Developmental single-cell transcriptomics in the Lytechinus variegatus sea urchin embryo

• DOI: 10.1242/dev.198614
• Publication Date: 2021-08-31T13:35:33Z
• Authors: Abdull J. Massri; Laura Greenstreet; Anton Afanassiev; Alejandro Berrio; Gregory A. Wray; Geoffrey Schiebinger; David R. McClay
• Keywords: Lytechinus variegatus; Developmental Biology; Germ layer; Cleavage (geology)

Using scRNA-seq coupled with computational approaches, we studied transcriptional changes in cell states of sea urchin embryos during development to the larval stage. Eighteen closely spaced time points were taken first 24 h Lytechinus variegatus (Lv). Developmental trajectories constructed using Waddington-OT, a approach 'stitch' together developmental points. Skeletogenic and primordial germ diverged early cleavage. Ectodermal progenitors distinct from other lineages by 6th cleavage, although small percentage ectoderm cells briefly co-expressed endoderm markers that indicated an ecto-endoderm state, likely originating equatorial region egg. Endomesoderm also originated at cleavage this state persisted for more than two cleavages, then into mesoderm fates asynchronously, some retaining intermediate specification status until gastrulation. Seventy-nine out 80 genes (99%) examined, included published gene regulatory networks (dGRNs), are present Lv-scRNA-seq dataset expressed correct which dGRN circuits operate.