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\begin{document}

\title{Benchmarking DNA Methylation Assays for Marine Invertebrates}



\author[1]{Groves Dixon}%
\author[2,2]{Mikhail Matz}%
\affil[1]{University of Texas}%
\affil[2]{University of Texas at Austin}%


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  \date{June 15, 2024}


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\begin{abstract}
Abstract: Interrogation of chromatin modifications, such as DNA
methylation, has potential to improve forecasting and conservation of
marine ecosystems. The standard method for assaying DNA methylation
(Whole Genome Bisulfite Sequencing), however, is too costly to apply at
the scales required for ecological research. Here we evaluate different
methods for measuring DNA methylation for ecological epigenetics. We
compare Whole Genome Bisulfite Sequencing (WGBS) with Methylated CpG
Binding Domain Sequencing (MBD-seq), and a modified version of MethylRAD
we term methylation-dependent Restriction site-Associated DNA sequencing
(mdRAD). We evaluate these three assays in measuring variation in
methylation across the genome, between genotypes, and between polyp
types in the reef-building coral Acropora millepora. We find that all
three assays measure absolute methylation levels similarly, with tight
correlations for methylation of gene bodies (gbM), as well as exons and
1Kb windows. Correlations for differential gbM between genotypes were
weaker, but still concurrent across assays. We detected little to no
reproducible differences in gbM between polyp types. We conclude that
MBD-seq and mdRAD are reliable cost-effective alternatives to WGBS.
Moreover, the considerably lower sequencing effort required for mdRAD to
produce comparable methylation estimates makes it particularly useful
for ecological epigenetics.%
\end{abstract}%



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