Author response: Accurate and versatile 3D segmentation of plant tissues at cellular resolution

Wolny, Adrian; Cerrone, Lorenzo; Vijayan, Athul; Tofanelli, Rachele; Barro, Amaya Vilches; Louveaux, Marion; Wenzl, Christian; Strauss, Soeren; Wilson-Sánchez, David; Lymbouridou, Rena; Steigleder, Susanne S; Pape, Constantin; Bailoni, Alberto; Duran-Nebreda, Salva; Bassel, George W.; Lohmann, Jan U.; Tsiantis, Miltos; Hamprecht, Fred A.; Schneitz, Kay; Maizel, Alexis; Kreshuk, Anna

doi:10.7554/elife.57613.sa2

Cited by 3 publications

(3 citation statements)

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“…In the past 20 years, plant science has been leading the emerging field of morphodynamics. Community efforts to capture growth and development in 4D have kept improving the capacity in data acquisition, processing, extraction and analysis (e.g., Barbier de Reuille et al, 2015;Wolny et al, 2020). Phenotypic platforms have been developed, driving innovative solutions to capture morphodynamics in situ, generating a wealth of quantitative data.…”

Section: Back To Society: Plants and Humansmentioning

confidence: 99%

What is quantitative plant biology?

et al. 2021

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Quantitative plant biology is an interdisciplinary field that builds on a long history of biomathematics and biophysics. Today, thanks to high spatiotemporal resolution tools and computational modelling, it sets a new standard in plant science. Acquired data, whether molecular, geometric or mechanical, are quantified, statistically assessed and integrated at multiple scales and across fields. They feed testable predictions that, in turn, guide further experimental tests. Quantitative features such as variability, noise, robustness, delays or feedback loops are included to account for the inner dynamics of plants and their interactions with the environment. Here, we present the main features of this ongoing revolution, through new questions around signalling networks, tissue topology, shape plasticity, biomechanics, bioenergetics, ecology and engineering. In the end, quantitative plant biology allows us to question and better understand our interactions with plants. In turn, this field opens the door to transdisciplinary projects with the society, notably through citizen science.

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Section: Back To Society: Plants and Humansmentioning

confidence: 99%

What is quantitative plant biology?

et al. 2021

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“…Over the past few years, the possibility to study many entire organs through complete reconstruction at the cellular level became a significant breakthrough (Wolny et al, 2020). The root tip of A. thaliana is the most abundant target for scRNAseq in plants.…”

Section: Modern Imaging Technologies For Obtaining Data On Plant Tissues With a Single-cell Resolutionmentioning

confidence: 99%

“…The dynamics of the development of A. thaliana lateral roots are also available for visualization at the cellular level from the earliest stages of their establishment (Goh, 2019). Using confocal and multiphoton microscopy approaches, apexes and leaf primordia can also be completely reconstructed (Kiss et al, 2017;Wolny et al, 2020), as well as adult leaves (Wuyts et al, 2010) and sepals (Tauriello et al, 2015).…”

Section: Modern Imaging Technologies For Obtaining Data On Plant Tissues With a Single-cell Resolutionmentioning

confidence: 99%

A Sight on Single-Cell Transcriptomics in Plants Through the Prism of Cell-Based Computational Modeling Approaches: Benefits and Challenges for Data Analysis

et al. 2021

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Single-cell technology is a relatively new and promising way to obtain high-resolution transcriptomic data mostly used for animals during the last decade. However, several scientific groups developed and applied the protocols for some plant tissues. Together with deeply-developed cell-resolution imaging techniques, this achievement opens up new horizons for studying the complex mechanisms of plant tissue architecture formation. While the opportunities for integrating data from transcriptomic to morphogenetic levels in a unified system still present several difficulties, plant tissues have some additional peculiarities. One of the plants’ features is that cell-to-cell communication topology through plasmodesmata forms during tissue growth and morphogenesis and results in mutual regulation of expression between neighboring cells affecting internal processes and cell domain development. Undoubtedly, we must take this fact into account when analyzing single-cell transcriptomic data. Cell-based computational modeling approaches successfully used in plant morphogenesis studies promise to be an efficient way to summarize such novel multiscale data. The inverse problem’s solutions for these models computed on the real tissue templates can shed light on the restoration of individual cells’ spatial localization in the initial plant organ—one of the most ambiguous and challenging stages in single-cell transcriptomic data analysis. This review summarizes new opportunities for advanced plant morphogenesis models, which become possible thanks to single-cell transcriptome data. Besides, we show the prospects of microscopy and cell-resolution imaging techniques to solve several spatial problems in single-cell transcriptomic data analysis and enhance the hybrid modeling framework opportunities.

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A morpho-transcriptomic map of brassinosteroid action in the Arabidopsis root

Graeff

Rana

Wendrich

et al. 2021

Preprint

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The effects of brassinosteroid signaling on shoot and root development have been characterized in great detail but did not identify a simple consistent positive or negative impact on a basic cellular parameter that would comprehensively explain the phenotype of brassinosteroid-related mutants. Here we combined digital 3D single-cell shape analysis and single-cell mRNA sequencing to characterize root meristems and mature root segments of brassinosteroid-blind mutants and wildtype. These data demonstrate that brassinosteroid signaling neither affects cell volume nor cell proliferation capacity. Instead, brassinosteroid signaling is essential for the precise orientation of cell division planes and the extent and timing of anisotropic cell expansion. Moreover, we found that the cell-aligning effects of brassinosteroid signaling can propagate to normalize the anatomy of both adjacent and distant brassinosteroid-blind cells through non-cell-autonomous functions, which are sufficient to restore overall root growth vigor. Finally, single-cell transcriptome data discern directly brassinosteroid-responsive genes from genes that can react to non-cell-autonomous brassinosteroid-dependent signals and highlight arabinogalactans as sentinels of brassinosteroid-dependent anisotropic cell expansion.

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Author response: Accurate and versatile 3D segmentation of plant tissues at cellular resolution

Cited by 3 publications

References 0 publications

What is quantitative plant biology?

What is quantitative plant biology?

A Sight on Single-Cell Transcriptomics in Plants Through the Prism of Cell-Based Computational Modeling Approaches: Benefits and Challenges for Data Analysis

A morpho-transcriptomic map of brassinosteroid action in the Arabidopsis root

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