Chromosome-Scale Genome Assembly Reveals How Repeat Elements Shape Non-Coding RNA Landscapes Active During Newt Limb Regeneration
(2024)- Abstract
- Newts have large genomes harbouring 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 20.3Gb genome of the Iberian ribbed newt, Pleurodeles waltl, with a hitherto unprecedented contiguity and completeness among giant genomes. We provide evidence that intronic repeat elements may drive newt-specific 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 distinct regulatory pattern in the regenerating limb. These data reveal links between repeat elements, non-coding... (More)
- Newts have large genomes harbouring 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 20.3Gb genome of the Iberian ribbed newt, Pleurodeles waltl, with a hitherto unprecedented contiguity and completeness among giant genomes. We provide evidence that intronic repeat elements may drive newt-specific 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 distinct regulatory pattern in the regenerating limb. These data reveal links between repeat elements, non-coding RNAs and adult regeneration, as well as provide a key resource for addressing developmental, regenerative, and evolutionary principles. (Less)
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- publishing date
- 2024-01-01
- type
- Working paper/Preprint
- publication status
- published
- subject
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- SSRN
- DOI
- 10.2139/ssrn.4890100
- language
- English
- LU publication?
- yes
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- b80db194-6287-4cb0-b733-c2e4fb718f77
- date added to LUP
- 2025-10-16 13:37:54
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- 2025-10-16 13:52:55
@misc{b80db194-6287-4cb0-b733-c2e4fb718f77, abstract = {{Newts have large genomes harbouring 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 20.3Gb genome of the Iberian ribbed newt, Pleurodeles waltl, with a hitherto unprecedented contiguity and completeness among giant genomes. We provide evidence that intronic repeat elements may drive newt-specific 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 distinct regulatory pattern in the regenerating limb. These data reveal links between repeat elements, non-coding RNAs and adult regeneration, as well as provide a key resource for addressing developmental, regenerative, and evolutionary principles.}}, author = {{Brown, Thomas and Mishra, Ketan and Elewa, Ahmed and Iarovenko, Svetlana and Subramanian, Elaiyaraja and Joven Araus, Alberto and Petzold, Andreas and Fromm, Bastian and Friedländer, Marc R. 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 Yun, Maximina H. and Simon, Andras}}, language = {{eng}}, month = {{01}}, note = {{Preprint}}, publisher = {{SSRN}}, title = {{Chromosome-Scale Genome Assembly Reveals How Repeat Elements Shape Non-Coding RNA Landscapes Active During Newt Limb Regeneration}}, url = {{http://dx.doi.org/10.2139/ssrn.4890100}}, doi = {{10.2139/ssrn.4890100}}, year = {{2024}}, }