Single-cell reconstruction of developmental trajectories across amphioxus embryogenesis reveals neural system regionalization along the anterior-posterior axis

Amphioxus is an invertebrate chordate that is phylogenetically well positioned for advancing our understanding of vertebrate evolution. Here we report the development of single-cell RNA-sequencing (scRNA-seq) data from seven amphioxus embryo stages from the blastula to late neurula stages. We also deployed scRNA-seq in an experimental framework to compare Brachyury double knock-out and wild type embryos. This demonstrated that Brachyury is essential for balancing posterior neural and mesodermal cell fate decisions and we provide evidence for the presence of neuromesodermal progenitor cells in amphioxus. We suggest that the evolution of these in a stem chordate led to a dramatic shift in posterior neural and mesodermal cell fate decisions and the body elongation that is part of the chordate body plan.