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

Thomas Brown; Ketan Mishra; Ahmed Elewa; Svetlana Iarovenko; Elaiyaraja Subramanian; Alberto Joven Araus; Andreas Petzold; Bastian Fromm; Marc R Friedländer; Lennart Rikk; Miyuki Suzuki; Ken-Ichi T Suzuki; Toshinori Hayashi; Atsushi Toyoda; Catarina R Oliveira; Ekaterina Osipova; Nicholas D Leigh; Maximina H Yun; András Simon

doi:10.1016/j.xgen.2025.100761

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

Thomas Brown, Ketan Mishra, Ahmed Elewa, Svetlana Iarovenko, Elaiyaraja Subramanian, Alberto Joven Araus, Andreas Petzold, Bastian Fromm, Marc R Friedländer, Lennart Rikk, Miyuki Suzuki, Ken-Ichi T Suzuki, Toshinori Hayashi, Atsushi Toyoda, Catarina R Oliveira, Ekaterina Osipova, Nicholas D Leigh, Maximina H Yun, András Simon

Forskningsoutput: Tidskriftsbidrag › Artikel i vetenskaplig tidskrift › Peer review

Sammanfattning

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.

Originalspråk	engelska
Artikelnummer	100761
Tidskrift	Cell Genomics
Volym	5
Nummer	2
DOI	https://doi.org/10.1016/j.xgen.2025.100761
Status	Published - 2025

Bibliografisk information

Ämnesklassifikation (UKÄ)

Genetik och genomik

Tillgång till dokument

10.1016/j.xgen.2025.100761Licens: CC BY

Andra filer och länkar

Link to publication in Scopus

Chromosome-Scale Genome Assembly Reveals How Repeat Elements Shape Non-Coding RNA Landscapes Active During Newt Limb Regeneration
Brown, T., Mishra, K., Elewa, A., Iarovenko, S., Subramanian, E., Joven Araus, A., Petzold, A., Fromm, B., Friedländer, M. R., Suzuki, M., Suzuki, K.-I. T., Hayashi, T., Toyoda, A., Oliveira, C., Osipova, E., Leigh, N. D., Yun, M. H. & Simon, A., 2024 jan. 1, SSRN.
Forskningsoutput: Working paper/Preprint › Preprint (i preprint-arkiv)

Deciphering the balance between regeneration and tumorigenesis
Leigh, N. (PI)
Cancerfonden
2024/01/01 → 2026/12/31
Projekt: Forskning

Citera det här

Brown, T., Mishra, K., Elewa, A., Iarovenko, S., Subramanian, E., Araus, A. J., Petzold, A., Fromm, B., Friedländer, M. R., Rikk, L., Suzuki, M., Suzuki, K.-I. T., Hayashi, T., Toyoda, A., Oliveira, C. R., Osipova, E., Leigh, N. D., Yun, M. H., & Simon, A. (2025). Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration. Cell Genomics, 5(2), Artikel 100761. https://doi.org/10.1016/j.xgen.2025.100761

@article{57b666d4342c4a099b38597c5151767a,

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

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 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.",

author = "Thomas Brown and Ketan Mishra and Ahmed Elewa and Svetlana Iarovenko and Elaiyaraja Subramanian and Araus, \{Alberto Joven\} and Andreas Petzold and Bastian Fromm and Friedl{\"a}nder, \{Marc R\} and Lennart Rikk and Miyuki Suzuki and Suzuki, \{Ken-Ichi T\} and Toshinori Hayashi and Atsushi Toyoda and Oliveira, \{Catarina R\} and Ekaterina Osipova and Leigh, \{Nicholas D\} and Yun, \{Maximina H\} and Andr{\'a}s Simon",

year = "2025",

doi = "10.1016/j.xgen.2025.100761",

language = "English",

volume = "5",

journal = "Cell Genomics",

issn = "2666-979X",

publisher = "Cell Press",

number = "2",

}

Brown, T, Mishra, K, Elewa, A, Iarovenko, S, Subramanian, E, Araus, AJ, Petzold, A, Fromm, B, Friedländer, MR, Rikk, L, Suzuki, M, Suzuki, K-IT, Hayashi, T, Toyoda, A, Oliveira, CR, Osipova, E, Leigh, ND, Yun, MH & Simon, A 2025, 'Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration', Cell Genomics, vol. 5, nr. 2, 100761. https://doi.org/10.1016/j.xgen.2025.100761

TY - JOUR

T1 - Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration

AU - Brown, Thomas

AU - Mishra, Ketan

AU - Elewa, Ahmed

AU - Iarovenko, Svetlana

AU - Subramanian, Elaiyaraja

AU - Araus, Alberto Joven

AU - Petzold, Andreas

AU - Fromm, Bastian

AU - Friedländer, Marc R

AU - Rikk, Lennart

AU - Suzuki, Miyuki

AU - Suzuki, Ken-Ichi T

AU - Hayashi, Toshinori

AU - Toyoda, Atsushi

AU - Oliveira, Catarina R

AU - Osipova, Ekaterina

AU - Leigh, Nicholas D

AU - Yun, Maximina H

AU - Simon, András

PY - 2025

Y1 - 2025

N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/85217502364

U2 - 10.1016/j.xgen.2025.100761

DO - 10.1016/j.xgen.2025.100761

M3 - Article

C2 - 39874962

SN - 2666-979X

VL - 5

JO - Cell Genomics

JF - Cell Genomics

IS - 2

M1 - 100761

ER -

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

Sammanfattning

Bibliografisk information

Ämnesklassifikation (UKÄ)

Tillgång till dokument

Andra filer och länkar

Fingeravtryck

Forskningsoutput

Chromosome-Scale Genome Assembly Reveals How Repeat Elements Shape Non-Coding RNA Landscapes Active During Newt Limb Regeneration

Projekt

Deciphering the balance between regeneration and tumorigenesis

Citera det här