A single-cell blueprint for cellular diversity in the Green Lineage

Abstract

The Green Lineage (Viridiplantae) represents one of the most successful evolutionary radiations on Earth, with remarkable morphological diversity from unicellular algae to complex multicellular land plants. Recent advances in single-cell genomics have transformed our understanding of plant cell-type diversity and evolution, revealing fundamental principles underlying cellular organization and specification. This review synthesizes current knowledge of plant cell-type identity and evolution through the lens of single-cell approaches. We examine how plant cell types are specified through combinatorial transcription factor networks analogous to animal terminal selector systems yet operate within a fundamentally different developmental framework characterized by positional determination, extensive plasticity, and environmental responsiveness. We highlight unique features of plant cells, including plastids, large vacuoles, cell walls, and plasmodesmata, that profoundly influence cellular identity and present distinct challenges for single-cell profiling. Comparative analysis across the Green Lineage reveals that new cell types arise through subfunctionalization following gene and genome duplications, co-option of ancestral gene regulatory networks, and cis -regulatory evolution driven by transposable elements. We address major analytical challenges, including orthology assignment in polyploid genomes, cross-species dataset integration, gene regulatory network reconstruction, and functional validation in diverse plant systems. Despite these challenges, plant single-cell genomics offers unprecedented opportunities to understand cellular evolution, with implications extending from fundamental biology to agricultural innovation.