Plant Single Cell Transcriptome Hub (PsctH): an integrated online tool to explore the plant single‐cell transcriptome landscape

Xu, Zhongping; Wang, Qiongqiong; Zhu, Xiangqian; Wang, Guanying; Qin, Yuan; Ding, Fang; Tu, Lili; Daniell, Henry; Zhang, Xianlong; Jin, Shuangxia

doi:10.1111/pbi.13725

Cited by 32 publications

(23 citation statements)

References 11 publications

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“…Furthermore, of the 6,836 cells that passed quality control, a total of 5,930 nuclei of high con dence represented their corresponding cells in the gene expression matrix (Table S2 and Figure S3-4). The integration of snRNA-seq and snATAC-seq resulted in the construction of 17 cell clusters in a coembedded 5,930 cell distribution UMAP (Figure 1C) based on previously reported cell markers (Figure 1D) and cluster correlation detection (Liu et al, 2021;Chen et al, 2021;Kim et al, 2021;Xu et al, 2022). These 17 clusters were further classi ed into different cell types, with clusters 0, 1, 3, 8, 11, and 12 representing mesophyll cells; clusters 2, 7, 10, and 15 classi ed as epidermal cells; guard cells were distributed in cluster 14.…”

Section: Resultsmentioning

confidence: 92%

Simultaneous Analysis of Single-nucleus Transcriptome and Chromatin Accessibility Unveils the Mechanisms of Leaf Cell Development in Arachis hypogaea L.

Líu

Deng

et al. 2023

Preprint

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Plant cell development is an asynchronous process that is governed by multiple layers of gene regulation. However, the correlation between transcriptome and chromatin regulatory events in an allotetraploid species at the single-cell resolution has not been widely studied. Herein, we employed fluorescence-activated nuclei sorting to isolate single nuclei and simultaneously investigate the transcriptome (snRNA-seq) and chromatin accessibility (snATAC-seq) landscapes in the same leaf single-cell of Arachis hypogaea. A total of 5,930 cells with 10,793 expressed genes were classified into 17 cell-clusters and 5,315 chromatin fragments were enriched to target 26,083 genes in the snATAC-seq landscape. The developmental trajectory revealed a conserved ethylene-AP2 module in leaf cell differentiation and provided novel insight for mesophyll and vascular cell development. Additionally, dual-omics described the epidermal progenitor cell development trajectory, primordium and palisade cells were able to convert into spongy cells, and bundle sheath cells developed earlier than other vascular-cells. Further cell-cycle analysis demonstrated that cytokinin biosynthesis promotes mesophyll cell genome replication and lipid pathway participates in guard cell development. snRNA-seq identified that the AT-hook transcription factor AhAHL11promotes leaf area growth by modulating auxin content, but snATAC-seq identified AhBHLH143 displaying contrasting results by repressing leaf development via the jasmonic acid pathway in ectopically expressed Arabidopsis. Conclusively, our study demonstrates that snRNA-seq combined with snATAC-seq is an effective platform for exploring the association between chromatin regulatory events and transcriptional activity across diverse cell types in peanut leaves. The broad application of this approach will enable significant advances in the functional research of tissue growth and development in plant species. Plant cell development is an asynchronous process that is governed by multiple layers of gene regulation. However, the correlation between transcriptome and chromatin regulatory events in an allotetraploid species at the single-cell resolution has not been widely studied. Herein, we employed fluorescence-activated nuclei sorting to isolate single nuclei and simultaneously investigate the transcriptome (snRNA-seq) and chromatin accessibility (snATAC-seq) landscapes in the same leaf single-cell of peanut. Totally 5,930 cells with 10,793 expressed genes were classified into 17 cell-clusters and 5,315 chromatin fragments were enriched to target 26,083 genes in the snATAC-seq landscape. Developmental trajectory revealed a conserved ethylene-AP2 module in leaf cell differentiation and provided novel insights for mesophyll and vascular cells development. Further ell-cycle demonstrated that cytokinin promotes mesophyll-cell genome replication and lipid pathway participates in guard cell development. snRNA-seq identified AhAHL11 promotes leaf area growth by modulating auxin content, but snATAC-seq identified AhBHLH143 repressing leaf development via jasmonic acid pathway. Conclusively, snRNA-seq combined with snATAC-seq is an effective platform for exploring the association between chromatin regulatory events and transcriptional activity across diverse cell-types. The broad application of this approach will enable significant advances in the functional research of tissue growth and development in plant species.

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Section: Resultsmentioning

confidence: 92%

Simultaneous Analysis of Single-nucleus Transcriptome and Chromatin Accessibility Unveils the Mechanisms of Leaf Cell Development in Arachis hypogaea L.

Líu

Deng

et al. 2023

Preprint

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“…The UMAP dimensionality reduction of the relative expression of cell matrix constructed a two-dimensional representation group of cells, 5930 leaf cells were divided into sixteen and ve cell clusters by only using the snRNA-seq and snATAC-seq data, respectively (Figure 1C-F). Furthermore, integration of snRNA-seq and snATAC-seq resulted in construction of 17 cell clusters in co-embed cell distribution map based on previous reported cell marker and cluster correlation detection (Liu et al, 2021;Chen et al, 2021;Kim et al, 2021;Xu et al, 2022). Interestingly, the clusters 0, 1, 3, 8, 11, and 12 represented the mesophyll cells, divided by RBCS and CAB3, and YAB1 transcript abundance, marker for spongy cell was enriched in cluster 8.…”

Section: Resultsmentioning

confidence: 92%

Simultaneous Establishing Single-cell Transcriptome Atlas and Chromatin Accessibility Landscapes in Allotetraploid Leguminous Plant

Líu

Deng

et al. 2022

Preprint

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Plant cell proliferation associated with multiple layers of gene regulation, including modulation of transcriptome by changes in chromatin accessibility. However, cell proliferation is an asynchronous process precluding a temporal understanding of regulatory events leading to single-cell fate commitment. Here, a robust single nucleus RNA sequencing approach, where single nucleus employed for simultaneous investigation of transcriptome (snRNA-seq) and chromatin accessibility (snATAC-seq) landscapes in the same single-cell of Arachis hypogaea leaves. A total of 5,930 leaf cells with 10,793 expressed genes were used to construct development trajectory and characterized large-scale critical differentially expressed genes (DEGs). Additionally, uncovered extending insights of chromatin opening guided 5,315 DEGs expression involved biological pathway determines differentiation direction in distinct cell-types. But obtained members in each cell-clusters not exhibits obvious difference in distinct cell-cycling regulated genome duplication phases. Furthermore, snRNA-seq identified AT-hook transcription factor AhAHL11 promotes leaf area growth by modulating auxin content, but snATAC-seq identified AhBHLH143 displays contrasting results to repress the leaf development by jasmonic acid pathway in ectopically expressed Arabidopsis. We concluded that, snRNA-seq combined with snATAC-seq is an extensible platform to explore association between the chromatin regulatory events and gene expression across diversity cell-types in peanut leaf, broadly application of this approach will enable significant advances in the functional research of tissues ontology in plant species.

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“…Moreover, several databases have been developed to facilitate the use of sc in plant biology, including PlantscRNAdb (Chen et al, 2021a), Single-Cell Portal (Svensson et al, 2020), PsctH (Xu et al, 2022d), PCMDB (Jin et al, 2022), IonFlow (Iacovacci et al, 2021), scDEC (Liu et al, 2021b), RA3 (Chen et al, 2021b), epiAnno (Chen et al, 2022), and PlantCADB (Ke et al, 2022). When combined with computational biology, these databases have provided opportunities for sc-genome-wide approaches to assess different molecules, such as DNA, RNA, protein, and chromatin, with the highest resolution in many organisms, including plants (Libault et al, 2017;Hu et al, 2018;Argelaguet et al, 2021).…”

Section: Era Of Single-cell Omics-assisted Breeding For Crop Improvementmentioning

confidence: 99%

Temperature‐smart plants: A new horizon with omics‐driven plant breeding

Raza,

Bashir,

Khare

et al. 2024

Physiologia Plantarum

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The adverse effects of mounting environmental challenges, including extreme temperatures, threaten the global food supply due to their impact on plant growth and productivity. Temperature extremes disrupt plant genetics, leading to significant growth issues and eventually damaging phenotypes. Plants have developed complex signaling networks to respond and tolerate temperature stimuli, including genetic, physiological, biochemical, and molecular adaptations. In recent decades, omics tools and other molecular strategies have rapidly advanced, offering crucial insights and a wealth of information about how plants respond and adapt to stress. This review explores the potential of an integrated omics‐driven approach to understanding how plants adapt and tolerate extreme temperatures. By leveraging cutting‐edge omics methods, including genomics, transcriptomics, proteomics, metabolomics, miRNAomics, epigenomics, phenomics, and ionomics, alongside the power of machine learning and speed breeding data, we can revolutionize plant breeding practices. These advanced techniques offer a promising pathway to developing climate‐proof plant varieties that can withstand temperature fluctuations, addressing the increasing global demand for high‐quality food in the face of a changing climate.

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Plant Single Cell Transcriptome Hub (PsctH): an integrated online tool to explore the plant single‐cell transcriptome landscape

Cited by 32 publications

References 11 publications

Simultaneous Analysis of Single-nucleus Transcriptome and Chromatin Accessibility Unveils the Mechanisms of Leaf Cell Development in Arachis hypogaea L.

Simultaneous Analysis of Single-nucleus Transcriptome and Chromatin Accessibility Unveils the Mechanisms of Leaf Cell Development in Arachis hypogaea L.

Simultaneous Establishing Single-cell Transcriptome Atlas and Chromatin Accessibility Landscapes in Allotetraploid Leguminous Plant

Temperature‐smart plants: A new horizon with omics‐driven plant breeding

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