Single cell atlas of Medicago sativa seedlings

Eukaryotic cellular functions are driven by specific gene expression programs, and inherent heterogeneity exists among distinct cell types. Recent advances in single-cell genomics allow us to explore the transcriptional dynamics of developmental processes and highly heterogeneous cell populations. Here, we present the first single-cell transcriptomic atlas of the world's most important forage crop, Medicago sativa, during seedling establishment. We identified novel marker genes defining distinct cell populations. By profiling RNA expression in 61,013 cells from young leaves, shoot apices, and root tips, we inferred transcription factors and gene expression dynamics associated with cell fate decisions, and delineated developmental trajectories and gene regulatory networks in specific cell types.