Early transcriptional similarities between two distinct neural lineages during ascidian embryogenesis

In chordates, the central nervous system arises from precursors that have distinct developmental and transcriptional trajectories. Anterior nervous system is ontogenically associated with ectoderm lineages while posterior nervous systems are associated with mesoderm. Taking advantage of the well-documented cell lineage of ascidian embryos, we addressed how early similarities in the transcriptional states of the different neural lineages become apparent. We performed single-cell RNA sequencing (scRNA-seq) analyses of hand-dissected neural precursor cells of these lineages, together with those of their sister cell lineages, with a high temporal resolution covering five successive cell cycles from 16-cell to neural plate stages. A transcription factor binding site enrichment analysis of neural specific genes at the neural plate stage revealed limited evidence for shared transcriptional control between the two neural lineages, consistent with their different ontogenies. Nevertheless, PCA analysis and hierarchical clustering showed that, by neural plate stages, the two neural lineages cluster together. Consistent with this, we identified a set of genes enriched in both neural lineages at the neural plate stage. Hand-dissected single-cell neural lineage precursors between 16-cell stage and neural plate (at least 6 replicates per cell type) Please note that the sample characteristics 'cell type' is based on the nomenclature of Conklin: "The organization and cell-lineage of the ascidian egg". J. Acad. Nat. Sci. Phila. 1905;13:1–119.