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De novo genome assembly and in natura epigenomics reveal salinity-induced DNA methylation in the mangrove tree Bruguiera gymnorhiza

Miryeganeh, M; Marlétaz, F; Gavriouchkina, D; Saze, H; (2022) De novo genome assembly and in natura epigenomics reveal salinity-induced DNA methylation in the mangrove tree Bruguiera gymnorhiza. New Phytologist , 233 (5) pp. 2094-2110. 10.1111/nph.17738. Green open access

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Abstract

Mangroves are adapted to harsh environments, such as high UV light, low nutrition, and fluctuating salinity in coastal zones. However, little is known about the transcriptomic and epigenomic basis of the resilience of mangroves due to limited available genome resources. We performed a de novo genome assembly and in natura epigenome analyses of the mangrove Bruguiera gymnorhiza, one of the dominant mangrove species. We also performed the first genome-guided transcriptome assembly for mangrove species. The 309 Mb of the genome is predicted to encode 34,403 genes and has a repeat content of 48%. Depending on its growing environment, the natural B. gymnorhiza population showed drastic morphological changes associated with expression changes in thousands of genes. Moreover, high-salinity environments induced genome-wide DNA hypermethylation of transposable elements (TEs) in the B. gymnorhiza. DNA hypermethylation was concurrent with the transcriptional regulation of chromatin modifier genes, suggesting robust epigenome regulation of TEs in the B. gymnorhiza genome under high-salinity environments. The genome and epigenome data in this study provide novel insights into the epigenome regulation of mangroves and a better understanding of the adaptation of plants to fluctuating, harsh natural environments.

Type: Article
Title: De novo genome assembly and in natura epigenomics reveal salinity-induced DNA methylation in the mangrove tree Bruguiera gymnorhiza
Location: England
Open access status: An open access version is available from UCL Discovery
DOI: 10.1111/nph.17738
Publisher version: https://doi.org/10.1111/nph.17738
Language: English
Additional information: Copyright © 2021 The Authors. New Phytologist copyright © 2021 New Phytologist Foundation. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License (http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.
Keywords: Abiotic stress, DNA methylation, Epigenome, Mangrove genome, Salt stress, Transposable elements
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
URI: https://discovery.ucl.ac.uk/id/eprint/10135934
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