Single-cell RNA landscape of the special fiber initiation process in Bombax ceiba

Single-Cell Transcriptome Reveals the Cellular Response to PEG-Induced Stress in Wheat Leaves

Drought is a major factor limiting the production and yield of wheat bread (Triticum aestivum). Therefore, investigating the wheat drought-related response mechanism is an urgent priority. Here, the single-cell transcriptome of drought-nonsusceptible and susceptible wheat seedlings subjected to PEG-induced stress was systematically analyzed to study the drought-related response at the cellular level. We identified five major cell types using known marker genes and constructed a wheat leaf cell atlas. On this foundation, several potential specific marker genes for each cell type were identified, which provide a reference for further cell type annotation. Moreover, we identified cellular heterogeneity in the drought-related response mechanisms and regulatory networks among cell types. Specifically, the drought response of mesophyll cells was correlated with the photosynthetic pathway. Pseudotime trajectory analysis revealed the transition of epidermal cells from their normal function to a defense response under stress. Moreover, we also characterized the genes associated with the drought response. Notably, we identified two transcription factors (TraesCS1D02G223600 and TraesCS1D02G072900) as master regulators in most cell types. Our study provides detailed insights into the response heterogeneity of cells under PEG-induced stress. The gene resources obtained in our study could be applied to breed better crop plants with improved drought tolerance.

Single-cell multiome reveals root hair-specific responses to salt stress

Soil salinization, exacerbated by environmental deterioration and improper cultivation, is a major challenge for sustainable agriculture. The root is the primary organ in plants to perceive and respond to salt stress. Utilizing single-cell sequencing, we have created the first single-cell transcriptional and chromatin accessibility landscape for normal and salt-stressed root tips in non-heading Chinese cabbage (NHCC). Our study reveals that salt stress disrupts the normal differentiation of root hairs, leaving many in an undifferentiated state and preventing stress response gene expression. Inter-species analyses show that both salt and osmotic stresses inhibit root hair differentiation and elongation similarly, resulting in fewer, malfunctioning root hairs. We found that high salinity affects root hair iron transport. Salt stress-responsive genes, cell type-specific transcriptional regulatory networks, and trajectory curves are linked to iron transport. Specifically, the expression of BcIRT2, a metal transporter gene, is influenced by salt stress. Silencing BcIRT2 causes chlorotic leaves and increases salt sensitivity, reducing iron content in NHCC roots. Our findings offer significant insights into plant salt stress responses and provide valuable information for breeding salt-tolerant NHCC and other crops.

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.

High-quality genomes of Bombax ceiba and Ceiba pentandra provide insights into the evolution of Malvaceae species and differences in their natural fiber development

Members of the Malvaceae family, including Corchorus spp., Gossypium spp., Bombax spp., and Ceiba spp., are important sources of natural fibers. In the past decade, the genomes of several Malvaceae species have been assembled; however, the evolutionary history of Malvaceae species and the differences in their fiber development remain to be clarified. Here, we report the genome assembly and annotation of two natural fiber plants from the Malvaceae, Bombax ceiba and Ceiba pentandra, whose assembled genome sizes are 783.56 Mb and 1575.47 Mb, respectively. Comparative analysis revealed that whole-genome duplication and Gypsy long terminal repeat retroelements have been the major causes of differences in chromosome number (2n = 14 to 2n = 96) and genome size (234 Mb to 2676 Mb) among Malvaceae species. We also used comparative genomic analyses to reconstruct the ancestral Malvaceae karyotype with 11 proto-chromosomes, providing new insights into the evolutionary trajectories of Malvaceae species. MYB-MIXTA-like 3 is relatively conserved among the Malvaceae and functions in fiber cell-fate determination in the epidermis. It appears to perform this function in any tissue where it is expressed, i.e. in fibers on the endocarp of B. ceiba and in ovule fibers of cotton. We identified a structural variation in a cellulose synthase gene and a higher copy number of cellulose synthase-like genes as possible causes of the finer, less spinnable, weaker fibers of B. ceiba. Our study provides two high-quality genomes of natural fiber plants and offers insights into the evolution of Malvaceae species and differences in their natural fiber formation and development through multi-omics analysis.

Application and prospects of single-cell and spatial omics technologies in woody plants

Over the past decade, high-throughput sequencing and high-resolution single-cell transcriptome sequencing technologies have undergone rapid development, leading to significant breakthroughs. Traditional molecular biology methods are limited in their ability to unravel cellular-level heterogeneity within woody plant tissues. Consequently, techniques such as single-cell transcriptomics, single-cell epigenetics, and spatial transcriptomics are rapidly gaining popularity in the study of woody plants. In this review, we provide a comprehensive overview of the development of these technologies, with a focus on their applications and the challenges they present in single-cell transcriptome research in woody plants. In particular, we delve into the similarities and differences among the results of current studies and analyze the reasons behind these differences. Furthermore, we put forth potential solutions to overcome the challenges encountered in single-cell transcriptome applications in woody plants. Finally, we discuss the application directions of these techniques to address key challenges in woody plant research in the future.

Application of single-cell multi-omics approaches in horticulture research

Cell heterogeneity shapes the morphology and function of various tissues and organs in multicellular organisms. Elucidation of the differences among cells and the mechanism of intercellular regulation is essential for an in-depth understanding of the developmental process. In recent years, the rapid development of high-throughput single-cell transcriptome sequencing technologies has influenced the study of plant developmental biology. Additionally, the accuracy and sensitivity of tools used to study the epigenome and metabolome have significantly increased, thus enabling multi-omics analysis at single-cell resolution. Here, we summarize the currently available single-cell multi-omics approaches and their recent applications in plant research, review the single-cell based studies in fruit, vegetable, and ornamental crops, and discuss the potential of such approaches in future horticulture research.