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

作者：Tom Brown, Ketan Mishra, Ahmed Elewa, Svetlana Iarovenko, Elaiyaraja Subramanian, Alberto Joven, A. Petzold, Bastian Fromm, Marc R. Friedländer, Lennart Rikk, Miyuki Suzuki, Kenichi Suzuki, Toshinori Hayashi, Atsushi Toyoda, Catarina R. Oliveira, Ekaterina Osipova, Nicholas D. Leigh, Maximina H. Yun, András Simon · 发表于：Cell Genomics · 年份：2025 · DOI：10.1016/j.xgen.2025.100761 · 被引用次数：23 · 研究领域：RNA Research and Splicing、Circular RNAs in diseases、Cancer-related molecular mechanisms research

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.