Cytology, transcriptomics, and mass spectrometry imaging reveal changes in late-maturation elm (Ulmus pumila) seeds

The Current Status and Prospects of the Application of Omics Technology in the Study of Ulmus

Elm (Ulmus) species are important components of forest resources with significant ecological and economic value. As tall hardwood trees that are drought-resistant, poor-soil-tolerant, and highly adaptable, Ulmus species are an excellent choice for ecologically protected forests and urban landscaping. Additionally, the bioactive substances identified in the fruits, leaves, bark, and roots of Ulmus have potential applications in the food and medical fields and as raw materials in industrial and cosmetic applications. However, the survival of Ulmus species in the natural environment has been threatened by recurrent outbreaks of Dutch elm disease, which have led to the death of large numbers of Ulmus trees. In addition, severe damage to the natural habitats of some Ulmus species is driving their populations to extinction. Omics technology has become an important tool for the collection, protection, and biological characteristic analysis of Ulmus species and their resources due to its recent advances. This article summarizes the current research and application status of omics technology in Ulmus. The remaining problems are noted, and future research directions are proposed. Our review is aimed at providing a reference for resource conservation of Ulmus and for scientific research into this genus.

Large-volume fully automated cell reconstruction generates a cell atlas of plant tissues

The geometric shape and arrangement of individual cells play a role in shaping organ functions. However, analyzing multicellular features and exploring their connectomes in centimeter-scale plant organs remain challenging. Here, we established a set of frameworks named Large-Volume Fully Automated Cell Reconstruction (LVACR), enabling the exploration of three-dimensional (3D) cytological features and cellular connectivity in plant tissues. Through benchmark testing, our framework demonstrated superior efficiency in cell segmentation and aggregation, successfully addressing the inherent challenges posed by light sheet fluorescence microscopy (LSFM) imaging. Using LVACR, we successfully established a cell atlas of different plant tissues. Cellular morphology analysis revealed differences of cell clusters and shapes in between different poplar (P. simonii Carr. and P. canadensis Moench.) seeds, whereas topological analysis revealed that they maintained conserved cellular connectivity. Furthermore, LVACR spatiotemporally demonstrated an initial burst of cell proliferation, accompanied by morphological transformations at an early stage in developing the shoot apical meristem. During subsequent development, cell differentiation produced anisotropic features, thereby resulting in various cell shapes. Overall, our findings provided valuable insights into the precise spatial arrangement and cellular behavior of multicellular organisms, thus enhancing our understanding of the complex processes underlying plant growth and differentiation.

Advances in mass spectrometry imaging for plant metabolomics-Expanding the analytical toolbox

Mass spectrometry imaging (MSI) has become increasingly popular in plant science due to its ability to characterize complex chemical, spatial, and temporal aspects of plant metabolism. Over the past decade, as the emerging and unique features of various MSI techniques have continued to support new discoveries in studies of plant metabolism closely associated with various aspects of plant function and physiology, spatial metabolomics based on MSI techniques has positioned it at the forefront of plant metabolic studies, providing the opportunity for far higher resolution than was previously available. Despite these efforts, profound challenges at the levels of spatial resolution, sensitivity, quantitative ability, chemical confidence, isomer discrimination, and spatial multi-omics integration, undoubtedly remain. In this Perspective, we provide a contemporary overview of the emergent MSI techniques widely used in the plant sciences, with particular emphasis on recent advances in methodological breakthroughs. Having established the detailed context of MSI, we outline both the golden opportunities and key challenges currently facing plant metabolomics, presenting our vision as to how the enormous potential of MSI technologies will contribute to progress in plant science in the coming years.

Variation pattern in the macromolecular (cellulose, hemicelluloses, lignin) composition of cell walls in Pinus tabulaeformis tree trunks at different ages as revealed using multiple techniques

The plant cell wall is a complex, heterogeneous structure primarily composed of cellulose, hemicelluloses, and lignin. Exploring the variations in these three macromolecules over time is crucial for understanding wood formation to enhance chemical processing and utilization. Here, we comprehensively analyzed the chemical composition of cell walls in the trunks of Pinus tabulaeformis using multiple techniques. In situ analysis showed that macromolecules accumulated gradually in the cell wall as the plant aged, and the distribution pattern of lignin was opposite that of polysaccharides, and both showed heterogenous distribution patterns. In addition, gel permeation chromatography (GPC) results revealed that the molecular weights of hemicelluloses decreased while that of lignin increased with age. Two-dimensional heteronuclear single quantum coherence nuclear magnetic resonance (2D-HSQC NMR) analysis indicated that hemicelluloses mainly comprised galactoglucomannan and arabinoglucuronoxylan, and the lignin types were mainly comprised guaiacyl (G) and p-hydroxyphenyl (H) units with three main linkage types: β-O-4, β-β, and β-5. Furthermore, the C-O bond (β-O-4) signals of lignin decreased while the C-C bonds (β-β and β-5) signals increased over time. Taken together, these findings shed light on wood formation in P. tabulaeformis and lay the foundation for enhancing the processing and use of wood and timber products.

Desorption electrospray ionization and matrix-assisted laser desorption/ionization as imaging approaches for biological samples analysis

The imaging of biological tissues can offer valuable information about the sample composition, which improves the understanding of analyte distribution in such complex samples. Different approaches using mass spectrometry imaging (MSI), also known as imaging mass spectrometry (IMS), enabled the visualization of the distribution of numerous metabolites, drugs, lipids, and glycans in biological samples. The high sensitivity and multiple analyte evaluation/visualization in a single sample provided by MSI methods lead to various advantages and overcome drawbacks of classical microscopy techniques. In this context, the application of MSI methods, such as desorption electrospray ionization-MSI (DESI-MSI) and matrix-assisted laser desorption/ionization-MSI (MALDI-MSI), has significantly contributed to this field. This review discusses the evaluation of exogenous and endogenous molecules in biological samples using DESI and MALDI imaging. It offers rare technical insights not commonly found in the literature (scanning speed and geometric parameters), making it a comprehensive guide for applying these techniques step-by-step. Furthermore, we provide an in-depth discussion of recent research findings on using these methods to study biological tissues.

Single-cell and spatial multi-omics in the plant sciences: Technical advances, applications, and perspectives

Plants contain a large number of cell types and exhibit complex regulatory mechanisms. Studies at the single-cell level have gradually become more common in plant science. Single-cell transcriptomics, spatial transcriptomics, and spatial metabolomics techniques have been combined to analyze plant development. These techniques have been used to study the transcriptomes and metabolomes of plant tissues at the single-cell level, enabling the systematic investigation of gene expression and metabolism in specific tissues and cell types during defined developmental stages. In this review, we present an overview of significant breakthroughs in spatial multi-omics in plants, and we discuss how these approaches may soon play essential roles in plant research.