Plant Single-Cell Multiomics: Cracking the Molecular Profiles of Plant Cells

Novel synthetic inducible promoters controlling gene expression during water-deficit stress with green tissue specificity in transgenic poplar

Synthetic promoters may be designed using short cis-regulatory elements (CREs) and core promoter sequences for specific purposes. We identified novel conserved DNA motifs from the promoter sequences of leaf palisade and vascular cell type-specific expressed genes in water-deficit stressed poplar (Populus tremula × Populus alba), collected through low-input RNA-seq analysis using laser capture microdissection. Hexamerized sequences of four conserved 20-base motifs were inserted into each synthetic promoter construct. Two of these synthetic promoters (Syn2 and Syn3) induced GFP in transformed poplar mesophyll protoplasts incubated in 0.5 M mannitol solution. To identify effect of length and sequence from a valuable 20 base motif, 5' and 3' regions from a basic sequence (GTTAACTTCAGGGCCTGTGG) of Syn3 were hexamerized to generate two shorter synthetic promoters, Syn3-10b-1 (5': GTTAACTTCA) and Syn3-10b-2 (3': GGGCCTGTGG). These promoters' activities were compared with Syn3 in plants. Syn3 and Syn3-10b-1 were specifically induced in transient agroinfiltrated Nicotiana benthamiana leaves in water cessation for 3 days. In stable transgenic poplar, Syn3 presented as a constitutive promoter but had the highest activity in leaves. Syn3-10b-1 had stronger induction in green tissues under water-deficit stress conditions than mock control. Therefore, a synthetic promoter containing the 5' sequence of Syn3 endowed both tissue-specificity and water-deficit inducibility in transgenic poplar, whereas the 3' sequence did not. Consequently, we have added two new synthetic promoters to the poplar engineering toolkit: Syn3-10b-1, a green tissue-specific and water-deficit stress-induced promoter, and Syn3, a green tissue-preferential constitutive promoter.

Plant genome information facilitates plant functional genomics

MAIN CONCLUSION

In this review, we give an overview of plant sequencing efforts and how this impacts plant functional genomics research. 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.

Advances in the Application of Single-Cell Transcriptomics in Plant Systems and Synthetic Biology

Plants are complex systems hierarchically organized and composed of various cell types. To understand the molecular underpinnings of complex plant systems, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for revealing high resolution of gene expression patterns at the cellular level and investigating the cell-type heterogeneity. Furthermore, scRNA-seq analysis of plant biosystems has great potential for generating new knowledge to inform plant biosystems design and synthetic biology, which aims to modify plants genetically/epigenetically through genome editing, engineering, or re-writing based on rational design for increasing crop yield and quality, promoting the bioeconomy and enhancing environmental sustainability. In particular, data from scRNA-seq studies can be utilized to facilitate the development of high-precision Build-Design-Test-Learn capabilities for maximizing the targeted performance of engineered plant biosystems while minimizing unintended side effects. To date, scRNA-seq has been demonstrated in a limited number of plant species, including model plants (e.g., Arabidopsis thaliana), agricultural crops (e.g., Oryza sativa), and bioenergy crops (e.g., Populus spp.). It is expected that future technical advancements will reduce the cost of scRNA-seq and consequently accelerate the application of this emerging technology in plants. In this review, we summarize current technical advancements in plant scRNA-seq, including sample preparation, sequencing, and data analysis, to provide guidance on how to choose the appropriate scRNA-seq methods for different types of plant samples. We then highlight various applications of scRNA-seq in both plant systems biology and plant synthetic biology research. Finally, we discuss the challenges and opportunities for the application of scRNA-seq in plants.

Introducing single cell stereo-sequencing technology to transform the plant transcriptome landscape

Single cell RNA-sequencing (scRNA-seq) advancements have helped detect transcriptional heterogeneities in biological samples. However, scRNA-seq cannot currently provide high-resolution spatial transcriptome information or identify subcellular organs in biological samples. These limitations have led to the development of spatially enhanced-resolution omics-sequencing (Stereo-seq), which combines spatial information with single cell transcriptomics to address the challenges of scRNA-seq alone. In this review, we discuss the advantages of Stereo-seq technology. We anticipate that the application of such an integrated approach in plant research will advance our understanding of biological process in the plant transcriptomics era. We conclude with an outlook of how such integration will enhance crop improvement.

Resolving plant development in space and time with single-cell genomics

Single-cell genomics technologies are ushering in a new research era. In this review, we summarize the benefits and current challenges of using these technologies to probe the transcriptional regulation of plant development. In addition to profiling cells at a single snapshot in time, researchers have recently produced time-resolved datasets to map cell responses to stimuli. Live-imaging and spatial transcriptomic techniques are rapidly being adopted to link a cell's transcriptional profile with its spatial location within a tissue. Combining these technologies is a powerful spatiotemporal approach to investigate cell plasticity and developmental responses that contribute to plant resilience. Although there are hurdles to overcome, we conclude by discussing how single-cell genomics is poised to address developmental questions in the coming years.

Systems biology of root development in Populus: Review and perspectives

The root system of plants consists of primary, lateral, and adventitious roots (ARs) (aka shoot-born roots). ARs arise from stem- or leaf-derived cells during post-embryonic development. Adventitious root development (ARD) through stem cuttings is the first requirement for successful establishment and growth of planted trees; however, the details of the molecular mechanisms underlying ARD are poorly understood. This knowledge is important to both basic plant biology and because of its necessary role in the successful propagation of superior cultivars of commercial woody bioenergy crops, like poplar. In this review article, the molecular mechanisms that control both endogenous (auxin) and environmentally (nutrients and microbes) regulated ARD and how these systems interact to control the rooting efficiency of poplar trees are described. Then, potential future studies in employing integrated systems biology approaches at cellular resolutions are proposed to more precisely identify the molecular mechanisms that cause AR. Using genetic transformation and genome editing approaches, this information can be used for improving ARD in economically important plants for which clonal propagation is a requirement.

Shoot-root signal circuit: Phytoremediation of heavy metal contaminated soil

High concentrations of heavy metals in the environment will cause serious harm to ecosystems and human health. It is urgent to develop effective methods to control soil heavy metal pollution. Phytoremediation has advantages and potential for soil heavy metal pollution control. However, the current hyperaccumulators have the disadvantages of poor environmental adaptability, single enrichment species and small biomass. Based on the concept of modularity, synthetic biology makes it possible to design a wide range of organisms. In this paper, a comprehensive strategy of "microbial biosensor detection - phytoremediation - heavy metal recovery" for soil heavy metal pollution control was proposed, and the required steps were modified by using synthetic biology methods. This paper summarizes the new experimental methods that promote the discovery of synthetic biological elements and the construction of circuits, and combs the methods of producing transgenic plants to facilitate the transformation of constructed synthetic biological vectors. Finally, the problems that should be paid more attention to in the remediation of soil heavy metal pollution based on synthetic biology were discussed.

Plant Single-Cell/Nucleus RNA-seq Workflow

Single-cell transcriptomics technologies allow researchers to investigate how individual cells, in complex multicellular organisms, differentially use their common genomic DNA. In plant biology, these technologies were recently applied to reveal the transcriptomes of various plant cells isolated from different organs and different species and in response to environmental stresses. These first studies support the potential of single-cell transcriptomics technology to decipher the biological function of plant cells, their developmental programs, cell-type-specific gene networks, programs controlling plant cell response to environmental stresses, etc. In this chapter, we provide information regarding the critical steps and important information to consider when developing an experimental design in plant single-cell biology. We also describe the current status of bioinformatics tools used to analyze single-cell RNA-seq datasets and how additional emerging technologies such as spatial transcriptomics and long-read sequencing technologies will provide additional information on the differential use of the genome by plant cells.

Review: Challenges and perspectives in applying single nuclei RNA-seq technology in plant biology

Plant single-cell RNA-seq technology quantifies the abundance of plant transcripts at a single-cell resolution. Deciphering the transcriptomes of each plant cell, their regulation during plant cell development, and their response to environmental stresses will support the functional study of genes, the establishment of precise transcriptional programs, the prediction of more accurate gene regulatory networks, and, in the long term, the design of de novo gene pathways to enhance selected crop traits. In this review, we will discuss the opportunities, challenges, and problems, and share tentative solutions associated with the generation and analysis of plant single-cell transcriptomes. We will discuss the benefit and limitations of using plant protoplasts vs. nuclei to conduct single-cell RNA-seq experiments on various plant species and organs, the functional annotation of plant cell types based on their transcriptomic profile, the characterization of the dynamic regulation of the plant genes during cell development or in response to environmental stress, the need to characterize and integrate additional layers of -omics datasets to capture new molecular modalities at the single-cell level and reveal their causalities, the deposition and access to single-cell datasets, and the accessibility of this technology to plant scientists.

Single-cell technologies: From research to application

In recent years, more and more single-cell technologies have been developed. A vast amount of single-cell omics data has been generated by large projects, such as the Human Cell Atlas, the Mouse Cell Atlas, the Mouse RNA Atlas, the Mouse ATAC Atlas, and the Plant Cell Atlas. Based on these single-cell big data, thousands of bioinformatics algorithms for quality control, clustering, cell-type annotation, developmental inference, cell-cell transition, cell-cell interaction, and spatial analysis are developed. With powerful experimental single-cell technology and state-of-the-art big data analysis methods based on artificial intelligence, the molecular landscape at the single-cell level can be revealed. With spatial transcriptomics and single-cell multi-omics, even the spatial dynamic multi-level regulatory mechanisms can be deciphered. Such single-cell technologies have many successful applications in oncology, assisted reproduction, embryonic development, and plant breeding. We not only review the experimental and bioinformatics methods for single-cell research, but also discuss their applications in various fields and forecast the future directions for single-cell technologies. We believe that spatial transcriptomics and single-cell multi-omics will become the next booming business for mechanism research and commercial industry.

Epigenetic regulation of thermomorphogenesis in Arabidopsis thaliana

Temperature is a key factor in determining plant growth and development, geographical distribution, and seasonal behavior. Plants accurately sense subtle changes in ambient temperature and alter their growth and development accordingly to improve their chances of survival and successful propagation. Thermomorphogenesis encompasses a variety of morphological changes that help plants acclimate to warm environmental temperatures. Revealing the molecular mechanism of thermomorphogenesis is important for breeding thermo-tolerant crops and ensuring food security under global climate change. Plant adaptation to elevated ambient temperature is regulated by multiple signaling pathways and epigenetic mechanisms such as histone modifications, histone variants, and non-coding RNAs. In this review, we summarize recent advances in the mechanism of epigenetic regulation during thermomorphogenesis with a focus on the model plant Arabidopsis thaliana and briefly discuss future prospects for this field.

Late-maturity α-amylase (LMA): exploring the underlying mechanisms and end-use quality effects in wheat

MAIN CONCLUSION

A comprehensive understanding of LMA from the underlying molecular aspects to the end-use quality effects will greatly benefit the global wheat industry and those whose livelihoods depend upon it. Late-maturity α-amylase (LMA) leads to the expression and protein accumulation of high pI α-amylases during late grain development. This α-amylase is maintained through harvest and leads to an unacceptable low falling number (FN), the wheat industry's standard measure for predicting end-use quality. Unfortunately, low FN leads to significant financial losses for growers. As a result, wheat researchers are working to understand and eliminate LMA from wheat breeding programs, with research aims that include unraveling the genetic, biochemical, and physiological mechanisms that lead to LMA expression. In addition, cereal chemists and quality scientists are working to determine if and how LMA-affected grain impacts end-use quality. This review is a comprehensive overview of studies focused on LMA and includes open questions and future directions.

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

Plants are composed of cells that physically interact and constantly adapt to their environment. To reveal the contribution of each plant cells to the biology of the entire organism, their molecular, morphological, and physiological attributes must be quantified and analyzed in the context of the morphology of the plant organs. The emergence of single-cell/nucleus omics technologies now allows plant biologists to access different modalities of individual cells including their epigenome and transcriptome to reveal the unique molecular properties of each cell composing the plant and their dynamic regulation during cell differentiation and in response to their environment. In this manuscript, we provide a perspective regarding the challenges and strategies to collect plant single-cell biological datasets and their analysis in the context of cellular interactions. As an example, we provide an analysis of the transcriptional regulation of the Arabidopsis genes controlling the differentiation of the root hair cells at the single-cell level. We also discuss the perspective of the use of spatial profiling to complement existing plant single-cell omics.

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

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.