Advances and Opportunities in Single-Cell Transcriptomics for Plant Research

Seyfferth, Carolin; Renema, Jim; Wendrich, Jos R.; Eekhout, Thomas; Seurinck, Ruth; Vandamme, Niels; Blob, Bernhard; Saeys, Yvan; Helariutta, Yrjö; Birnbaum, Kenneth D.; Rybel, Bert De

doi:10.1146/annurev-arplant-081720-010120

Cited by 126 publications

(94 citation statements)

References 103 publications

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“…The plates were incubated for 24h at 37°C. Antagonistic activity was estimated by identifying zones of inhibited growth ( Seyfferth et al, 2021 ).…”

Section: Methodsmentioning

confidence: 99%

Drought Stress Triggers Shifts in the Root Microbial Community and Alters Functional Categories in the Microbial Gene Pool

et al. 2021

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Drought is a major threat to crop productivity and causes decreased plant growth, poor yields, and crop failure. Nevertheless, the frequency of droughts is expected to increase in the coming decades. The microbial communities associated with crop plants can influence how plants respond to various stresses; hence, microbiome manipulation is fast becoming an effective strategy for improving the stress tolerance of plants. The effect of drought stress on the root microbiome of perennial woody plants is currently poorly understood. Using Populus trees as a model ecosystem, we found that the diversity of the root microbial community decreased during drought treatment and that compositional shifts in microbes during drought stress were driven by the relative abundances of a large number of dominant phyla, including Actinobacteria, Firmicutes, and Proteobacteria. A subset of microbes, including Streptomyces rochei, Bacillus arbutinivorans, B. endophyticus, B. megaterium, Aspergillus terreus, Penicillium raperi, Trichoderma ghanense, Gongronella butleri, and Rhizopus stolonifer, was isolated from the drought-treated poplar rhizosphere soils, which have potentially beneficial to plant fitness. Further controlled inoculation experiments showed that the isolated bacterial and fungal isolates positively impacted plant growth and drought tolerance. Collectively, our results demonstrate the impact of drought on root microbiome structure and provide a novel example of manipulating root microbiomes to improve plant tolerance.

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“…The plates were incubated for 24h at 37°C. Antagonistic activity was estimated by identifying zones of inhibited growth ( Seyfferth et al, 2021 ).…”

Section: Methodsmentioning

confidence: 99%

Drought Stress Triggers Shifts in the Root Microbial Community and Alters Functional Categories in the Microbial Gene Pool

et al. 2021

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“…This issue can otherwise be assessed with pipelines such as Doublet Finder and Scrublet [43,44] (Figure 2). While data quality control and analysis pipelines for plant scRNA-Seq studies are now being discussed (e.g., [29,30]), this requires further work and is complicated by the metazoan-tailored tools commonly used. For example, a better understanding of mRNA content across plant cells in a given tissue would mean that cell-calling thresholds based on UMIs can be positioned more accurately.…”

Section: Balancing Sequencing Reads Against Cell Numbersmentioning

confidence: 99%

“…Principal among these are guaranteeing a viable cell selection, dealing with noise resulting from cell-isolation procedures, accommodating biotic/abiotic stress responses in this context, and interpreting the 'cluster cloud' and the detailed information inherent, beyond just coarse identification of cell types. There are many fine reviews that detail the state-of-the-art technology and data analysis methods, for example, [25][26][27][28], and several that focus specifically on plant applications, for example, [29,30]. However, undertaking an experiment of this nature on a plant tissue requires navigating some novel practical issues.…”

mentioning

confidence: 99%

Crafting a blueprint for single-cell RNA sequencing

Denyer

Timmermans

2022

Trends in Plant Science

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Droplet-based single-cell RNA sequencing (scRNA-Seq) has moved rapidly from a technology with great potential to a method applied to ever-broader questions. The detailed information that scRNA-Seq offers has proven incredibly powerful in resolving cell responses to developmental and environmental cues. However, to maximize the potential of this technology, a panoply of upstream, practical points require consideration. Principal among these are the optimization of cell-isolation procedures, accommodating biotic/abiotic stress responses, and discerning the number of cells and sequencing reads needed. To complement excellent reviews outlining applications and data analysis tools for scRNA-Seq, we here discuss these considerations and provide practical tips to tailor experimental design and ensure the best possible outcome. HighlightsHigh-throughput single-cell RNA sequencing (scRNA-Seq) offers huge potential to plant research.Optimization of a cell-isolation procedure is critical.Cell numbers and sequencing depth per cell must be balanced to maximize results.Appreciating the broader dynamics of scRNA-Seq data can aid initial understanding.Here, we discuss practical approaches to make the most of scRNA-Seq.

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“…To overcome this resolution barrier, single-cell transcriptomics was developed. A glance at the papers about using the single-cell transcriptomics in plant science showed that it became very popular (see Table S1) and is widely discussed technology today [126,[188][189][190]. Several groups undertook the first attempts for single-cell transcriptome assessment in 2013 [191] and 2015-2016 [192,193].…”

Section: Single-cell Transcriptomicsmentioning

confidence: 99%

OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security

Gogolev

Ahmar

Akpınar³

et al. 2021

Plants

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The incredible success of crop breeding and agricultural innovation in the last century greatly contributed to the Green Revolution, which significantly increased yields and ensures food security, despite the population explosion. However, new challenges such as rapid climate change, deteriorating soil, and the accumulation of pollutants require much faster responses and more effective solutions that cannot be achieved through traditional breeding. Further prospects for increasing the efficiency of agriculture are undoubtedly associated with the inclusion in the breeding strategy of new knowledge obtained using high-throughput technologies and new tools in the future to ensure the design of new plant genomes and predict the desired phenotype. This article provides an overview of the current state of research in these areas, as well as the study of soil and plant microbiomes, and the prospective use of their potential in a new field of microbiome engineering. In terms of genomic and phenomic predictions, we also propose an integrated approach that combines high-density genotyping and high-throughput phenotyping techniques, which can improve the prediction accuracy of quantitative traits in crop species.

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Advances and Opportunities in Single-Cell Transcriptomics for Plant Research

Cited by 126 publications

References 103 publications

Drought Stress Triggers Shifts in the Root Microbial Community and Alters Functional Categories in the Microbial Gene Pool

Drought Stress Triggers Shifts in the Root Microbial Community and Alters Functional Categories in the Microbial Gene Pool

Crafting a blueprint for single-cell RNA sequencing

OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security

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