The axolotl genome and the evolution of key tissue formation regulators

Sergej Nowoshilow, Siegfried Schloissnig (), Ji-Feng Fei, Andreas Dahl, Andy W. C. Pang, Martin Pippel, Sylke Winkler, Alex R. Hastie, George Young, Juliana G. Roscito, Francisco Falcon, Dunja Knapp, Sean Powell, Alfredo Cruz, Han Cao, Bianca Habermann, Michael Hiller (), Elly M. Tanaka () and Eugene W. Myers
Additional contact information
Sergej Nowoshilow: Max Planck Institute of Molecular Cell Biology and Genetics
Siegfried Schloissnig: Heidelberg Institute for Theoretical Studies
Ji-Feng Fei: Institute for Brain Research and Rehabilitation, South China Normal University
Andreas Dahl: DFG Research Center for Regenerative Therapies, Technische Universität Dresden
Andy W. C. Pang: Bionano Genomics, San Diego
Martin Pippel: Heidelberg Institute for Theoretical Studies
Sylke Winkler: Max Planck Institute of Molecular Cell Biology and Genetics
Alex R. Hastie: Bionano Genomics, San Diego
George Young: The Francis Crick Institute
Juliana G. Roscito: Max Planck Institute of Molecular Cell Biology and Genetics
Francisco Falcon: Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada, Langebio-Cinvestav
Dunja Knapp: DFG Research Center for Regenerative Therapies, Technische Universität Dresden
Sean Powell: Heidelberg Institute for Theoretical Studies
Alfredo Cruz: Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada, Langebio-Cinvestav
Han Cao: Bionano Genomics, San Diego
Bianca Habermann: IBDM – Institut de Biologie du Développement de Marseille, CNRS & Aix-Marseille Université
Michael Hiller: Max Planck Institute of Molecular Cell Biology and Genetics
Elly M. Tanaka: Max Planck Institute of Molecular Cell Biology and Genetics
Eugene W. Myers: Max Planck Institute of Molecular Cell Biology and Genetics

Nature, 2018, vol. 554, issue 7690, 50-55

Abstract: Abstract Salamanders serve as important tetrapod models for developmental, regeneration and evolutionary studies. An extensive molecular toolkit makes the Mexican axolotl (Ambystoma mexicanum) a key representative salamander for molecular investigations. Here we report the sequencing and assembly of the 32-gigabase-pair axolotl genome using an approach that combined long-read sequencing, optical mapping and development of a new genome assembler (MARVEL). We observed a size expansion of introns and intergenic regions, largely attributable to multiplication of long terminal repeat retroelements. We provide evidence that intron size in developmental genes is under constraint and that species-restricted genes may contribute to limb regeneration. The axolotl genome assembly does not contain the essential developmental gene Pax3. However, mutation of the axolotl Pax3 paralogue Pax7 resulted in an axolotl phenotype that was similar to those seen in Pax3−/− and Pax7−/− mutant mice. The axolotl genome provides a rich biological resource for developmental and evolutionary studies.

Date: 2018
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DOI: 10.1038/nature25458

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