High-resolution anatomical and spatial transcriptome analyses reveal two types of meristematic cell pools within the secondary vascular tissue of poplar stem

C2H2 zinc finger protein PagIDD15A regulates secondary wall thickening and lignin biosynthesis in poplar

Wood production is largely determined by the activity of cambial cell proliferation, and the secondary cell wall (SCW) thickening of xylem cells determines the wood property. In this study, we identified an INDETERMINATE DOMAIN (IDD) type C2H2 zinc finger transcription factor PagIDD15A as a regulator of wood formation in Populus alba × Populus glandulosa. Downregulation of PagIDD15A expression by RNA interference (RNAi) inhibited xylem development and xylem cell secondary wall thickening. RNA-seq analysis showed that PagPAL1, PagCCR2 and PagCCoAOMT1 were downregulated in the differentiating xylem of the PagIDD15A-RNAi transgenic plants, showing that PagIDD15A may regulate SCW biosynthesis through inhibiting lignin biosynthesis. The downregulation of PagVND6-B2, PagMYB10 and PagMYC4 and upregulation of PagWRKY12 in the differentiating xylem of RNAi transgenic plants suggest that PagIDD15A may also regulate these transcription factor (TF) genes to affect SCW thickening. RT-qPCR analysis in the phloem-cambium of RNAi transgenic demonstrates that PagIDD15A may regulate the expression of the genes associated with cell proliferation, including, PagSHR (SHORTROOT), PagSCR (SCARECROW), PagCYCD3;1 (CYCLIN D3;1) and PagSMR4 (SIAMESE-RELATED4), to affect the cambial activity. This study provides the knowledge of the IDD-type C2H2 zinc finger protein in regulating wood formation.

Integrating evolutionary genomics of forest trees to inform future tree breeding amid rapid climate change

Global climate change is leading to rapid and drastic shifts in environmental conditions, posing threats to biodiversity and nearly all life forms worldwide. Forest trees serve as foundational components of terrestrial ecosystems and play a crucial and leading role in combating and mitigating the adverse effects of extreme climate events, despite their own vulnerability to these threats. Therefore, understanding and monitoring how natural forests respond to rapid climate change is a key priority for biodiversity conservation. Recent progress in evolutionary genomics, driven primarily by cutting-edge multi-omics technologies, offers powerful new tools to address several key issues. These include precise delineation of species and evolutionary units, inference of past evolutionary histories and demographic fluctuations, identification of environmentally adaptive variants, and measurement of genetic load levels. As the urgency to deal with more extreme environmental stresses grows, understanding the genomics of evolutionary history, local adaptation, future responses to climate change, and conservation and restoration of natural forest trees will be critical for research at the nexus of global change, population genomics, and conservation biology. In this review, we explore the application of evolutionary genomics to assess the effects of global climate change using multi-omics approaches and discuss the outlook for breeding of climate-adapted trees.

Aerogel-Involved Triple-State Gels Resemble Natural Living Leaves in Structure and Multi-Functions

Natural plant leaves with multiple functions, for example, spectral features, transpiration, photosynthesis, etc., have played a significant role in the ecosystem, and artificial synthesis of plant leaves with multiple functions of natural ones is still a great challenge. Herein, this work presents an aerogel-involved living leaf (AL), most similar to natural ones so far, by embedding super-hydrophobic SiO2 aerogel microparticles in polyvinyl alcohol hydrogel in the presence of hygroscopic salt and chlorophyllin copper sodium to form solid-liquid-vapor triple-state gel. The AL shows a high spectral similarity with all sampled 15 species of natural leaves and exhibits ≈4-7 times transpiration speed higher than natural leaves. More importantly, AL can achieve several times higher photosynthesis than natural leaves without the energy provided by the respiratory action of natural ones. This work demonstrates the feasibility of creating ALs with natural leaf-like triple-state gel structures and multiple functions, opening up new avenues for energy conversion, environmental engineering, and biomimetic applications.

Opportunities and Challenges in Advancing Plant Research with Single-cell Omics

Plants possess diverse cell types and intricate regulatory mechanisms to adapt to the ever-changing environment of nature. Various strategies have been employed to study cell types and their developmental progressions, including single-cell sequencing methods which provide high-dimensional catalogs to address biological concerns. In recent years, single-cell sequencing technologies in transcriptomics, epigenomics, proteomics, metabolomics, and spatial transcriptomics have been increasingly used in plant science to reveal intricate biological relationships at the single-cell level. However, the application of single-cell technologies to plants is more limited due to the challenges posed by cell structure. This review outlines the advancements in single-cell omics technologies, their implications in plant systems, future research applications, and the challenges of single-cell omics in plant systems.

Stem Cells and Differentiation in Vascular Tissues

Plant vascular tissues are crucial for the long-distance transport of water, nutrients, and a multitude of signal molecules throughout the plant body and, therefore, central to plant growth and development. The intricate development of vascular tissues is orchestrated by unique populations of dedicated stem cells integrating endogenous as well as environmental cues. This review summarizes our current understanding of vascular-related stem cell biology and of vascular tissue differentiation. We present an overview of the molecular and cellular mechanisms governing the maintenance and fate determination of vascular stem cells and highlight the interplay between intrinsic and external cues. In this context, we emphasize the role of transcription factors, hormonal signaling, and epigenetic modifications. We also discuss emerging technologies and the large repertoire of cell types associated with vascular tissues, which have the potential to provide unprecedented insights into cellular specialization and anatomical adaptations to distinct ecological niches.

Advances in Single-Cell Transcriptome Sequencing and Spatial Transcriptome Sequencing in Plants

"Omics" typically involves exploration of the structure and function of the entire composition of a biological system at a specific level using high-throughput analytical methods to probe and analyze large amounts of data, including genomics, transcriptomics, proteomics, and metabolomics, among other types. Genomics characterizes and quantifies all genes of an organism collectively, studying their interrelationships and their impacts on the organism. However, conventional transcriptomic sequencing techniques target population cells, and their results only reflect the average expression levels of genes in population cells, as they are unable to reveal the gene expression heterogeneity and spatial heterogeneity among individual cells, thus masking the expression specificity between different cells. Single-cell transcriptomic sequencing and spatial transcriptomic sequencing techniques analyze the transcriptome of individual cells in plant or animal tissues, enabling the understanding of each cell's metabolites and expressed genes. Consequently, statistical analysis of the corresponding tissues can be performed, with the purpose of achieving cell classification, evolutionary growth, and physiological and pathological analyses. This article provides an overview of the research progress in plant single-cell and spatial transcriptomics, as well as their applications and challenges in plants. Furthermore, prospects for the development of single-cell and spatial transcriptomics are proposed.

Anchoring Active Li Metal in Oriented Channel by In Situ Formed Nucleation Sites Enabling Durable Lithium-Metal Batteries

Lithium metal is the ultimate anode material for pursuing the increased energy density of rechargeable batteries. However, fatal dendrites growth and huge volume change seriously hinder the practical application of lithium metal batteries (LMBs). In this work, a lithium host that preinstalled CoSe nanoparticles on vertical carbon vascular tissues (VCVT/CoSe) is designed and fabricated to resolve these issues, which provides sufficient Li plating space with a robust framework, enabling dendrite-free Li deposition. Their inherent N sites coupled with the in situ formed lithiophilic Co sites loaded at the interface of VCVT not only anchor the initial Li nucleation seeds but also accelerate the Li+ transport kinetics. Meanwhile, the Li2Se originated from the CoSe conversion contributes to constructing a stable solid-electrolyte interphase with high ionic conductivity. This optimized Li/VCVT/CoSe composite anode exhibits a prominent long-term cycling stability over 3000 h with a high areal capacity of 10 mAh cm-2. When paired with a commercial nickel-rich LiNi0.83Co0.12Mn0.05O2 cathode, the full-cell presents substantially enhanced cycling performance with 81.7% capacity retention after 300 cycles at 0.2 C. Thus, this work reveals the critical role of guiding Li deposition behavior to maintain homogeneous Li morphology and pave the way to stable LMBs.

Morpho-histology of co-occurrence of somatic embryos, shoots, and inflorescences within a callus of Limonium 'Misty Blue'

This is the first attempt to report the co-occurrence of somatic embryos, shoots, and inflorescences and their sequential development from stem cell niches of an individual callus mass through morpho-histological study of any angiosperm. In the presence of a proper auxin/cytokinin combination, precambial stem cells from the middle layer of a compact callus, which was derived from the thin cell layer of the inflorescence rachis of Limonium, expressed the highest level of totipotency and pluripotency and simultaneously developed somatic embryos, shoots, and inflorescences. This study also proposed the concept of programmed cell death during bipolar somatic embryo and unipolar shoot bud pattern formation. The unique feature of this research was the stepwise histological description of in vitro racemose inflorescence development. Remarkably, during the initiation of inflorescence development, either a unipolar structure with open vascular elements or an independent bipolar structure with closed vascular elements were observed. The protocol predicted the production of 6.6 ± 0.24 and 7.4 ± 0.24 somatic embryos and shoots, respectively, from 400 mg of callus, which again multiplied, rooted, and acclimatised. The plants' ploidy level and genetic fidelity were assessed randomly before acclimatisation by flow cytometry and inter simple sequence repeats (ISSR) marker analysis. Finally, the survivability and flower quality of the regenerated plants were evaluated in the field.

TARGET OF MONOPTEROS: key transcription factors orchestrating plant development and environmental response

Plants have an incredible ability to sustain root and vascular growth after initiation of the embryonic root and the specification of vascular tissue in early embryos. Microarray assays have revealed that a group of transcription factors, TARGET OF MONOPTEROS (TMO), are important for embryonic root initiation in Arabidopsis. Despite the discovery of their auxin responsiveness early on, their function and mode of action remained unknown for many years. The advent of genome editing has accelerated the study of TMO transcription factors, revealing novel functions for biological processes such as vascular development, root system architecture, and response to environmental cues. This review covers recent achievements in understanding the developmental function and the genetic mode of action of TMO transcription factors in Arabidopsis and other plant species. We highlight the transcriptional and post-transcriptional regulation of TMO transcription factors in relation to their function, mainly in Arabidopsis. Finally, we provide suggestions for further research and potential applications in plant genetic engineering.

Single-cell and spatial RNA sequencing reveal the spatiotemporal trajectories of fruit senescence

The senescence of fruit is a complex physiological process, with various cell types within the pericarp, making it highly challenging to elucidate their individual roles in fruit senescence. In this study, a single-cell expression atlas of the pericarp of pitaya (Hylocereus undatus) is constructed, revealing exocarp and mesocarp cells undergoing the most significant changes during the fruit senescence process. Pseudotime analysis establishes cellular differentiation and gene expression trajectories during senescence. Early-stage oxidative stress imbalance is followed by the activation of resistance in exocarp cells, subsequently senescence-associated proteins accumulate in the mesocarp cells at late-stage senescence. The central role of the early response factor HuCMB1 is unveiled in the senescence regulatory network. This study provides a spatiotemporal perspective for a deeper understanding of the dynamic senescence process in plants.

Studying plant vascular development using single-cell approaches

Vascular cells form a highly complex and heterogeneous tissue. Its composition, function, shape, and arrangement vary with the developmental stage and between organs and species. Understanding the transcriptional regulation underpinning this complexity thus requires a high-resolution technique that is capable of capturing rapid events during vascular cell formation. Single-cell and single-nucleus RNA sequencing (sc/snRNA-seq) approaches provide powerful tools to extract transcriptional information from these lowly abundant and dynamically changing cell types, which allows the reconstruction of developmental trajectories. Here, we summarize and reflect on recent studies using single-cell transcriptomics to study vascular cell types and discuss current and future implementations of sc/snRNA-seq approaches in the field of vascular development.

Wood of trees: Cellular structure, molecular formation, and genetic engineering

Wood is an invaluable asset to human society due to its renewable nature, making it suitable for both sustainable energy production and material manufacturing. Additionally, wood derived from forest trees plays a crucial role in sequestering a significant portion of the carbon dioxide fixed during photosynthesis by terrestrial plants. Nevertheless, with the expansion of the global population and ongoing industrialization, forest coverage has been substantially decreased, resulting in significant challenges for wood production and supply. Wood production practices have changed away from natural forests toward plantation forests. Thus, understanding the underlying genetic mechanisms of wood formation is the foundation for developing high-quality, fast-growing plantation trees. Breeding ideal forest trees for wood production using genetic technologies has attracted the interest of many. Tremendous studies have been carried out in recent years on the molecular, genetic, and cell-biological mechanisms of wood formation, and considerable progress and findings have been achieved. These studies and findings indicate enormous possibilities and prospects for tree improvement. This review will outline and assess the cellular and molecular mechanisms of wood formation, as well as studies on genetically improving forest trees, and address future development prospects.

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.

Spatial transcriptomics drives a new era in plant research

The plant community lags far behind the animal and human fields concerning the application of single‐cell methodologies. This is primarily due to the challenges associated with plant tissue dissection and the limitations of the available technologies. However, recent advances in spatial transcriptomics enable the study of single‐cells derived from plant tissues from a spatial perspective. This technology is already successfully used to identify cell types, reconstruct cell‐fate lineages, and reveal cell‐to‐cell interactions. Future technological advancements will overcome the challenges in sample processing, data analysis, and the integration of multiple‐omics technologies. Thanks to spatial transcriptomics, we anticipate several plant research projects to significantly advance our understanding of critical aspects of plant biology.

How to explore what is hidden? A review of techniques for vascular tissue expression profile analysis

The evolution of plants to efficiently transport water and assimilates over long distances is a major evolutionary success that facilitated their growth and colonization of land. Vascular tissues, namely xylem and phloem, are characterized by high specialization, cell heterogeneity, and diverse cell components. During differentiation and maturation, these tissues undergo an irreversible sequence of events, leading to complete protoplast degradation in xylem or partial degradation in phloem, enabling their undisturbed conductive function. Due to the unique nature of vascular tissue, and the poorly understood processes involved in xylem and phloem development, studying the molecular basis of tissue differentiation is challenging. In this review, we focus on methods crucial for gene expression research in conductive tissues, emphasizing the importance of initial anatomical analysis and appropriate material selection. We trace the expansion of molecular techniques in vascular gene expression studies and discuss the application of single-cell RNA sequencing, a high-throughput technique that has revolutionized transcriptomic analysis. We explore how single-cell RNA sequencing will enhance our knowledge of gene expression in conductive tissues.

Engineering custom morpho- and chemotypes of Populus for sustainable production of biofuels, bioproducts, and biomaterials

Humans have been modifying plant traits for thousands of years, first through selection (i.e., domestication) then modern breeding, and in the last 30 years, through biotechnology. These modifications have resulted in increased yield, more efficient agronomic practices, and enhanced quality traits. Precision knowledge of gene regulation and function through high-resolution single-cell omics technologies, coupled with the ability to engineer plant genomes at the DNA sequence, chromatin accessibility, and gene expression levels, can enable engineering of complex and complementary traits at the biosystem level. Populus spp., the primary genetic model system for woody perennials, are among the fastest growing trees in temperate zones and are important for both carbon sequestration and global carbon cycling. Ample genomic and transcriptomic resources for poplar are available including emerging single-cell omics datasets. To expand use of poplar outside of valorization of woody biomass, chassis with novel morphotypes in which stem branching and tree height are modified can be fabricated thereby leading to trees with altered leaf to wood ratios. These morphotypes can then be engineered into customized chemotypes that produce high value biofuels, bioproducts, and biomaterials not only in specific organs but also in a cell-type-specific manner. For example, the recent discovery of triterpene production in poplar leaf trichomes can be exploited using cell-type specific regulatory sequences to synthesize high value terpenes such as the jet fuel precursor bisabolene specifically in the trichomes. By spatially and temporally controlling expression, not only can pools of abundant precursors be exploited but engineered molecules can be sequestered in discrete cell structures in the leaf. The structural diversity of the hemicellulose xylan is a barrier to fully utilizing lignocellulose in biomaterial production and by leveraging cell-type-specific omics data, cell wall composition can be modified in a tailored and targeted specific manner to generate poplar wood with novel chemical features that are amenable for processing or advanced manufacturing. Precision engineering poplar as a multi-purpose sustainable feedstock highlights how genome engineering can be used to re-imagine a crop species.

Exploring the identity of individual plant cells in space and time

In recent years, single-cell genomics, coupled to imaging techniques, have become the state-of-the-art approach for characterising biological systems. In plant sciences, a variety of tissues and species have been profiled, providing an enormous quantity of data on cell identity at an unprecedented resolution, but what biological insights can be gained from such data sets? Using recently published studies in plant sciences, we will highlight how single-cell technologies have enabled a better comprehension of tissue organisation, cell fate dynamics in development or in response to various stimuli, as well as identifying key transcriptional regulators of cell identity. We discuss the limitations and technical hurdles to overcome, as well as future directions, and the promising use of single-cell omics to understand, predict, and manipulate plant development and physiology.

Harnessing the Genetic Basis of Sorghum Biomass-Related Traits to Facilitate Bioenergy Applications

The extensive use of fossil fuels and global climate change have raised ever-increasing attention to sustainable development, global food security and the replacement of fossil fuels by renewable energy. Several C4 monocot grasses have excellent photosynthetic ability, stress tolerance and may rapidly produce biomass in marginal lands with low agronomic inputs, thus representing an important source of bioenergy. Among these grasses, Sorghum bicolor has been recognized as not only a promising bioenergy crop but also a research model due to its diploidy, simple genome, genetic diversity and clear orthologous relationship with other grass genomes, allowing sorghum research to be easily translated to other grasses. Although sorghum molecular genetic studies have lagged far behind those of major crops (e.g., rice and maize), recent advances have been made in a number of biomass-related traits to dissect the genetic loci and candidate genes, and to discover the functions of key genes. However, molecular and/or targeted breeding toward biomass-related traits in sorghum have not fully benefited from these pieces of genetic knowledge. Thus, to facilitate the breeding and bioenergy applications of sorghum, this perspective summarizes the bioenergy applications of different types of sorghum and outlines the genetic control of the biomass-related traits, ranging from flowering/maturity, plant height, internode morphological traits and metabolic compositions. In particular, we describe the dynamic changes of carbohydrate metabolism in sorghum internodes and highlight the molecular regulators involved in the different stages of internode carbohydrate metabolism, which affects the bioenergy utilization of sorghum biomass. We argue the way forward is to further enhance our understanding of the genetic mechanisms of these biomass-related traits with new technologies, which will lead to future directions toward tailored designing sorghum biomass traits suitable for different bioenergy applications.

Spatial transcriptomics reveals light-induced chlorenchyma cells involved in promoting shoot regeneration in tomato callus

Callus is a reprogrammed cell mass involved in plant regeneration and gene transformation in crop engineering. Pluripotent callus cells develop into fertile shoots through shoot regeneration. The molecular basis of the shoot regeneration process in crop callus remains largely elusive. This study pioneers the exploration of the spatial transcriptome of tomato callus during shoot regeneration. The findings reveal the presence of highly heterogeneous cell populations within the callus, including epidermis, vascular tissue, shoot primordia, inner callus, and outgrowth shoots. By characterizing the spatially resolved molecular features of shoot primordia and surrounding cells, specific factors essential for shoot primordia formation are identified. Notably, chlorenchyma cells, enriched in photosynthesis-related processes, play a crucial role in promoting shoot primordia formation and subsequent shoot regeneration. Light is shown to promote shoot regeneration by inducing chlorenchyma cell development and coordinating sugar signaling. These findings significantly advance our understanding of the cellular and molecular aspects of shoot regeneration in tomato callus and demonstrate the immense potential of spatial transcriptomics in plant biology.

Spatially resolved transcriptomic analysis of the germinating barley grain

Seeds are a vital source of calories for humans and a unique stage in the life cycle of flowering plants. During seed germination, the embryo undergoes major developmental transitions to become a seedling. Studying gene expression in individual seed cell types has been challenging due to the lack of spatial information or low throughput of existing methods. To overcome these limitations, a spatial transcriptomics workflow was developed for germinating barley grain. This approach enabled high-throughput analysis of spatial gene expression, revealing specific spatial expression patterns of various functional gene categories at a sub-tissue level. This study revealed over 14 000 genes differentially regulated during the first 24 h after imbibition. Individual genes, such as the aquaporin gene family, starch degradation, cell wall modification, transport processes, ribosomal proteins and transcription factors, were found to have specific spatial expression patterns over time. Using spatial autocorrelation algorithms, we identified auxin transport genes that had increasingly focused expression within subdomains of the embryo over time, suggesting their role in establishing the embryo axis. Overall, our study provides an unprecedented spatially resolved cellular map for barley germination and identifies specific functional genomics targets to better understand cellular restricted processes during germination. The data can be viewed at https://spatial.latrobe.edu.au/.

A method for analyzing programmed cell death in xylem development by flow cytometry

Programmed cell death (PCD) is a genetically regulated developmental process leading to the death of specific types of plant cells, which plays important roles in plant development and growth such as wood formation. However, an efficient method needs to be established to study PCD in woody plants. Flow cytometry is widely utilized to evaluate apoptosis in mammalian cells, while it is rarely used to detect PCD in plants, especially in woody plants. Here, we reported that the xylem cell protoplasts from poplar stem were stained with a combination of fluorescein annexin V-FITC and propidium iodide (PI) and then sorted by flow cytometry. As expected, living cells (annexin V-FITC negative/PI negative), early PCD cells (annexin V-FITC positive/PI negative), and late PCD cells (annexin V-FITC positive/PI positive) could be finely distinguished through this method and then subjected for quantitative analysis. The expression of cell-type- and developmental stages-specific marker genes was consistent with the cell morphological observation. Therefore, the newly developed fluorescence-activated cell sorting (FACS) method can be used to study PCD in woody plants, which will be beneficial for studying the molecular mechanisms of wood formation.