A unified cell atlas of vascular plants reveals cell-type foundational genes and accelerates gene discovery

Abstract

The pace of gene discovery in plants has slowed as forward genetic screens reach saturation. To address this, we built a unified single-cell atlas of shoot apices from six vascular plant species spanning major evolutionary groups. This cross-species resource allowed us to identify a core set of cell-type foundational genes linked to key tissues such as the epidermis, xylem, and phloem, streamlining gene discovery with greater accuracy. Among these, we uncovered a previously unrecognized clade of X8 domain proteins and JULGI-LIKE as regulators of phloem development. We also identified companion-cell-like cells in ferns and gymnosperms that cannot be distinguished by conventional histological methods and developed an automated cell-type annotation tool for vascular plant cell types, expanding the utility of our approach. Our findings establish a high-resolution framework for identifying key regulators of plant cell types and set an innovative paradigm for studying plant cell-type evolution.

Keywords: cell type; cell-type foundational gene; cross-species analysis; evo-devo; gene discovery; phloem; plant cell atlas; scRNA-seq; vascular plants.