PlantscRNAdb: A database for plant single-cell RNA analysis

Chen, Hongyu; Yin, Xinxin; Guo, Longbiao; Yao, Jie; Ding, Yiwen; Xu, Xiaoxu; Liu, Lu; Zhu, Qian; Chu, Qinjie; Fan, Longjiang

doi:10.1016/j.molp.2021.05.002

Cited by 54 publications

(43 citation statements)

References 15 publications

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“…Single-cell sequencing has ushered in a new era of biology where it is possible to characterize cell types and function with unprecedented detail. In plants, this has resulted in detailed single-cell RNA-seq and Assay for Transposase-Accessible Chromatin (scATAC-seq) datasets primarily on different organ types from well-studied model organisms ( Denyer et al, 2019 ; Ryu et al, 2019 ; Dorrity et al, 2021 ; Gujas et al, 2020 ; Marand et al, 2020 ; Song et al, 2020 ; Liu et al, 2020a , 2020b ; Chen et al, 2021 ; Lopez-Anido et al, 2021 ; Xu et al, 2021 ). Most plant studies to date start with protoplast isolation, which has the potential to miss some recalcitrant cell types and often require correction to control for transcriptional changes elicited by lengthy enzyme treatment and centrifugation steps ( Ryu et al, 2019 ; Cuperus, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

The genome and preliminary single-nuclei transcriptome ofLemna minutareveals mechanisms of invasiveness

et al. 2021

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The ability to trace every cell in some model organisms has led to the fundamental understanding of development and cellular function. However, in plants the complexity of cell number, organ size and developmental time makes this a challenge even in the diminutive model plant Arabidopsis (Arabidopsis thaliana). Duckweed, basal non-grass aquatic monocots, provide an opportunity to follow every cell of an entire plant due to their small size, reduced body plan, and fast clonal growth habit. Here we present a chromosome-resolved genome for the highly invasive Lesser Duckweed (Lemna minuta) and generate a preliminary cell atlas leveraging low cell coverage single-nuclei sequencing. We resolved the 360 megabase genome into 21 chromosomes, revealing a core non-redundant gene set with only the ancient tau whole genome duplication shared with all monocots, and paralog expansion as a result of tandem duplications related to phytoremediation. Leveraging SMARTseq2 single-nuclei sequencing, which provided higher gene coverage yet lower cell count, we profiled 269 nuclei covering 36.9% (8,457) of the L. minuta transcriptome. Since molecular validation was not possible in this non-model plant, we leveraged gene orthology with model organism single cell expression datasets, gene ontology, and cell trajectory analysis to define putative cell types. We found that the tissue that we computationally defined as mesophyll expressed high levels of elemental transport genes consistent with this tissue playing a role in L. minuta wastewater detoxification. The L. minuta genome and preliminary cell map provide a paradigm to decipher developmental genes and pathways for an entire plant.

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Section: Introductionmentioning

confidence: 99%

The genome and preliminary single-nuclei transcriptome ofLemna minutareveals mechanisms of invasiveness

et al. 2021

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“…First, we compared SIM0 scRNA-seq data with the previously reported scRNA-seq data obtained from root 38 and shoot apex 29 , respectively. We found that there were 2,623 and 2,632 genes up-regulated in callus compared with root and shoot apex, respectively.…”

Section: Resultsmentioning

confidence: 99%

“…The cell identity scores were calculated using Hypergeometric Distribution Enrichment Analysis (HDEA). Specifically, the root cell type-specific markers from the online database 38 and the leaf cell type-specific markers from Arabidopsis shoot apex 29 were used as reference (Supplementary Table 2). The cluster-specific markers were calculated using Seurat “FindAllMarkers” function log-fold change >= 0.25, present in >= 25% cells.…”

Section: Methodsmentioning

confidence: 99%

Single-cell transcriptome reveals the redifferentiation trajectories of the early stage of de novo shoot regeneration in Arabidopsis thaliana

Liu

et al. 2022

Preprint

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De novo shoot regeneration from a callus plays a crucial role in both plant biotechnology and the fundamental research of plant cell totipotency. Recent studies have revealed many regulatory factors involved in this developmental process. However. our knowledge of the cell heterogeneity and cell fate transition during de novo shoot regeneration is still limited. Here, we performed time-series single-cell transcriptome experiments to reveal the cell heterogeneity and redifferentiation trajectories during the early stage of de novo shoot regeneration. Based on the single-cell transcriptome data of 35,669 cells at five-time points, we successfully determined seven major cell populations in this developmental process and reconstructed the redifferentiation trajectories. We found that all cell populations resembled root identities and undergone gradual cell-fate transitions. In detail, the totipotent callus cells differentiated into pluripotent QC-like cells and then gradually developed into less differentiated cells that have multiple root-like cell identities, such as pericycle-like cells. According to the reconstructed redifferentiation trajectories, we discovered that the canonical regeneration-related genes were dynamically expressed at certain stages of the redifferentiation process. Moreover, we also explored potential transcription factors and regulatory networks that might be involved in this process. The transcription factors detected at the initial stage, QC-like cells, and the end stage provided a valuable resource for future functional verifications. Overall, this dataset offers a unique glimpse into the early stages of de novo shoot regeneration, providing a foundation for a comprehensive analysis of the mechanism of de novo shoot regeneration.

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“…scRNA-seq has been used by plant scientists since 2013 and related publications have dramatically increased recently due to the advent of droplet-based scRNA-seq technologies (Chen et al, 2021). While the increasing number of scRNA-seq studies has advanced our knowledge about plant cell heterogeneity, mining public data is challenging for researchers with limited computational expertise.…”

Section: Discussionmentioning

confidence: 99%

Single Cell App: An App for Single Cell RNA-sequencing Data Visualization, Comparison and Discovery

Lewsey

Berkowitz

et al. 2021

Preprint

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The Single Cell App is a cloud-based application that allows visualisation and comparison of scRNA-seq data and is scalable according to use. Users upload their own or publicly available scRNA-seq datasets after pre-processing to be visualised using a web browser. The data can be viewed in two colour modes, Cluster - representing cell identity, and Values - level of expression, and data queried using keyword or gene identification number(s). Using the app to compare four different studies we determined that some genes frequently used as cell-type markers are in fact study specific. Phosphate transporter and hormone response genes were exemplary investigated with the app. This showed that the apparent cell specific expression of PHO1;H3 differed between GFP-tagging and scRNA-seq studies. Some phosphate transporter genes were induced by protoplasting, they retained cell specificity, indicating that cell specific stress responses (i.e. protoplasting). Examination of the cell specificity of hormone response genes revealed that 132 hormone responsive genes display restricted expression and that the jasmonate response gene TIFY8 is expressed in endodermal cells which differs from previous reports. It also appears that JAZ repressors have cell-type specific functions. These differences, identified using the Single Cell App, highlight the need for resources to enable researchers to find common and different patterns of cell specific gene expression. Thus, the Single Cell App enables researchers to form new hypothesis, perform comparative studies, allows for easy re-use of data for this emerging technology to provide novel avenues to crop improvement.

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PlantscRNAdb: A database for plant single-cell RNA analysis

Cited by 54 publications

References 15 publications

The genome and preliminary single-nuclei transcriptome ofLemna minutareveals mechanisms of invasiveness

The genome and preliminary single-nuclei transcriptome ofLemna minutareveals mechanisms of invasiveness

Single-cell transcriptome reveals the redifferentiation trajectories of the early stage of de novo shoot regeneration in Arabidopsis thaliana

Single Cell App: An App for Single Cell RNA-sequencing Data Visualization, Comparison and Discovery

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