MorphoSeq: Full Single-Cell Transcriptome Dynamics Up to Gastrulation in a Chordate

Single-cell RNA sequencing (scRNA-seq) provides a leap forward in resolving cellular diversity and developmental trajectories but fails to comprehensively delineate the spatial organization and precise cellular makeup of individual embryos. Here, we reconstruct from scRNA-seq and light sheet imaging data a canonical digital embryo that captures the genome-wide gene expression trajectory of every single cell at every cell division in the 18 lineages up to gastrulation in the ascidian Phallusia mammillata. By using high-coverage scRNA-seq, we devise a computational framework that stratifies single cells of individual embryos into cell types without prior knowledge. Unbiased transcriptome data analysis mapped each cell’s physical position and lineage history, yielding the complete history of gene expression at the genome-wide level for every single cell in a developing embryo. A comparison of individual embryos reveals both extensive reproducibility between symmetric embryo sides and a large inter-embryonic variability due to small differences in embryogenesis timing. [Display omitted] •Integration of scRNA-seq and imaging data yield a canonical digital embryo•Cell type classification without prior knowledge•De novo reconstruction of the lineage history and spatial organization of the embryo•Timing differences contribute to inter-embryo variability in gene expression The complete gene expression history and physical position of every single cell at every cell division in an embryo up to gastrulation is reconstructed using a combination of single-cell transcriptomics and light sheet imaging.