Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration
Newts have large genomes harboring many repeat elements. How these elements shape the genome and relate to newts' unique regeneration ability remains unknown. We present here the chromosome-scale assembly of the 20.3 Gb genome of the Iberian ribbed newt, Pleurodeles waltl, with a hitherto unprecedented contiguity and completeness among giant genomes. Utilizing this assembly, we demonstrate conserved synteny as well as genetic rearrangements, such as in the major histocompatibility complex locus. We provide evidence suggesting that intronic repeat elements drive newt-specific circular RNA (circRNA) biogenesis and show their regeneration-specific expression. We also present a comprehensive in-depth annotation and chromosomal mapping of microRNAs, highlighting genomic expansion profiles as well as a distinct regulatory pattern in the regenerating limb. These data reveal links between repeat elements, non-coding RNAs, and adult regeneration and provide key resources for addressing developmental, regenerative, and evolutionary principles.
Authors
- Miyuki Suzuki (ORCID: https://orcid.org/0000-0002-7284-7505)
- Marc R. Friedländer (ORCID: https://orcid.org/0000-0001-6577-4363)
- Toshinori Hayashi (ORCID: https://orcid.org/0000-0003-3676-5710)
- Ketan Mishra (ORCID: https://orcid.org/0000-0001-6175-6643)
- Atsushi Toyoda (ORCID: https://orcid.org/0000-0002-0728-7548)
- Ekaterina Osipova (ORCID: https://orcid.org/0000-0002-6769-7223)
- Ahmed Elewa (ORCID: https://orcid.org/0000-0002-1988-7970)
- Kenichi Suzuki (ORCID: https://orcid.org/0000-0002-4502-831X)
- Tom Brown (ORCID: https://orcid.org/0000-0001-8293-4816)
- András Simon (ORCID: https://orcid.org/0000-0002-1018-1891)
- A. Petzold (ORCID: https://orcid.org/0000-0001-9599-8632)
- Bastian Fromm (ORCID: https://orcid.org/0000-0003-0352-3037)
- Nicholas D. Leigh (ORCID: https://orcid.org/0000-0002-6978-6254)
- Svetlana Iarovenko (ORCID: https://orcid.org/0000-0002-5759-6496)
- Elaiyaraja Subramanian
- Alberto Joven (ORCID: https://orcid.org/0000-0002-0926-4665)
- Maximina H. Yun (ORCID: https://orcid.org/0000-0001-9019-2453)
- Catarina R. Oliveira (ORCID: https://orcid.org/0000-0003-3595-9329)
- Lennart Rikk
Institutions
- National Institute of Genetics (JP)
- Hiroshima University (JP)
- Augsburg University (US)
- California Institute of Technology (US)
- National Institute for Basic Biology (JP)
- Lund University (SE)
- Karolinska Institutet (SE)
- Centre for Arctic Gas Hydrate, Environment and Climate (NO)
- LOEWE Centre for Translational Biodiversity Genomics (DE)
- Wenner-Gren Foundations (SE)
- Center for Systems Biology Dresden (DE)
- Max Planck Institute of Molecular Cell Biology and Genetics (DE)
- UiT The Arctic University of Norway (NO)
- Technische Universität Dresden (DE)
Publication Details
- Journal
- Cell Genomics
- Published
- 2025-01-27
- DOI
- https://doi.org/10.1016/j.xgen.2025.100761
- Citations
- 20
- Primary Topic
- RNA Research and Splicing
- Type
- article
- Field-Weighted Citation Impact
- 15.31
Funders
- European Resuscitation Council
- Deutsche Forschungsgemeinschaft
- Cancerfonden
- Technische Universität Dresden
- Karolinska Institutet
- Knut och Alice Wallenbergs Stiftelse
- Vetenskapsrådet
- Zentrum für Regenerative Therapien Dresden
- Science for Life Laboratory
- Japan Society for the Promotion of Science
- Uppsala Multidisciplinary Center for Advanced Computational Science
- Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden