snRNA-seq analysis of the moss Physcomitrium patens identifies a conserved cytokinin-ESR module promoting pluripotent stem cell identity

The shoot apical meristem (SAM), which contains pluripotent stem cells, serves as the source of the entire shoot system in land plants. To find the mechanisms underlying SAM development and its origin, we employed single-nucleus RNA sequencing technology in Physcomitrium patens, which contains a single stem cell known as the gametophore apical cell. We identified distinct cell clusters representing major cell types of the P. patens gametophyte, including the gametophore apical cells. We showed dynamic gene expression changes during cell fate progression in the gametophore apical cell and found upregulation of cytokinin biosynthesis genes in this cell. We also identified ENHANCER OF SHOOT REGENERATION 1 (ESR1) orthologs as important regulators of gametophore apical cells downstream of cytokinin. Given that ESRs promote SAM formation under cytokinin in angiosperms, we propose that the cytokinin-ESR module represents a conserved mechanism promoting stem cell identity that evolved in the common ancestor of land plants.