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Nature. 2018 Feb 1;554(7690):50-55. doi: 10.1038/nature25458. Epub 2018 Jan 24.

The axolotl genome and the evolution of key tissue formation regulators.

Author information

1
Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
2
Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
3
DFG Research Center for Regenerative Therapies, Technische Universität Dresden, Dresden, Germany.
4
Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.
5
Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, China.
6
Deep Sequencing Group, Biotechnology Center (Biotec) Technische Universität Dresden, Dresden, Germany.
7
Bionano Genomics, San Diego, California, USA.
8
The Francis Crick Institute, London, UK.
9
Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.
10
Center for Systems Biology, Dresden, Germany.
11
Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada, Langebio-Cinvestav, Irapuato, Mexico.
12
IBDM - Institut de Biologie du Développement de Marseille, CNRS & Aix-Marseille Université, Marseille, France.

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.

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PMID:
29364872
DOI:
10.1038/nature25458
[Indexed for MEDLINE]

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