Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer

The germ layer concept has been one of the foremost organizing principles in developmental biology, classification, systematics and evolution for 150 years(1-3). Of the three germ layers, the mesoderm is found in bilaterian animals but is absent in species in the phyla Cnidaria and Ctenophora, which has been taken as evidence that the mesoderm was the final germ layer to evolve(1,4,5). The origin of the ectoderm and endoderm germ layers, however, remains unclear with models supporting the antecedence of each as well as a simultaneous origin(4,6-9). Here, we determine the temporal and spatial components of gene expression spanning embryonic development for all Caenorhabditis elegans genes and use it to determine the evolutionary ages of the germ layers. The gene expression program of the mesoderm is induced after those of the ectoderm and endoderm, thus making it the last germ layer to both evolve and develop. Strikingly, the C. elegans endoderm and ectoderm expression programs do not co-induce; rather the endoderm activates earlier, and this is observed also in the expression of endoderm orthologs during the embryology of Xenopus tropicalis, Nematostella vectensis, and the sponge Amphimedon queenslandica. Querying for the phylogenetic ages of specifically expressed genes revealed that the endoderm is comprised of older genes. Taken together, we propose that the endoderm program dates back to the origin of multicellularity, while the ectoderm originated as a secondary germ layer freed from ancestral feeding functions.