Single-cell transcriptomics reveals cellular and genetic mechanisms of alpine adaptation in <i>Rosa sericea</i>

<h4>Introduction</h4>Plant development is shaped by environmental conditions, and its adaptation to climate change is crucial for biodiversity conservation. The extreme climate of the Qinghai-Tibet Plateau makes it an ideal system for studying plant adaptive strategies. <i>Rosa sericea</i>, a dominant alpine shrub, exhibits remarkable morphological plasticity, but its molecular and cellular adaptation mechanisms are still unclear. In this study, we integrated single-nucleus RNA sequencing (snRNA-seq) with high-dimensional weighted gene co-expression network analysis (hdWGCNA), gene ontology (GO) enrichment, gene set enrichment analysis (GSEA), pseudotime trajectory inference, and gene overexpression techniques to profile 31,796 cells from <i>R. sericea</i> leaves.<h4>Methods</h4>We constructed a draft single-cell transcriptional atlas with putative annotation of 11 leaf cell types and identified eight co-expression gene modules linked to key cell types.<h4>Results</h4>The leaf development spatiotemporal dynamics uncovered a developmental continuum from cell proliferation to photosynthetically specialized maturation. Furthermore, we identified several developmental and physiological features potentially associated with high-altitude adaptation, including presence of transcriptionally active nuclear-encoded genes involved in chloroplast function in epidermal pavement cells, the potential role of SPL7-mediated copper homeostasis, and a putative <i>RO6G37307-TTG2-TCP4</i> regulatory module associated with trichome development.<h4>Discussion</h4>Together, this study provides the first single-cell-resolved transcriptional framework for <i>R. sericea</i> leaves and suggests adaptive developmental mechanisms at the cellular and genetic levels, enhancing our understanding of how alpine plants respond to climate change.