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The axolotl genome and the evolution of key tissue formation regulators

Author

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  • Sergej Nowoshilow

    (Max Planck Institute of Molecular Cell Biology and Genetics
    Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)
    DFG Research Center for Regenerative Therapies, Technische Universität Dresden
    Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC))

  • 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
    Deep Sequencing Group, Biotechnology Center (Biotec) 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
    Max Planck Institute for the Physics of Complex Systems
    Center for Systems Biology)

  • 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
    Max Planck Institute for the Physics of Complex Systems
    Center for Systems Biology)

  • Elly M. Tanaka

    (Max Planck Institute of Molecular Cell Biology and Genetics
    Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)
    DFG Research Center for Regenerative Therapies, Technische Universität Dresden
    Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC))

  • Eugene W. Myers

    (Max Planck Institute of Molecular Cell Biology and Genetics
    Center for Systems Biology)

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.

Suggested Citation

  • 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, 2018. "The axolotl genome and the evolution of key tissue formation regulators," Nature, Nature, vol. 554(7690), pages 50-55, February.
    • Handle: RePEc:nat:nature:v:554:y:2018:i:7690:d:10.1038_nature25458
    DOI: 10.1038/nature25458
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    Citations

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    Cited by:

    1. Jessen V. Bredeson & Austin B. Mudd & Sofia Medina-Ruiz & Therese Mitros & Owen Kabnick Smith & Kelly E. Miller & Jessica B. Lyons & Sanjit S. Batra & Joseph Park & Kodiak C. Berkoff & Christopher Plo, 2024. "Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    2. Peng Liu & Jessica Ewald & Zhiqiang Pang & Elena Legrand & Yeon Seon Jeon & Jonathan Sangiovanni & Orcun Hacariz & Guangyan Zhou & Jessica A. Head & Niladri Basu & Jianguo Xia, 2023. "ExpressAnalyst: A unified platform for RNA-sequencing analysis in non-model species," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    3. Yenny Villuendas-Rey & José L. Velázquez-Rodríguez & Mariana Dayanara Alanis-Tamez & Marco-Antonio Moreno-Ibarra & Cornelio Yáñez-Márquez, 2021. "Mexican Axolotl Optimization: A Novel Bioinspired Heuristic," Mathematics, MDPI, vol. 9(7), pages 1-20, April.
    4. Adriana Arneson & Amin Haghani & Michael J. Thompson & Matteo Pellegrini & Soo Bin Kwon & Ha Vu & Emily Maciejewski & Mingjia Yao & Caesar Z. Li & Ake T. Lu & Marco Morselli & Liudmilla Rubbi & Bret B, 2022. "A mammalian methylation array for profiling methylation levels at conserved sequences," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    5. Fang Ye & Guodong Zhang & Weigao E. & Haide Chen & Chengxuan Yu & Lei Yang & Yuting Fu & Jiaqi Li & Sulei Fu & Zhongyi Sun & Lijiang Fei & Qile Guo & Jingjing Wang & Yanyu Xiao & Xinru Wang & Peijing , 2022. "Construction of the axolotl cell landscape using combinatorial hybridization sequencing at single-cell resolution," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    6. Cassie L. Kemmler & Jana Smolikova & Hannah R. Moran & Brandon J. Mannion & Dunja Knapp & Fabian Lim & Anna Czarkwiani & Viviana Hermosilla Aguayo & Vincent Rapp & Olivia E. Fitch & Seraina Bötschi & , 2023. "Conserved enhancers control notochord expression of vertebrate Brachyury," Nature Communications, Nature, vol. 14(1), pages 1-18, December.

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