This repository includes data and analysis scripts to accompany:
Title: Dynamic DNA methylation contributes to carryover effects and beneficial acclimatization in geoduck clams
Authors: Hollie M. Putnam1, Shelly A. Trigg, Samuel J. White2, Laura H. Spencer2, Brent Vadopalas2,3, Aparna Natarajan4, Jonathan Hetzel4, Erich Jaeger4, Jonathan Soohoo4, Cristian Gallardo-Escárate5,6, Frederick W. Goetz7, Steven B. Roberts2
Abstract: To investigate the role of DNA methylation in environmental acclimatization in the long-lived and commercially important geoduck clam Panopea generosa, we generated the first draft reference genome and surveyed the physiology and DNA methylomes of juveniles initially exposed to environments differing in seawater pH and then following depuration and reexposure. Juveniles were initially exposed to one of three conditions (pH 7.9, 7.4, or 7.0) for 23 days, followed by an ambient common garden (~4 months), then a second reciprocal exposure to pH 7.9 or pH 7.4 for 23 days. Within 10 days of the initial exposure to pH 7.4 and 7.0, juvenile clams showed decreased shell size relative to ambient pH (7.9), which was associated with differentially methylated regions (DMRs) and genes (DMGs). After several months under ambient common-garden conditions, juveniles initially exposed to low pH (pH 7.4 and 7.0) grew larger than those initially exposed to ambient. DMRs and DMGs reflected these phenotypic differences, demonstrating epigenetic carryover effects persisted months after initial exposure. Functional enrichment analysis of the DMGs revealed regulation of signal transduction through widespread changes in the Wnt signaling pathways that influence cell growth, proliferation, tissue and skeletal formation, and cytoskeletal change. Correspondingly, developmental processes, protein metabolism, and transport were also enriched within the DMGs. Upon secondary exposure to pH 7.4, naive juvenile clams (pH 7.9) were more sensitive to low pH, with more reduced growth compared to those initially exposed to lower pH (pH 7.4 and 7.0). Similarly, naive clam methylation had a nearly 2-fold greater magnitude of methylation change in differentially methylated genes after 10 days of secondary exposure. Collectively, this new genomic resource and coordinated phenotypic and methylomic response support that environmental hardening via epigenetic mechanisms can provide beneficial phenotypes in molluscs, with important implications for wild and aquaculture populations under climate change.
Data:
Figs: This directory contains main and supplemental manuscript figures
Output: The directory containing the analysis results, figures, tables, and supplementary material.
Scripts: R scripts for all statistical analysis
Geoduck_Meth.RProj: Is this RProj needed?