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

Ahmed Elewa (), Heng Wang, Carlos Talavera-López, Alberto Joven, Gonçalo Brito, Anoop Kumar, L. Shahul Hameed, May Penrad-Mobayed, Zeyu Yao, Neda Zamani, Yamen Abbas, Ilgar Abdullayev, Rickard Sandberg, Manfred Grabherr, Björn Andersson and András Simon ()
Additional contact information
Ahmed Elewa: Karolinska Institute
Heng Wang: Huazhong Agricultural University
Carlos Talavera-López: Karolinska Institute
Alberto Joven: Karolinska Institute
Gonçalo Brito: Karolinska Institute
Anoop Kumar: Karolinska Institute
L. Shahul Hameed: Karolinska Institute
May Penrad-Mobayed: CNRS & University Paris-Diderot
Zeyu Yao: Karolinska Institute
Neda Zamani: Uppsala University
Yamen Abbas: Harvard Stem Cell Institute, Harvard University
Ilgar Abdullayev: Karolinska Institute
Rickard Sandberg: Karolinska Institute
Manfred Grabherr: Uppsala University
Björn Andersson: Karolinska Institute
András Simon: Karolinska Institute

Nature Communications, 2017, vol. 8, issue 1, 1-9

Abstract: Abstract 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 Pleurodeles waltl, 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 Myb-like proto-oncogene have expanded dramatically in the Pleurodeles waltl 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, Pax3 is present and necessary for development and that contrary to mammals, muscle regeneration is normal without functional Pax7 gene. Our data provide a foundation for comparative genomic studies that generate models for the uneven distribution of regenerative capacities among vertebrates.

Date: 2017
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DOI: 10.1038/s41467-017-01964-9

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