Single-cell and spatial multi-omics in the plant sciences: Technical advances, applications, and perspectives

Yu, Xiaole; Liu, Zhixin; Sun, Xuwu

doi:10.1016/j.xplc.2022.100508

Cited by 26 publications

(9 citation statements)

References 132 publications

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“…The field of single cell genomics will also expand and will also come with technical challenges such as capturing more cells, capturing low-abundance cells, cell-type annotation, new sequencing and analysis methods (Efroni and Birnbaum 2016 ; Conde and Kirst 2022 ; Cuperus 2022 ). Moreover, this will not only apply to transcriptomics, but in all omics fields we are going to see a rapid expansion, from single cell omics , single cell multi- omics , spatial genomics and other omics , new omics analysis methods, and to inference of gene regulatory networks using single cell omics data, among others (Thibivilliers and Libault 2021 ; Clark et al 2022 ; Yu et al 2023 ; Baysoy et al 2023 ).…”

Section: Conclusion and Perspectivementioning

confidence: 99%

Plant genome information facilitates plant functional genomics

Bernal-Gallardo,

de Folter

2024

Planta

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Main conclusion In this review, we give an overview of plant sequencing efforts and how this impacts plant functional genomics research. Abstract Plant genome sequence information greatly facilitates the studies of plant biology, functional genomics, evolution of genomes and genes, domestication processes, phylogenetic relationships, among many others. More than two decades of sequencing efforts have boosted the number of available sequenced plant genomes. The first plant genome, of Arabidopsis, was published in the year 2000 and currently, 4604 plant genomes from 1482 plant species have been published. Various large sequence initiatives are running, which are planning to produce tens of thousands of sequenced plant genomes in the near future. In this review, we give an overview on the status of sequenced plant genomes and on the use of genome information in different research areas.

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Section: Conclusion and Perspectivementioning

confidence: 99%

Plant genome information facilitates plant functional genomics

Bernal-Gallardo,

de Folter

2024

Planta

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“…The Cd-tolerant varieties upregulated genes related to oxidation–reduction, catabolism of aminoglycan, iron binding, and heme binding, and downregulated genes related to oxidoreductase activity, photosynthesis, and thylakoid. In contrast, Cd-sensitive varieties upregulated genes involved in heme binding, iron binding, oxidation–reduction, zinc ion transmembrane transport, and tetrapyrrole, and downregulated genes related to carbohydrate metabolism, hydrolyzing of O-glycosyl compounds, and apoplasts (Yu et al 2021 ).…”

Section: Advances In Three Major Omics Approaches For Enhancing Metal...mentioning

confidence: 99%

Transcriptomics, proteomics, and metabolomics interventions prompt crop improvement against metal(loid) toxicity

Raza,

Salehi,

Bashir

et al. 2024

Plant Cell Rep

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The escalating challenges posed by metal(loid) toxicity in agricultural ecosystems, exacerbated by rapid climate change and anthropogenic pressures, demand urgent attention. Soil contamination is a critical issue because it significantly impacts crop productivity. The widespread threat of metal(loid) toxicity can jeopardize global food security due to contaminated food supplies and pose environmental risks, contributing to soil and water pollution and thus impacting the whole ecosystem. In this context, plants have evolved complex mechanisms to combat metal(loid) stress. Amid the array of innovative approaches, omics, notably transcriptomics, proteomics, and metabolomics, have emerged as transformative tools, shedding light on the genes, proteins, and key metabolites involved in metal(loid) stress responses and tolerance mechanisms. These identified candidates hold promise for developing high-yielding crops with desirable agronomic traits. Computational biology tools like bioinformatics, biological databases, and analytical pipelines support these omics approaches by harnessing diverse information and facilitating the mapping of genotype-to-phenotype relationships under stress conditions. This review explores: (1) the multifaceted strategies that plants use to adapt to metal(loid) toxicity in their environment; (2) the latest findings in metal(loid)-mediated transcriptomics, proteomics, and metabolomics studies across various plant species; (3) the integration of omics data with artificial intelligence and high-throughput phenotyping; (4) the latest bioinformatics databases, tools and pipelines for single and/or multi-omics data integration; (5) the latest insights into stress adaptations and tolerance mechanisms for future outlooks; and (6) the capacity of omics advances for creating sustainable and resilient crop plants that can thrive in metal(loid)-contaminated environments.

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“…Additionally, spatially resolved multi-omics approaches beyond the transcriptome level are also currently being developed and adapted to achieve single-cell, or at least, near single-cell, resolution. These include spatially resolved epigenomics, proteomics, and metabolomics ( Yu et al., 2022 ; Yin et al., 2023 ) techniques. The ultimate aim is to establish and integrate multi-omics atlases and to recapitulate these cellular processes simultaneously in their native spatiotemporal context.…”

Section: Floral Meristem Development In 4d: Spatiotemporally Resolved...mentioning

confidence: 99%

Old school, new rules: floral meristem development revealed by 3D gene expression atlases and high-resolution transcription factor–chromatin dynamics

Pelayo,

Yamaguchi

2023

Front. Plant Sci.

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The intricate morphology of the flower is primarily established within floral meristems in which floral organs will be defined and from where the developing flower will emerge. Floral meristem development involves multiscale-level regulation, including lineage and positional mechanisms for establishing cell-type identity, and transcriptional regulation mediated by changes in the chromatin environment. However, many key aspects of floral meristem development remain to be determined, such as: 1) the exact role of cellular location in connecting transcriptional inputs to morphological outcomes, and 2) the precise interactions between transcription factors and chromatin regulators underlying the transcriptional networks that regulate the transition from cell proliferation to differentiation during floral meristem development. Here, we highlight recent studies addressing these points through newly developed spatial reconstruction techniques and high-resolution transcription factor–chromatin environment interactions in the model plant Arabidopsis thaliana. Specifically, we feature studies that reconstructed 3D gene expression atlases of the floral meristem. We also discuss how the precise timing of floral meristem specification, floral organ patterning, and floral meristem termination is determined through temporally defined epigenetic dynamics for fine-tuning of gene expression. These studies offer fresh insights into the well-established principles of floral meristem development and outline the potential for further advances in this field in an age of integrated, powerful, multiscale resolution approaches.

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Single-cell and spatial multi-omics in the plant sciences: Technical advances, applications, and perspectives

Cited by 26 publications

References 132 publications

Plant genome information facilitates plant functional genomics

Plant genome information facilitates plant functional genomics

Transcriptomics, proteomics, and metabolomics interventions prompt crop improvement against metal(loid) toxicity

Old school, new rules: floral meristem development revealed by 3D gene expression atlases and high-resolution transcription factor–chromatin dynamics

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