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

التفاصيل البيبلوغرافية
العنوان: A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence.
المؤلفون: Ivanković M; Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany., Brand JN; Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany., Pandolfini L; Center for Human Technologies, Non-coding RNA and RNA-based therapeutics, Istituto Italiano di Tecnologia, Genova, Italy., Brown T; Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany., Pippel M; Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany., Rozanski A; Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany., Schubert T; Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany., Grohme MA; Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany., Winkler S; Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany., Robledillo L; Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany., Zhang M; Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany., Codino A; Center for Human Technologies, Non-coding RNA and RNA-based therapeutics, Istituto Italiano di Tecnologia, Genova, Italy., Gustincich S; Center for Human Technologies, Non-coding RNA and RNA-based therapeutics, Istituto Italiano di Tecnologia, Genova, Italy., Vila-Farré M; Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany., Zhang S; Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany., Papantonis A; Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany., Marques A; Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany., Rink JC; Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany. jochen.rink@mpinat.mpg.de.; Faculty of Biology und Psychology, Georg-August-University Göttingen, Göttingen, Germany. jochen.rink@mpinat.mpg.de.
المصدر: Nature communications [Nat Commun] 2024 Sep 19; Vol. 15 (1), pp. 8215. Date of Electronic Publication: 2024 Sep 19.
نوع المنشور: Journal Article; Comparative Study
اللغة: English
بيانات الدورية: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE
أسماء مطبوعة: Original Publication: [London] : Nature Pub. Group
مواضيع طبية MeSH: Planarians*/genetics , Genome, Helminth* , Evolution, Molecular*, Animals ; Synteny ; Phylogeny ; Chromosome Inversion/genetics ; Retroelements/genetics ; Molecular Sequence Annotation ; Regulatory Sequences, Nucleic Acid/genetics ; Genome/genetics ; Conserved Sequence/genetics
مستخلص: 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.
(© 2024. The Author(s).)
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المشرفين على المادة: 0 (Retroelements)
تواريخ الأحداث: Date Created: 20240918 Date Completed: 20240918 Latest Revision: 20240921
رمز التحديث: 20240921
مُعرف محوري في PubMed: PMC11410931
DOI: 10.1038/s41467-024-52380-9
PMID: 39294119
قاعدة البيانات: MEDLINE
الوصف
تدمد:2041-1723
DOI:10.1038/s41467-024-52380-9