts to increase the spatiotemporal solution with techniques such as laser capture microdissection (LCM) (Asano et al., 2002; Cai & Lashbrook, 2006; Tomlins et al., 2007), capturing cells with fluorescence‐activated cell sorting (FACS) (Birnbaum et al., 2003; Brady et al., 2007), or isolation of nuclei tagged in individual cell types (INTACT) (Deal & Henikoff, 2011) could only analyze hundreds of cells at very high resolution.…”

Section: Single‐cell Transcriptomicsmentioning

confidence: 99%

Going broad and deep: sequencing‐driven insights into plant physiology, evolution, and crop domestication

et al. 2023

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SUMMARY Deep sequencing is a term that has become embedded in the plant genomic literature in recent years and with good reason. A torrent of (largely) high‐quality genomic and transcriptomic data has been collected and most of this has been publicly released. Indeed, almost 1000 plant genomes have been reported (http://www.plabipd.de) and the 2000 Plant Transcriptomes Project has long been completed. The EarthBioGenome project will dwarf even these milestones. That said, massive progress in understanding plant physiology, evolution, and crop domestication has been made by sequencing broadly (across a species) as well as deeply (within a single individual). We will outline the current state of the art in genome and transcriptome sequencing before we briefly review the most visible of these broad approaches, namely genome‐wide association and transcriptome‐wide association studies, as well as the compilation of pangenomes. This will include both (i) the most commonly used methods reliant on single nucleotide polymorphisms and short InDels and (ii) more recent examples which consider structural variants. We will subsequently present case studies exemplifying how their application has brought insight into either plant physiology or evolution and crop domestication. Finally, we will provide conclusions and an outlook as to the perspective for the extension of such approaches to different species, tissues, and biological processes.

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Section: Single‐cell Transcriptomicsmentioning

confidence: 99%

Going broad and deep: sequencing‐driven insights into plant physiology, evolution, and crop domestication

et al. 2023

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“…The first scRNA-seq atlas was accomplished in Arabidopsis roots, demonstrating the viability of this technology in plants ( Ryu et al., 2019 ). The single cell transcriptome technique can actually characterize common cell types and cell states, uncover rare cell types, and reveal, in particular, the relationship between cell differentiation and development among various cell types ( Bawa et al., 2022 ). Since its invention, the single cell suspension technique has been used to study the genetics of maize, the regulation of tomato root initiation, and the differentiation trajectory of peanut leaf ( Nelms and Walbot, 2019 ; Liu et al., 2021a ; Xu et al., 2021 ; Omary et al., 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Single-cell transcriptome sequencing atlas of cassava tuberous root

et al. 2023

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IntroductionSingle-cell transcriptome sequencing (ScRNA-seq) has emerged as an effective method for examining cell differentiation and development. In non-model plants, it hasn't been employed very much, especially in sink organs that are abundant in secondary metabolites.ResultsIn this study, we sequenced the single-cell transcriptomes at two developmental phases of cassava tuberous roots using the technology known as 10x Genomics (S1, S2). In total, 14,566 cells were grouped into 15 different cell types, primarily based on the marker genes of model plants known to exist. In the pseudotime study, the cell differentiation trajectory was defined, and the difference in gene expression between the two stages on the pseudotime axis was compared. The differentiation process of the vascular tissue and cerebral tissue was identified by the trajectory. We discovered the rare cell type known as the casparian strip via the use of up-regulated genes and pseudotime analysis, and we explained how it differentiates from endodermis. The successful creation of a protoplast isolation technique for organs rich in starch was also described in our study.DiscussionTogether, we created the first high-resolution single-cell transcriptome atlas of cassava tuberous roots, which made significant advancements in our understanding of how these roots differentiate and develop.

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“…Recent years have witnessed a major increase in the application of single‐cell RNA‐sequencing (scRNA‐seq) technology in plant research (Bawa et al., 2022; Giacomello, 2021; Luo et al., 2020; Mironova & Xu, 2019; Rich‐Griffin et al., 2020; Rodriguez‐Villalon & Brady, 2019; Ryu et al., 2021). However, the majority of current research has focused on plant roots (Graeff et al., 2021;Serrano‐Ron et al., 2021; Wendrich et al., 2020; Zhang, Xu, et al., 2019) as a result of the availability of improved root cell protoplast preparation protocols, a better understanding of root cell types, and the presence of representative marker genes (Serrano‐Ron et al., 2021; Wendrich et al., 2020; Zhang, Xu, et al., 2019).…”

Section: Introductionmentioning

confidence: 99%

Research strategies for single‐cell transcriptome analysis in plant leaves

Liu

Qin

et al. 2022

The Plant Journal

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The recent and continuous improvement in single-cell RNA sequencing (scRNA-seq) technology has led to its emergence as an efficient experimental approach in plant research. However, compared with single-cell research in animals and humans, the application of scRNA-seq in plant research is limited by several challenges, including cell separation, cell type annotation, cellular function analysis, and cell-cell communication networks. In addition, the unavailability of corresponding reliable and stable analysis methods and standards has resulted in the relative decentralization of plant single-cell research. Considering these shortcomings, this review summarizes the research progress in plant leaf using scRNA-seq. In addition, it describes the corresponding feasible analytical methods and associated difficulties and problems encountered in the current research. In the end, we provide a speculative overview of the development of plant single-cell transcriptome research in the future.

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

Cited by 27 publications

References 89 publications

Going broad and deep: sequencing‐driven insights into plant physiology, evolution, and crop domestication

Going broad and deep: sequencing‐driven insights into plant physiology, evolution, and crop domestication

Single-cell transcriptome sequencing atlas of cassava tuberous root

Research strategies for single‐cell transcriptome analysis in plant leaves

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