The inbred newt genome unveils molecular mechanisms of behavior, development, and regeneration in urodele amphibians

Salamanders provide excellent models for studying vertebrate evolution, development, and regeneration. To further advance the newt as a model organism in biology, we conducted draft genome sequencing of 20 Gb of an inbred newt (Pleurodeles waltl). As part of this study, the Hoxd11–d13 intergenic region is expanded by over 1 Mb owing to the massive insertion of repetitive sequences including newt-specific satellite DNA. Interestingly, Myod and Bmp4, genes that are typically involved in vertebrate development, are absent in salamanders. Co-option of Sodefrin Precursor-like Factor genes, which encode sex pheromone ligands, suggests a diversification of reproductive behavior among salamanders. Moreover, a limb enhancer of Shh, MFCS1/ZRS, retains its function, even though it is positioned approximately 5 Mb away from the promoter. Furthermore, we have identified a functional cis-element potentially associated with limb regeneration in this enhancer. The newt genome yields crucial insights into amphibian evolution, behavior, development, and regeneration.