The giant axolotl genome uncovers the evolution, scaling, and transcriptional control of complex gene loci

Siegfried Schloissnig; Akane Kawaguchi; Sergej Nowoshilow; Francisco Falcon; Leo Otsuki; Pietro Tardivo; Nataliya Timoshevskaya; Melissa C. Keinath; Jeramiah James Smith; S. Randal Voss; Elly M. Tanaka

doi:10.1073/pnas.2017176118

The giant axolotl genome uncovers the evolution, scaling, and transcriptional control of complex gene loci

Siegfried Schloissnig, Akane Kawaguchi, Sergej Nowoshilow, Francisco Falcon, Leo Otsuki, Pietro Tardivo, Nataliya Timoshevskaya, Melissa C. Keinath, Jeramiah James Smith, S. Randal Voss, Elly M. Tanaka

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52 Scopus citations

Abstract

Vertebrates harbor recognizably orthologous gene complements but vary 100-fold in genome size. How chromosomal organization scales with genome expansion is unclear, and how acute changes in gene regulation, as during axolotl limb regeneration, occur in the context of a vast genome has remained a riddle. Here, we describe the chromosome-scale assembly of the giant, 32 Gb axolotl genome. Hi-C contact data revealed the scaling properties of interphase and mitotic chromosome organization. Analysis of the assembly yielded understanding of the evolution of large, syntenic multigene clusters, including the Major Histocompatibility Complex (MHC) and the functional regulatory landscape of the Fibroblast Growth Factor 8 (Axfgf8) region. The axolotl serves as a primary model for studying successful regeneration.

Original language	English
Article number	e2017176118
Journal	Proceedings of the National Academy of Sciences of the United States of America
Volume	118
Issue number	15
DOIs	https://doi.org/10.1073/pnas.2017176118
State	Published - Apr 13 2021

Bibliographical note

Publisher Copyright:
© This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).

Funding

We thank the Institute of Molecular Pathology (IMP) axolotl caretakers for their dedicated work. We are grateful to Alex Schleiffer, Roman Stocsits, Oleg Simakov, Jim Kaufman, and Anton Goloborodko for sharing the data, help with the analyses and advice, and Gordana Wutz, Yuka Taniguchi-Sugiura, Alex Vogt, and the VBCF NGS as well as the IMP IT department for advice and assistance. We thank Meinrad Busslinger for reading part of the manuscript. E.M.T. was supported by core funding from the IMP and ERC AdG 742046, RegGeneMems. A.K. was supported by a JSPS Postdoctoral Fellowship for Overseas Researchers. L.O. was supported by a fellowship from the HFSP. N.T., M.C.K., J.J.S., and S.R.V. were supported by NIH R24OD010435 and P40OD019794, and ARO W911NF1810168. ACKNOWLEDGMENTS. We thank the Institute of Molecular Pathology (IMP) axolotl caretakers for their dedicated work. We are grateful to Alex Schleiffer, Roman Stocsits, Oleg Simakov, Jim Kaufman, and Anton Golobor-odko for sharing the data, help with the analyses and advice, and Gordana Wutz, Yuka Taniguchi-Sugiura, Alex Vogt, and the VBCF NGS as well as the IMP IT department for advice and assistance. We thank Meinrad Busslinger for reading part of the manuscript. E.M.T. was supported by core funding from the IMP and ERC AdG 742046, RegGeneMems. A.K. was supported by a JSPS Postdoctoral Fellowship for Overseas Researchers. L.O. was supported by a fellowship from the HFSP. N.T., M.C.K., J.J.S., and S.R.V. were supported by NIH R24OD010435 and P40OD019794, and ARO W911NF1810168.

Funders	Funder number
Institute of Molecular Pathology
VBCF
National Institutes of Health (NIH)	ARO W911NF1810168, P40OD019794
NIH Office of the Director	R24OD010435
National Council for Eurasian and East European Research	742046
International Human Frontier Science Program Organization
Japan Society for the Promotion of Science
Instituto Mexicano del Petróleo

Keywords

Axolotl
Genome assembly
Regeneration
Topological associating domains

ASJC Scopus subject areas

General

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10.1073/pnas.2017176118

Cite this

Schloissnig, S., Kawaguchi, A., Nowoshilow, S., Falcon, F., Otsuki, L., Tardivo, P., Timoshevskaya, N., Keinath, M. C., Smith, J. J., Voss, S. R., & Tanaka, E. M. (2021). The giant axolotl genome uncovers the evolution, scaling, and transcriptional control of complex gene loci. Proceedings of the National Academy of Sciences of the United States of America, 118(15), Article e2017176118. https://doi.org/10.1073/pnas.2017176118

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abstract = "Vertebrates harbor recognizably orthologous gene complements but vary 100-fold in genome size. How chromosomal organization scales with genome expansion is unclear, and how acute changes in gene regulation, as during axolotl limb regeneration, occur in the context of a vast genome has remained a riddle. Here, we describe the chromosome-scale assembly of the giant, 32 Gb axolotl genome. Hi-C contact data revealed the scaling properties of interphase and mitotic chromosome organization. Analysis of the assembly yielded understanding of the evolution of large, syntenic multigene clusters, including the Major Histocompatibility Complex (MHC) and the functional regulatory landscape of the Fibroblast Growth Factor 8 (Axfgf8) region. The axolotl serves as a primary model for studying successful regeneration.",

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Schloissnig, S, Kawaguchi, A, Nowoshilow, S, Falcon, F, Otsuki, L, Tardivo, P, Timoshevskaya, N, Keinath, MC, Smith, JJ , Voss, SR & Tanaka, EM 2021, 'The giant axolotl genome uncovers the evolution, scaling, and transcriptional control of complex gene loci', Proceedings of the National Academy of Sciences of the United States of America, vol. 118, no. 15, e2017176118. https://doi.org/10.1073/pnas.2017176118

The giant axolotl genome uncovers the evolution, scaling, and transcriptional control of complex gene loci. / Schloissnig, Siegfried; Kawaguchi, Akane; Nowoshilow, Sergej et al.
In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 118, No. 15, e2017176118, 13.04.2021.

Research output: Contribution to journal › Article › peer-review

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AU - Smith, Jeramiah James

AU - Voss, S. Randal

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The giant axolotl genome uncovers the evolution, scaling, and transcriptional control of complex gene loci

Abstract

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Keywords

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