An Arabidopsis single-nucleus atlas decodes leaf senescence and nutrient allocation

With rapid advancements in single-cell RNA sequencing (scRNA-seq) technologies, exploration of the systemic coordination of critical physiological processes has entered a new era. Here, we generated a comprehensive Arabidopsis single-nucleus transcriptomic atlas using over 1 million nuclei from 20 tissues encompassing multiple developmental stages. Our analyses identified cell types that have not been characterized in previous single-protoplast studies and revealed cell-type conservation and specificity across different organs. Through time-resolved sampling, we revealed highly coordinated onset and progression of senescence among the major leaf cell types. We originally formulated two molecular indexes to quantify the aging state of leaf cells at single-cell resolution. Additionally, facilitated by weighted gene co-expression network analysis, we identified hundreds of promising hub genes that may integratively regulate leaf senescence. Inspired by the functional validation of identified hub genes, we built a systemic scenario of carbon and nitrogen allocation among different cell types from source leaves to sink organs.