Single-cell genomics in plants: current state, future directions, and hurdles to overcome

Cuperus, Josh T.

doi:10.1093/plphys/kiab478

Cited by 38 publications

(25 citation statements)

References 77 publications

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“…These advances have not only expanded our knowledge about plant cell compositions, but also laid the groundwork for PCA construction. One of the major challenges for PCA is to generate a reference cell map that includes all the cell types (or as much as possible) in various tissues (Cuperus, 2022). However, current plant cell atlases are constructed in specific tissues and we still lack of a reference cell map of the entire plant.…”

Section: Discussionmentioning

confidence: 99%

Comprehensive integration of single-cell transcriptomic data illuminates the regulatory network architecture of plant cell fate specification

Cao

Zhao

et al. 2022

Preprint

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Plant morphogenesis relies on precise gene expression programs at the proper time and position which is orchestrated by transcription factors (TFs) in intricate regulatory networks at a cell-type specific manner. Here we presented a reference single-cell transcriptomic atlas of Arabidopsis seedlings by integration of 40 published scRNA-seq datasets from representative tissues as well as the entire under- and above-ground parts. We identified 34 distinct cell types or states, largely expanding our current view of plant cell compositions. We then mapped the developmental trajectory of root-shoot lineage separation and identified differential gene expression programs that may regulate the cell fate determination of under- and above-ground organs. Lastly, we systematically constructed cell-type specific gene regulatory networks and uncovered key regulators that act in a coordination manner to control cell-type specific gene expression. Taken together, our study not only offers a valuable resource plant cell atlas exploration but also provides molecular insights into gene-regulatory programs that determines organ specify, particularly the differentiation between root and shoot.

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Section: Discussionmentioning

confidence: 99%

Comprehensive integration of single-cell transcriptomic data illuminates the regulatory network architecture of plant cell fate specification

Cao

Zhao

et al. 2022

Preprint

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“…The comparison of the transcriptomes of different genotypes from different tissues or cell types at different stages of development and under different environmental conditions allows for the discovery of the genes that control plant traits and has become a key approach in plant biology and the discovery of genes for selection in plant breeding. Single-cell transcriptomics has become a powerful tool for understanding gene expression at the cell and tissue level but has had limited application in plants [71], partly due to the difficulty in isolating specific plant cells without disrupting expression.…”

Section: Transcriptomesmentioning

confidence: 99%

Progress in Plant Genome Sequencing

Henry

2022

Applied Biosciences

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The genome sequence of any organism is key to understanding the biology and utility of that organism. Plants have diverse, complex and sometimes very large nuclear genomes, mitochondrial genomes and much smaller and more highly conserved chloroplast genomes. Plant genome sequences underpin our understanding of plant biology and serve as a key platform for the genetic selection and improvement of crop plants to achieve food security. The development of technology that can capture large volumes of sequence data at low costs and with high accuracy has driven the acceleration of plant genome sequencing advancements. More recently, the development of long read sequencing technology has been a key advance for supporting the accurate sequencing and assembly of chromosome-level plant genomes. This review explored the progress in the sequencing and assembly of plant genomes and the outcomes of plant genome sequencing to date. The outcomes support the conservation of biodiversity, adaptations to climate change and improvements in the sustainability of agriculture, which support food and nutritional security.

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“…The PCA's vision of developing a platform that brings together data at multiple scales, from molecular to cellular to organismal, comes with many challenges. While the vision of a PCA will require a large amount of high quality data from a variety of technologies, studies which generate this data are being performed with rapidly increasing frequency and with ever‐greater data output since the first plant single‐cell studies were published in 2018–2019 (Cole et al, 2021 ; Cuperus, 2021 ). As technology becomes increasingly accessible, we expect that the problem of the PCA will become less about data availability, and more about data analysis, integration, and interpretation.…”

Section: Data Analysis Tools and Annotation Standardsmentioning

confidence: 99%

First Plant Cell Atlas symposium report

et al. 2022

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The Plant Cell Atlas (PCA) community hosted a virtual symposium on December 9 and 10, 2021 on single cell and spatial omics technologies. The conference gathered almost 500 academic, industry, and government leaders to identify the needs and directions of the PCA community and to explore how establishing a data synthesis center would address these needs and accelerate progress. This report details the presentations and discussions focused on the possibility of a data synthesis center for a PCA and the expected impacts of such a center on advancing science and technology globally. Community discussions focused on topics such as data analysis tools and annotation standards; computational expertise and cyber‐infrastructure; modes of community organization and engagement; methods for ensuring a broad reach in the PCA community; recruitment, training, and nurturing of new talent; and the overall impact of the PCA initiative. These targeted discussions facilitated dialogue among the participants to gauge whether PCA might be a vehicle for formulating a data synthesis center. The conversations also explored how online tools can be leveraged to help broaden the reach of the PCA (i.e., online contests, virtual networking, and social media stakeholder engagement) and decrease costs of conducting research (e.g., virtual REU opportunities). Major recommendations for the future of the PCA included establishing standards, creating dashboards for easy and intuitive access to data, and engaging with a broad community of stakeholders. The discussions also identified the following as being essential to the PCA's success: identifying homologous cell‐type markers and their biocuration, publishing datasets and computational pipelines, utilizing online tools for communication (such as Slack), and user‐friendly data visualization and data sharing. In conclusion, the development of a data synthesis center will help the PCA community achieve these goals by providing a centralized repository for existing and new data, a platform for sharing tools, and new analytical approaches through collaborative, multidisciplinary efforts. A data synthesis center will help the PCA reach milestones, such as community‐supported data evaluation metrics, accelerating plant research necessary for human and environmental health.

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Single-cell genomics in plants: current state, future directions, and hurdles to overcome

Cited by 38 publications

References 77 publications

Comprehensive integration of single-cell transcriptomic data illuminates the regulatory network architecture of plant cell fate specification

Comprehensive integration of single-cell transcriptomic data illuminates the regulatory network architecture of plant cell fate specification

Progress in Plant Genome Sequencing

First Plant Cell Atlas symposium report

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