Distinct gene expression dynamics in developing and regenerating crustacean limbs

Regenerating animals have the ability to reproduce body parts that were originally made in the embryo and subsequently lost due to injury. Understanding whether the process of regeneration mirrors development is an open question in most regenerative species. Here we take a transcriptomics approach to examine to what extent leg regeneration shows the same temporal patterns of gene expression as leg development in the embryo, in the crustacean Parhyale hawaiensis. We find that leg development in the embryo shows stereotypic temporal patterns of gene expression. In contrast, global patterns of gene expression during leg regeneration show a high degree of variation, related to the physiology of individual animals. A major driver of this variation is the molting cycle. After dissecting the transcriptional signals of individual physiology from regeneration, we obtain temporal signals that mark distinct phases of leg regeneration. Comparing the transcriptional dynamics of development and regeneration we find that, although both processes use largely the same genes, the temporal patterns in which these gene sets are deployed are different and cannot be systematically aligned. Overall design: Regeneration Dataset (Rd); Regeneration dataset (Rp); Development dataset (Ef and Ed): 212 mRNAseq leg samples during time courses of development or regeneration in the Crustacean Parhyale hawaiensis: 70 samples were collected during development, 60 limbs were amputated and the most-distal and moore proximal parts of the leg were collected separately throughout regeneration, for a total of 120 samples (60 samples corresponding to the regenerating most-distal part of the leg, as well as the 60 samples corresponding to the non-regenerating most distal part of the leg). 20 entire legs were collected at different moments of the molting cycle. Finally two entire legs were also collected, with to tracking of their molting stage, for the purpose of genome annotation.