Hydra Genome Code from Emergence of form in embryogenesis

The development of form in an embryo is the result of a series of topological and informational symmetry breakings. We introduce the vector–reaction-diffusion–drift (VRDD) system where the limit cycle of spatial dynamics is morphogen concentrations with Dirac delta-type distributions. This is fundamentally different from Turing reaction–diffusion system, as VRDD generates system-wide broken symmetry. We developed ‘Fundamental Forms’ from spherical blastula with a single organizing axis (rotational symmetry), double axis (mirror symmetry) and triple axis (no symmetry operator in three dimensions). We then introduced dynamics for cell differentiation, where genetic regulatory states are modelled as a finite-state machine (FSM). The state-switching of FSM is based on local morphogen concentrations as epigenetic information that changes dynamically. We grow complicated forms hierarchically in spatial subdomains using the FSM model coupled with VRDD system. Using our integrated simulation model with four layers (topological, physical, chemical and regulatory), we generated life-like forms such as hydra. Genotype–phenotype mapping was investigated with continuous and jump mutations. Our study can have applications in morphogenetic engineering, soft robotics and biomimetic design