Plant single-cell solutions for energy and the environment

Abstract

Progress in sequencing, microfluidics, and analysis strategies has revolutionized the granularity at which multicellular organisms can be studied. In particular, single-cell transcriptomics has led to fundamental new insights into animal biology, such as the discovery of new cell types and cell type-specific disease processes. However, the application of single-cell approaches to plants, fungi, algae, or bacteria (environmental organisms) has been far more limited, largely due to the challenges posed by polysaccharide walls surrounding these species’ cells. In this perspective, we discuss opportunities afforded by single-cell technologies for energy and environmental science and grand challenges that must be tackled to apply these approaches to plants, fungi and algae. We highlight the need to develop better and more comprehensive single-cell technologies, analysis and visualization tools, and tissue preparation methods. We advocate for the creation of a centralized, open-access database to house plant single-cell data. Finally, we consider how such efforts should balance the need for deep characterization of select model species while still capturing the diversity in the plant kingdom. Investments into the development of methods, their application to relevant species, and the creation of resources to support data dissemination will enable groundbreaking insights to propel energy and environmental science forward.

Autopolyploidization affects transcript patterns and gene targeting frequencies in Physcomitrella

“…However, we did not observe different transformation efficiencies between haploid and diploid protoplasts based on the highly standardized procedures developed by us (Hohe et al 2004). Single-cell transcriptomic studies are gaining popularity (Cole et al 2021) but are still in their infancy in Physcomitrella (Kubo et al 2019) and thus not highly standardized for a series of quantitative studies we performed here. The differences in gene expression between haploids and diploids having an identical, albeit duplicated, genome might be to some extent caused by ploidy-dependent epigenetic regulation of the transcriptome.…”

Synthetic genetic circuits as a means of reprogramming plant roots

“…To efficiently engineer genetic circuits that meet specific design requirements, researchers can leverage the growing number of transient expression methods available for plants ( 34 , 35 ). Advances in single-cell measurements and spatially resolved omics will also support the construction of circuits in multicellular organisms by enabling more precise measurements ( 36 , 37 ). Ultimately, methods for programming novel traits in plants will become increasingly useful as climate challenges grow and new agricultural solutions are needed.…”

First Plant Cell Atlas symposium report

“…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.…”