Transcriptome age of embryo development and regeneration in axolotl

Tracing the evolutionary origin of genes in organisms offers valuable insights into the ontogenetic progression and developmental process. Combination of phylostratigraphy analysis with stage-specific gene expression data can revealed the evolutionary age of transcriptome. The transcriptome age index (TAI) is a measurement that has been applied to embryonic developmental process of several species. Phylostratigraphy analysis offers an evolutionary perspective to explore the age of genes in various species. Throughout the course of evolution, new genes gradually evolve indispensable roles in fundamental biological processes. However, the transcriptome age of genes and the significant role of new genes in tissue regeneration, also the relationship with embryogenesis remain unexplored. Here, we used axolotl (Ambystoma mexicanum), a species renowned for its remarkable regenerative capacity, to trace the phylogenetic age of genes and categorize them into 18 phylostratas corresponding to different taxonomies. By analyzing bulk transcriptomic data, we observed an hourglass model throughout axolotl embryonic development, with the gastrula phase representing the phylotypic stage characterized by the oldest transcriptome. In addition, phylostratigraphy analysis identified 324 axolotl lineage-specific new genes, which have been partly recruited into co-expression networks associated with DNA damage response biological process. Furthermore, analysis of single-cell transcriptome data revealed that the pattern of limb regeneration recapitulated the developmental hourglass model. Taken the single-cell transcriptome data of limb and telencephalon regeneration together, we found that the cell types with lower differentiation potency expressed younger transcriptomes and vice versa. Finally, we observed that the majority of newly evolved genes demonstrated cell type- and stage-specific expression patterns in axolotls, suggesting their potential contribution to evolution and regeneration processes. These results greatly expand our understanding for new gene evolution in regeneration and phenotypic evolution in general.