snRNA-seq analysis of the moss Physcomitrium patens identifies a conserved cytokinin-ESR module promoting pluripotent stem cell identity
Yuki Hata, Nicola Hetherington, Kai Battenberg, Atsuko Hirota, Aki Minoda, Makoto Hayashi, Junko Kyozuka
Abstract
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. • Gene expression profiles in a moss meristem are identified at a single-cell resolution • Cytokinin biosynthesis is specifically activated in a stem cell of the moss meristem • Cytokinin-ESR is a conserved module promoting stem cell identity in land plants • Expressions of auxin response genes are high during organ/tissue differentiation Pluripotent stem cells in the apical meristem have been a key innovation that allows plants to flourish. Hata et al. identified transcriptomic characters of a pluripotent stem cell in Physcomitrium patens using single-nucleus RNA sequencing and found a conserved cytokinin-ESR module promoting pluripotent stem cell identity in land plants.