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

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posted on 2024-05-02, 09:21 authored by Anurag Chaturvedi, Xiaojing Li, Vignesh Dhandapani, Hollie Marshall, Stephen Kissane, Maria Cuenca-Cambronero, Giovanni Asole, Ferriol Calvet, Marina Ruiz-Romero, Paolo Marangio, Roderic Guigó, Daria Rago, Leda Mirbahai, Niamh Eastwood, John K Colbourne, Jiarui Zhou, Eamonn Mallon, Luisa Orsini

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.

Funding

Cracking the Code of Adaptive Evolution (deCODE)

Natural Environment Research Council

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Toward Precision Toxicology: New Approach Methodologies for Chemical Safety

European Commission

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This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101028700; China−UK Research of Safeguarding Natural Water project, funded by the Royal Society International Collaboration Award [IC160121]. Funding for open access charge: Natural Environment Research Council.

History

Author affiliation

College of Life Sciences/Genetics & Genome Biology

Version

  • VoR (Version of Record)

Published in

Nucleic Acids Research

Volume

51

Issue

18

Pagination

9785 - 9803

Publisher

Oxford University Press (OUP)

issn

0305-1048

eissn

1362-4962

Copyright date

2023

Available date

2024-05-02

Spatial coverage

England

Language

en

Deposited by

Dr Hollie Marshall

Deposit date

2024-04-25

Data Access Statement

The Illumina short read sequences can be found at the following NCBI BioProject ID: PRJNA727483. The ONT and Hi-C data, including the mtDNA genome, can be found at the following NCBI BioProject ID: PRJNA777104. The metagenome has been submitted to NCBI at the following BioProject: PRJNA906625. The methylation data can be found at the following BioProject: PRJNA991497.

Rights Retention Statement

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