A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence

Mario Ivanković, Jeremias N. Brand, Luca Pandolfini, Thomas Brown, Martin Pippel, Andrei Rozanski, Til Schubert, Markus A. Grohme, Sylke Winkler, Laura Robledillo, Meng Zhang, Azzurra Codino, Stefano Gustincich, Miquel Vila-Farré, Shu Zhang, Argyris Papantonis, André Marques and Jochen C. Rink ()
Additional contact information
Mario Ivanković: Max Planck Institute for Multidisciplinary Sciences
Jeremias N. Brand: Max Planck Institute for Multidisciplinary Sciences
Luca Pandolfini: Istituto Italiano di Tecnologia
Thomas Brown: Max Planck Institute of Molecular Cell Biology and Genetics
Martin Pippel: Max Planck Institute of Molecular Cell Biology and Genetics
Andrei Rozanski: Max Planck Institute for Multidisciplinary Sciences
Til Schubert: Max Planck Institute for Multidisciplinary Sciences
Markus A. Grohme: Max Planck Institute of Molecular Cell Biology and Genetics
Sylke Winkler: Max Planck Institute of Molecular Cell Biology and Genetics
Laura Robledillo: Max Planck Institute for Plant Breeding Research
Meng Zhang: Max Planck Institute for Plant Breeding Research
Azzurra Codino: Istituto Italiano di Tecnologia
Stefano Gustincich: Istituto Italiano di Tecnologia
Miquel Vila-Farré: Max Planck Institute for Multidisciplinary Sciences
Shu Zhang: University Medical Center Göttingen
Argyris Papantonis: University Medical Center Göttingen
André Marques: Max Planck Institute for Plant Breeding Research
Jochen C. Rink: Max Planck Institute for Multidisciplinary Sciences

Nature Communications, 2024, vol. 15, issue 1, 1-21

Abstract: Abstract The planarian Schmidtea mediterranea is being studied as a model species for regeneration, but the assembly of planarian genomes remains challenging. Here, we report a high-quality haplotype-phased, chromosome-scale genome assembly of the sexual S2 strain of S. mediterranea and high-quality chromosome-scale assemblies of its three close relatives, S. polychroa, S. nova, and S. lugubris. Using hybrid gene annotations and optimized ATAC-seq and ChIP-seq protocols for regulatory element annotation, we provide valuable genome resources for the planarian research community and a first comparative perspective on planarian genome evolution. Our analyses reveal substantial divergence in protein-coding sequences and regulatory regions but considerable conservation within promoter and enhancer annotations. We also find frequent retrotransposon-associated chromosomal inversions and interchromosomal translocations within the genus Schmidtea and, remarkably, independent and nearly complete losses of ancestral metazoan synteny in Schmidtea and two other flatworm groups. Overall, our results suggest that platyhelminth genomes can evolve without syntenic constraints.

Date: 2024
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-024-52380-9 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-52380-9

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-024-52380-9

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().