Chia-Chen Chu

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.