Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration

<jats:title>Abstract</jats:title><jats:p>Salamanders exhibit an extraordinary ability among vertebrates to regenerate complex body parts. However, scarce genomic resources have limited our understanding of regeneration in adult salamanders. Here, we present the ~20 Gb genome and transcriptome of the Iberian ribbed newt <jats:italic>Pleurodeles waltl</jats:italic>, a tractable species suitable for laboratory research. We find that embryonic stem cell-specific miRNAs mir-93b and mir-427/430/302, as well as Harbinger DNA transposons carrying the <jats:italic>Myb</jats:italic>-like proto-oncogene have expanded dramatically in the <jats:italic>Pleurodeles</jats:italic><jats:italic>waltl</jats:italic> genome and are co-expressed during limb regeneration. Moreover, we find that a family of salamander methyltransferases is expressed specifically in adult appendages. Using CRISPR/Cas9 technology to perturb transcription factors, we demonstrate that, unlike the axolotl, <jats:italic>Pax3</jats:italic> is present and necessary for development and that contrary to mammals, muscle regeneration is normal without functional <jats:italic>Pax7</jats:italic> gene. Our data provide a foundation for comparative genomic studies that generate models for the uneven distribution of regenerative capacities among vertebrates.</jats:p>