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The hologenome of Daphnia magna reveals possible DNA methylation and microbiome-mediated evolution of the host genome.

التفاصيل البيبلوغرافية
العنوان: The hologenome of Daphnia magna reveals possible DNA methylation and microbiome-mediated evolution of the host genome.
المؤلفون: Chaturvedi A; Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK., Li X; Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK., Dhandapani V; Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK., Marshall H; Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK.; Department of Genetics and Genome Biology, the University of Leicester, Leicester LE1 7RH, UK., Kissane S; Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK., Cuenca-Cambronero M; Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK.; Aquatic Ecology Group, University of Vic - Central University of Catalonia, 08500 Vic, Spain., Asole G; Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain., Calvet F; Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain., Ruiz-Romero M; Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain., Marangio P; Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain., Guigó R; Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain., Rago D; Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK., Mirbahai L; Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK., Eastwood N; Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK., Colbourne JK; Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK., Zhou J; Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK., Mallon E; Department of Genetics and Genome Biology, the University of Leicester, Leicester LE1 7RH, UK., Orsini L; Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK.; The Alan Turing Institute, British Library, London NW1 2DB, UK.
المصدر: Nucleic acids research [Nucleic Acids Res] 2023 Oct 13; Vol. 51 (18), pp. 9785-9803.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE
أسماء مطبوعة: Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.
مستخلص: Properties that make organisms ideal laboratory models in developmental and medical research are often the ones that also make them less representative of wild relatives. The waterflea Daphnia magna is an exception, by both sharing many properties with established laboratory models and being a keystone species, a sentinel species for assessing water quality, an indicator of environmental change and an established ecotoxicology model. Yet, Daphnia's full potential has not been fully exploited because of the challenges associated with assembling and annotating its gene-rich genome. Here, we present the first hologenome of Daphnia magna, consisting of a chromosomal-level assembly of the D. magna genome and the draft assembly of its metagenome. By sequencing and mapping transcriptomes from exposures to environmental conditions and from developmental morphological landmarks, we expand the previously annotates gene set for this species. We also provide evidence for the potential role of gene-body DNA-methylation as a mutagen mediating genome evolution. For the first time, our study shows that the gut microbes provide resistance to commonly used antibiotics and virulence factors, potentially mediating Daphnia's environmental-driven rapid evolution. Key findings in this study improve our understanding of the contribution of DNA methylation and gut microbiota to genome evolution in response to rapidly changing environments.
(© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)
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معلومات مُعتمدة: NE/N016777/1 NERC; 965406 European Union; 101028700 Marie Skłodowska-Curie; IC160121 Royal Society International Collaboration Award
تواريخ الأحداث: Date Created: 20230828 Latest Revision: 20231015
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC10570034
DOI: 10.1093/nar/gkad685
PMID: 37638757
قاعدة البيانات: MEDLINE
الوصف
تدمد:1362-4962
DOI:10.1093/nar/gkad685