Ying-Lan Chen

Summary: Plants are constantly challenged by environmental stressors, yet their sessile nature demands highly flexible developmental programs to maintain growth and survival. With the advent of single‐cell technologies, developmental plasticity can now be dissected at cellular resolution. Two recent Populus studies show that both mechanical and drought stress induce xylem remodeling by shifting cell‐type ratios or altering differentiation speed, while preserving the underlying developmental lineages. Highly similar patterns have been recently observed in Arabidopsis and cabbage, in which osmotic and salt stress alter the tempo of root hair differentiation without changing lineage identity. The recurrence of this developmental program across woody and herbaceous species, spanning distinct taxonomic orders, suggests that lineage‐stable yet flexible stress responses are evolutionarily conserved in plants. Moreover, these insights were enabled by the application of advanced single‐cell and spatially resolved approaches, with several of these studies incorporating single‐cell/nucleus transcriptomics with spatial multi‐omics analyses to link developmental dynamics with tissue context. This balance between flexibility and developmental order may represent a fundamental principle by which plants maintain resilience under diverse environmental challenges and may offer a valid framework for this field of study.

NanoPrePro is a streamlined read preprocessor specifically designed for high precision in identifying full-length reads from Oxford Nanopore Technology (ONT) transcriptomic sequencing results, achieved through the precise identification of adapters/primers. However, the preprocessing of ONT reads has been a long-term neglected and ambiguous area without thorough and systematic investigation. Here, we developed NanoPrePro that outperformed the current best preprocessor, Pychopper, using simulated and real datasets. Through sequence similarity, adapter/primer location, and adapter/primer length, NanoPrePro exerted a self-optimizing function to extract the best parameters in each sequencing file for users to customize their analyses. Furthermore, NanoPrePro shows a 38-times faster speed with less memory cost. NanoPrePro can be regarded as the state-of-the-art preprocessor with forward adaptability of ONT sequencing.

Secondary growth is a key characteristic evolved from seed plants and generates secondary xylem—the most abundant tissue on Earth. Recent studies have uncovered xylem developmental lineages in eudicots and magnoliids of angiosperms. However, xylem development in gymnosperms, the other representative clade of seed plants, remained elusive. We performed single-cell transcriptomics for xylem cells of conifers (Cunninghamia lanceolata), the major clade in gymnosperms. Using Seurat and scVI-based cross-species integration, we reconstructed the xylem differentiation trajectories and revealed that the radial system is conserved across seed plants, while the axial system in C. lanceolata exhibits a composite lineage architecture resembling both eudicots and magnoliids. To validate these trajectories, we established a multi-modal spatial framework incorporating spatial transcriptomics, spatial proteomics, and spatial metabolomics. These three spatial layers provided orthogonal evidence confirming cell-type identities and trajectory inference. Additionally, we identified a xylem cell population unique to gymnosperms, suggesting a lineage-specific specialization. Together, our findings uncover a more complex ancestral xylem architecture in gymnosperms and propose a progressive simplification of axial developmental programs from gymnosperms to angiosperms, highlighting a trajectory of reductive evolution in seed plant vascular development.

Single‐cell RNA sequencing (scRNA‐seq) has emerged as a transformative tool for decoding plant development, particularly in elucidating xylem differentiation. By capturing transcriptomic changes at single‐cell resolution, scRNA‐seq enables reconstruction of developmental trajectories across diverse plant tissues. In this review, we summarize recent advances in the application of scRNA‐seq to study both primary and secondary xylem development in monocots and eudicots. These studies have revealed distinct xylem cell types, including vessel elements, libriform fibers, and ray parenchyma cells, and provided insight into their lineage relationships. We also highlight key technical and analytical challenges that limit cross‐study comparisons, including inconsistent bioinformatic pipelines, variability in protoplasting efficiency, and the use of potentially misannotated marker genes. To address these limitations, we discuss the integration of in situ transcriptomic profiling using laser microdissection, which provides more accurate cell‐type annotation and supports the current best working model of xylem developmental lineages. Finally, we suggest future directions for improving xylem developmental studies, including deeper integration of spatial and single‐cell technologies to overcome current limitations in resolving lignified tissues and to better understand xylem responses to environmental perturbations.

Microbial biostimulants can be applied to reliably improve crop productivity and quality. One such biostimulant is 3‐methyl‐1‐butanol (3MB), a microbial volatile compound released by various plant growth‐promoting microbes, which has gained recent attention due to its ability to promote plant growth and enhance stress tolerance. Previous studies have shown that 3MB induces stomatal closure and enhances salt stress tolerance in plants; however, its mode of action in these processes remains poorly understood. In this study, 6‐day‐old Arabidopsis seedlings were fumigated with 3MB (1 mg L ⁻¹ ) for 3 days, resulting in significant transcriptomic changes compared to untreated controls. Transcriptome analysis revealed 452 differentially expressed genes (256 upregulated and 196 downregulated by 3MB), among which several ethylene (ET)‐ and jasmonate (JA)‐related genes were upregulated. Interestingly, 3MB induced stomatal closure and salt stress tolerance in wild‐type plants but not in ethylene‐responsive factor 4 (erf4) and jasmonate resistant1 (jar1‐1) mutants. A metabolomic analysis further revealed a significant increase in JA and anthocyanin contents following 3MB treatment. Together, these findings suggest that 3MB‐induced stomatal closure and salt stress tolerance are mediated by ET and JA signaling pathways in Arabidopsis, with potential involvement of anthocyanins. This study deepens our understanding of plant immune responses and highlights the potential of microbial biostimulants for sustainable crop improvement strategies.

Plant long-distance signaling peptides travel through the vascular system to coordinate development and respond to environmental cues, yet their precursor genes and expression origins remain elusive. We characterized 4,804 sap peptide precursor genes in Populus trichocarpa using an integrated approach that combined liquid chromatography tandem mass spectrometry (LC-MS/MS) peptidomics, transcriptomics, and comparative genomics. This study expands the known precursor families from approximately 50 to thousands, the majority of which are conserved across angiosperms. Transcriptome analysis across xylem developmental stages revealed that living xylem cells, typically viewed as precursors to non-living structures, predominantly express these specifically at transitions between primary and secondary growth stages, indicating an active role in plant-wide signaling coordination. The precursor genes show conservation at the transcriptome level and are under strong purifying selection. Our findings provide a comprehensive overview of the gene families encoding sap peptides, redefining xylem as an active participant in plant communication and adaptation.