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PreprintCited by 37Chromosomal and Genetic VariationsGenomics and Phylogenetic StudiesDevelopmental Biology and Gene Regulation

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

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Brown, Thomas, Elewa, Ahmed, Iarovenko, Svetlana, Subramanian, Elaiyaraja, Araus, Alberto Joven, Petzold, Andreas, Suzuki, Miyuki, Suzuki, Ken-ichi T. +7 more·2022·Cell Genomics
DOI 10.1101/2022.10.19.512763PMC PMC11872487

Preprint — published as 10.1016/j.xgen.2025.100761

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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.

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  • The Spanish ribbed newt, Pleurodeles waltl, has a high-quality de novo transcriptome and more recently a high-quality genome but no available common SNPs VCF file.

    “The Spanish ribbed newt, Pleurodeles waltl, is ar reemerging regenerative model organism, which has a high-quality de novo transcriptome (Matsunami et al, 2019) and more recently a high-quality genome (Brown et al, 2022, Preprint) but no available common SNPs VCF file.”

    From Evaluation of genetic demultiplexing of single-cell sequencing data from model species (2023) · cites this paper as Brown et al, 2022, Preprint

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Cited by

Sorted by citations

Authors
Brown, T., Elewa, A., Iarovenko, S., Subramanian, E., Araus, A. J., Petzold, A., Suzuki, M., Suzuki, K.-I. T., Hayashi, T., Toyoda, A., Oliveira, C., Osipova, E., Leigh, N. D., Simon, A., & Yun, M. H.
Affiliations
  • Augsburg University (US)
  • Center for Regenerative Therapies Dresden (DE)
  • Karolinska Institutet (SE)
  • DRESDEN-concept Genome Center (DE)
  • California Institute of Technology (US)
  • Hiroshima University (JP)
  • National Institute of Genetics (JP)
  • LOEWE Centre for Translational Biodiversity Genomics (DE)
  • Lund University (SE)
  • Max Planck Institute of Molecular Cell Biology and Genetics (DE)
Corresponding author
  • Leigh, Nicholas D.
  • Yun, Maximina H.
ORCID
Venue
Cell Genomics
Publisher
openRxiv
Published
2022-10-20
Volume
5
Issue
2
Pages
100761-100761
ISSN
2666-979X (ISSN-L)
DOI
10.1101/2022.10.19.512763
PMC
PMC11872487
OpenAlex
W4406867198
Cited by
37
References
0
Citations by year
2026: 8 · 2025: 16 · 2024: 6 · 2023: 7
FWCI
12.97
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Cell Genomics (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • SSRN Electronic Journal (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Lund University Publications (Lund University) (submittedVersion)
Funders
  • Rosalind Franklin Institute
  • European Resuscitation Council
  • Deutsche Forschungsgemeinschaft (2018-05973, 2018-2022, 450807335, 497658823, DFG 22137416, INST 269/768-1, 22137416, INST 269/768)
  • Cancerfonden (22 2424 Pj)
  • Technische Universität Dresden
  • Karolinska Institutet (450807335, 2020-01486, 23 3047 Pj, 22137416, 497658823)
  • Knut och Alice Wallenbergs Stiftelse (2018-05973, 2018-2022, 2020-01486, 2018.0040)
  • Vetenskapsrådet (2018-02443, 05973, 2020-01486, 2018-, 201805973, 2018-2022, 2023-02820)
  • Zentrum für Regenerative Therapien Dresden
  • Science for Life Laboratory (2018-2022)
  • European Research Council (951477)
  • Japan Society for the Promotion of Science (2018-05973, 16H06279, 22H04925, 21H03829, 18K06257, 23K24058, 2018-2022)
  • Uppsala Multidisciplinary Center for Advanced Computational Science
  • Zentrum für Informationsdienste und Hochleistungsrechnen, Technische Universität Dresden
  • Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden
  • H2020 European Research Council (951477)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
Keywords
Pleurodeles waltl, chromosome-level genome assembly, repetitive elements, non-coding RNA, limb regeneration, circular RNA biogenesis, conserved synteny, genome rearrangement, major histocompatibility complex, large genomes
MeSH terms
RNA, Circular, Animals, Chromosome Mapping, Chromosomes, Extremities, Pleurodeles, Regeneration, Repetitive Sequences, Nucleic Acid, Salamandridae, Genome, RNA, Untranslated, MicroRNAs

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