Evolutionary flexibility in the maternal-to-zygotic transition reveals alternative routes to embryogenesis across eukaryotes

SUMMARY The maternal-to-zygotic transition (MZT), during which developmental control shifts from maternal products to the zygotic genome, is a fundamental feature of embryogenesis. The prevailing model, established from animal systems, holds that maternal provisioning and nuclear-to-cytoplasmic (N/C) ratio determine the timing of zygotic genome activation (ZGA). Whether this developmental logic is conserved across multicellular eukaryotes remains unknown. Using brown algae, an independently evolved multicellular lineage spanning broad natural variation in maternal provisioning, we generated comparative embryonic transcriptomes across three species and resolved parental contributions through reciprocal crosses and allele-specific expression. Contrary to canonical animal models, all species activated their zygotic genomes immediately after fertilisation, including highly provisioned species with low N/C ratios, and showed no evidence of stable parental imprinting. These findings reveal that timing and regulation of MZT during embryogenesis is evolutionarily flexible and independently shaped across the tree of life.