Enhancing Our Understanding of Plant Cell-to-Cell Interactions Using Single-Cell Omics

Thibivilliers, Sandra; Libault, Marc

doi:10.3389/fpls.2021.696811

Cited by 9 publications

(9 citation statements)

References 66 publications

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“…Intercellular interaction in multicellular organisms regulates their activities and guarantees their ordered and efficient operation. One type of cell‐to‐cell interaction relies on direct contact between neighboring cells; another requires signaling molecules such as receptor‐ligands (Armingol et al., 2021; Thibivilliers & Libault, 2021). ST technology has evolved into an effective approach to capture the complete morphology of individual cells, examine the cellular microenvironment, and understand the interactions between individual cells (Rao et al., 2021; Tian et al., 2022; Walker et al., 2022).…”

Section: Understanding Plant Biology Using Stmentioning

confidence: 99%

Spatial transcriptomics drives a new era in plant research

Yin,

Xia,

2023

The Plant Journal

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SUMMARYThe plant community lags far behind the animal and human fields concerning the application of single‐cell methodologies. This is primarily due to the challenges associated with plant tissue dissection and the limitations of the available technologies. However, recent advances in spatial transcriptomics enable the study of single‐cells derived from plant tissues from a spatial perspective. This technology is already successfully used to identify cell types, reconstruct cell‐fate lineages, and reveal cell‐to‐cell interactions. Future technological advancements will overcome the challenges in sample processing, data analysis, and the integration of multiple‐omics technologies. Thanks to spatial transcriptomics, we anticipate several plant research projects to significantly advance our understanding of critical aspects of plant biology.

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Section: Understanding Plant Biology Using Stmentioning

confidence: 99%

Spatial transcriptomics drives a new era in plant research

Yin,

Xia,

2023

The Plant Journal

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“…The molecular dynamics of plant cells with different layers of information exhibit diversity in the regulatory mechanisms [224,225]. Despite our knowledge of apoplast involvement in cell growth and stress responses, its dynamics are still poorly known.…”

Section: Single-cell and Spatial Metabolomicsmentioning

confidence: 99%

Advances in Plant Metabolomics and Its Applications in Stress and Single-Cell Biology

Katam

Lin

Grant

et al. 2022

IJMS

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In the past two decades, the post-genomic era envisaged high-throughput technologies, resulting in more species with available genome sequences. In-depth multi-omics approaches have evolved to integrate cellular processes at various levels into a systems biology knowledge base. Metabolomics plays a crucial role in molecular networking to bridge the gaps between genotypes and phenotypes. However, the greater complexity of metabolites with diverse chemical and physical properties has limited the advances in plant metabolomics. For several years, applications of liquid/gas chromatography (LC/GC)-mass spectrometry (MS) and nuclear magnetic resonance (NMR) have been constantly developed. Recently, ion mobility spectrometry (IMS)-MS has shown utility in resolving isomeric and isobaric metabolites. Both MS and NMR combined metabolomics significantly increased the identification and quantification of metabolites in an untargeted and targeted manner. Thus, hyphenated metabolomics tools will narrow the gap between the number of metabolite features and the identified metabolites. Metabolites change in response to environmental conditions, including biotic and abiotic stress factors. The spatial distribution of metabolites across different organs, tissues, cells and cellular compartments is a trending research area in metabolomics. Herein, we review recent technological advancements in metabolomics and their applications in understanding plant stress biology and different levels of spatial organization. In addition, we discuss the opportunities and challenges in multiple stress interactions, multi-omics, and single-cell metabolomics.

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“…Although the greatest technical hurdles to adopting single-cell protocols to plants are related to dissociating cells from the appropriate tissues, obtaining sufficiently high numbers of cells for high-throughput analysis, the technical noise associated with single-cell assays, and the lack of true biological replicates ( Efroni and Birnbaum, 2016 ), matching SCT analysis tools and algorithms are being developed to facilitate the use of SCT approach in molecular biology research ( Gogolev et al, 2021 ). Recently, some researchers have used isolated protoplast or nuclei to successfully establish Arabidopsis roots and stomatal cells ( Jean-Baptiste et al, 2019 ; Liu Z. et al, 2020 ), as well as maize anther cell transcriptomes ( Nelms and Walbot, 2019 ; Xu et al, 2021 ) at the single-cell level ( Thibivilliers and Libault, 2021 ). Further, single-cell ATAC-seq (Assay for Transposase Accessible Chromatin-sequencing) has been applied on nuclei isolated from Arabidopsis roots and different maize organs to divulge the differential chromatin accessibility between plant cell types ( Thibivilliers and Libault, 2021 ).…”

Section: Omics Facilitated Crop Improvement For Abiotic and Biotic Stress Resistancesmentioning

confidence: 99%

“…Recently, some researchers have used isolated protoplast or nuclei to successfully establish Arabidopsis roots and stomatal cells ( Jean-Baptiste et al, 2019 ; Liu Z. et al, 2020 ), as well as maize anther cell transcriptomes ( Nelms and Walbot, 2019 ; Xu et al, 2021 ) at the single-cell level ( Thibivilliers and Libault, 2021 ). Further, single-cell ATAC-seq (Assay for Transposase Accessible Chromatin-sequencing) has been applied on nuclei isolated from Arabidopsis roots and different maize organs to divulge the differential chromatin accessibility between plant cell types ( Thibivilliers and Libault, 2021 ). For instance, single cell RNA-seq has been applied to Arabidopsis root cells to capture gene expressions in 3121 root cells and hundreds of genes with cell-type–specific expressions were identified, revealing both known and novel genes that are expressed along the developmental trajectories of cell lineages ( Jean-Baptiste et al, 2019 ).…”

Section: Omics Facilitated Crop Improvement For Abiotic and Biotic Stress Resistancesmentioning

confidence: 99%

Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value

et al. 2021

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Novel crop improvement approaches, including those that facilitate for the exploitation of crop wild relatives and underutilized species harboring the much-needed natural allelic variation are indispensable if we are to develop climate-smart crops with enhanced abiotic and biotic stress tolerance, higher nutritive value, and superior traits of agronomic importance. Top among these approaches are the “omics” technologies, including genomics, transcriptomics, proteomics, metabolomics, phenomics, and their integration, whose deployment has been vital in revealing several key genes, proteins and metabolic pathways underlying numerous traits of agronomic importance, and aiding marker-assisted breeding in major crop species. Here, citing several relevant examples, we appraise our understanding on the recent developments in omics technologies and how they are driving our quest to breed climate resilient crops. Large-scale genome resequencing, pan-genomes and genome-wide association studies are aiding the identification and analysis of species-level genome variations, whilst RNA-sequencing driven transcriptomics has provided unprecedented opportunities for conducting crop abiotic and biotic stress response studies. Meanwhile, single cell transcriptomics is slowly becoming an indispensable tool for decoding cell-specific stress responses, although several technical and experimental design challenges still need to be resolved. Additionally, the refinement of the conventional techniques and advent of modern, high-resolution proteomics technologies necessitated a gradual shift from the general descriptive studies of plant protein abundances to large scale analysis of protein-metabolite interactions. Especially, metabolomics is currently receiving special attention, owing to the role metabolites play as metabolic intermediates and close links to the phenotypic expression. Further, high throughput phenomics applications are driving the targeting of new research domains such as root system architecture analysis, and exploration of plant root-associated microbes for improved crop health and climate resilience. Overall, coupling these multi-omics technologies to modern plant breeding and genetic engineering methods ensures an all-encompassing approach to developing nutritionally-rich and climate-smart crops whose productivity can sustainably and sufficiently meet the current and future food, nutrition and energy demands.

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Enhancing Our Understanding of Plant Cell-to-Cell Interactions Using Single-Cell Omics

Cited by 9 publications

References 66 publications

Spatial transcriptomics drives a new era in plant research

Spatial transcriptomics drives a new era in plant research

Advances in Plant Metabolomics and Its Applications in Stress and Single-Cell Biology

Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value

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