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Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration

Brown, Thomas ; Mishra, Ketan ; Elewa, Ahmed ; Iarovenko, Svetlana ; Subramanian, Elaiyaraja ; Araus, Alberto Joven ; Petzold, Andreas ; Fromm, Bastian ; Friedländer, Marc R and Rikk, Lennart , et al. (2025) In Cell Genomics 5(2).
Abstract

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... (More)

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.

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organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Cell Genomics
volume
5
issue
2
article number
100761
publisher
Cell Press
external identifiers
  • pmid:39874962
  • scopus:85217502364
ISSN
2666-979X
DOI
10.1016/j.xgen.2025.100761
project
Deciphering the balance between regeneration and tumorigenesis
language
English
LU publication?
yes
additional info
Copyright © 2025 The Author(s). Published by Elsevier Inc. All rights reserved.
id
57b666d4-342c-4a09-9b38-597c5151767a
date added to LUP
2025-01-30 07:16:21
date last changed
2025-07-10 22:47:07
@article{57b666d4-342c-4a09-9b38-597c5151767a,
  abstract     = {{<p>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.</p>}},
  author       = {{Brown, Thomas and Mishra, Ketan and Elewa, Ahmed and Iarovenko, Svetlana and Subramanian, Elaiyaraja and Araus, Alberto Joven and Petzold, Andreas and Fromm, Bastian and Friedländer, Marc R and Rikk, Lennart and Suzuki, Miyuki and Suzuki, Ken-Ichi T and Hayashi, Toshinori and Toyoda, Atsushi and Oliveira, Catarina R and Osipova, Ekaterina and Leigh, Nicholas D and Yun, Maximina H and Simon, András}},
  issn         = {{2666-979X}},
  language     = {{eng}},
  number       = {{2}},
  publisher    = {{Cell Press}},
  series       = {{Cell Genomics}},
  title        = {{Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration}},
  url          = {{http://dx.doi.org/10.1016/j.xgen.2025.100761}},
  doi          = {{10.1016/j.xgen.2025.100761}},
  volume       = {{5}},
  year         = {{2025}},
}