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. DMRs and DMGs reflected these phenotypic differences, demonstrating epigenetic carryover effects persisted months after initial exposure. 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. 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). 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.
Roberts2Ībstract: 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. Spencer2, Brent Vadopalas2,3, Aparna Natarajan4, Jonathan Hetzel4, Erich Jaeger4, Jonathan Soohoo4, Cristian Gallardo-Escárate5,6, Frederick W. Title: Dynamic DNA methylation contributes to carryover effects and beneficial acclimatization in geoduck clamsĪuthors: Hollie M. This repository includes data and analysis scripts to accompany:
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