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DNA METHYLATION PROFILING OF A CNIDARIAN-ALGAL SYMBIOSIS USING NANOPORE SEQUENCING

View ORCID ProfileJames L. Dimond, Nhung Nguyen, Steven B. Roberts
doi: https://doi.org/10.1101/2021.02.01.429278
James L. Dimond
1University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA 98195
2Western Washington University, Shannon Point Marine Center, Anacortes, WA 98221
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  • For correspondence: jdimond@gmail.com
Nhung Nguyen
3Department of Biology, Hobart and William Smith Colleges, Geneva, NY 14456
4South Texas Center for Emerging Infectious Diseases, Department of Biology, The University of Texas at San Antonio, San Antonio, TX 78249
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Steven B. Roberts
1University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA 98195
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ABSTRACT

Symbiosis with protists is common among cnidarians such as corals and sea anemones, and is associated with homeostatic and phenotypic changes in the host that could have epigenetic underpinnings, such as methylation of CpG dinucleotides. We leveraged the sensitivity to base modifications of nanopore sequencing to probe the effect of symbiosis with the chlorophyte Elliptochloris marina on methylation in the sea anemone Anthopleura elegantissima. We first validated the approach by comparison of nanopore-derived methylation levels with CpG depletion analysis of a published transcriptome, finding that high methylation levels are associated with CpG depletion as expected. Next, using reads generated exclusively from aposymbiotic anemones, a largely complete draft genome comprising 243 Mb was assembled. Reads from aposymbiotic and symbiotic sea anemones were then mapped to this genome and assessed for methylation using the program Nanopolish, which detects signal disruptions from base modifications as they pass through the nanopore. Based on assessment of 452,841 CpGs for which there was adequate read coverage (approximately 8% of the CpGs in the genome), symbiosis with E. marina was, surprisingly, associated with only subtle changes in the host methylome. However, we did identify one extended genomic region with consistently higher methylation among symbiotic individuals. The region was associated with a DNA polymerase zeta that is noted for its role in translesion synthesis, which opens interesting questions about the biology of this symbiosis. Our study highlights the power and relative simplicity of nanopore sequencing for studies of nucleic acid base modifications in non-model species.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 02, 2021.
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DNA METHYLATION PROFILING OF A CNIDARIAN-ALGAL SYMBIOSIS USING NANOPORE SEQUENCING
James L. Dimond, Nhung Nguyen, Steven B. Roberts
bioRxiv 2021.02.01.429278; doi: https://doi.org/10.1101/2021.02.01.429278
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DNA METHYLATION PROFILING OF A CNIDARIAN-ALGAL SYMBIOSIS USING NANOPORE SEQUENCING
James L. Dimond, Nhung Nguyen, Steven B. Roberts
bioRxiv 2021.02.01.429278; doi: https://doi.org/10.1101/2021.02.01.429278

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