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Sequencing and chromosome-scale assembly of the giant Pleurodeles waltl genome

Brown, Thomas ; Elewa, Ahmed ; Iarovenko, Svetlana ; Subramanian, Elaiyaraja ; Araus, Alberto Joven ; Petzold, Andreas ; Suzuki, Miyuki ; Suzuki, Ken-Ichi T. ; Hayashi, Toshinori and Toyoda, Atsushi , et al. (2023)
Abstract
The Iberian ribbed newt (Pleurodeles waltl) constitutes a central model for probing the basis of vertebrate regeneration. Here, we present the sequencing and chromosome-scale assembly of the 20.3Gb P. waltl genome, which exhibits the highest level of contiguity and completeness among giant genome assemblies. We uncover that DNA transposable elements are the major contributors to its expansion, with hAT transposons comprising a large portion of repeats. Several hATs are actively transcribed and differentially expressed during adult P. waltl limb regeneration, along with domesticated hAT transposons of the ZBED transcription factor family. Despite its size, syntenic relationships are conserved. As an example, we show the high degree of... (More)
The Iberian ribbed newt (Pleurodeles waltl) constitutes a central model for probing the basis of vertebrate regeneration. Here, we present the sequencing and chromosome-scale assembly of the 20.3Gb P. waltl genome, which exhibits the highest level of contiguity and completeness among giant genome assemblies. We uncover that DNA transposable elements are the major contributors to its expansion, with hAT transposons comprising a large portion of repeats. Several hATs are actively transcribed and differentially expressed during adult P. waltl limb regeneration, along with domesticated hAT transposons of the ZBED transcription factor family. Despite its size, syntenic relationships are conserved. As an example, we show the high degree of conservation of the regeneration-associated Tig1 locus with several neighbouring genes. Together, the P. waltl genome provides a fundamental resource for the study of regenerative, developmental and evolutionary principles. (Less)
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type
Working paper/Preprint
publication status
published
subject
publisher
bioRxiv
DOI
10.1101/2022.10.19.512763
language
English
LU publication?
yes
id
e7d8fb15-2df2-4be6-9645-8d9169265854
date added to LUP
2025-10-21 16:33:48
date last changed
2025-10-21 16:42:04
@misc{e7d8fb15-2df2-4be6-9645-8d9169265854,
  abstract     = {{The Iberian ribbed newt (Pleurodeles waltl) constitutes a central model for probing the basis of vertebrate regeneration. Here, we present the sequencing and chromosome-scale assembly of the 20.3Gb P. waltl genome, which exhibits the highest level of contiguity and completeness among giant genome assemblies. We uncover that DNA transposable elements are the major contributors to its expansion, with hAT transposons comprising a large portion of repeats. Several hATs are actively transcribed and differentially expressed during adult P. waltl limb regeneration, along with domesticated hAT transposons of the ZBED transcription factor family. Despite its size, syntenic relationships are conserved. As an example, we show the high degree of conservation of the regeneration-associated Tig1 locus with several neighbouring genes. Together, the P. waltl genome provides a fundamental resource for the study of regenerative, developmental and evolutionary principles.}},
  author       = {{Brown, Thomas and Elewa, Ahmed and Iarovenko, Svetlana and Subramanian, Elaiyaraja and Araus, Alberto Joven and Petzold, Andreas and Suzuki, Miyuki and Suzuki, Ken-Ichi T. and Hayashi, Toshinori and Toyoda, Atsushi and Oliveira, Catarina and Osipova, Ekaterina and Leigh, Nicholas D. and Simon, Andras and Yun, Maximina H.}},
  language     = {{eng}},
  month        = {{08}},
  note         = {{Preprint}},
  publisher    = {{bioRxiv}},
  title        = {{Sequencing and chromosome-scale assembly of the giant <i>Pleurodeles waltl</i> genome}},
  url          = {{http://dx.doi.org/10.1101/2022.10.19.512763}},
  doi          = {{10.1101/2022.10.19.512763}},
  year         = {{2023}},
}