Dynamic DNA methylation contributes to carryover effects and beneficial acclimatization in geoduck clams

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.

Acclimatory gene expression of primed clams enhances robustness to elevated pCO2

“…Raw TagSeq reads were trimmed of Illumina adapters, poly‐A sequence and quality filtered with fastp (Chen et al, 2018); quality control for filter optimization was completed using multiqc (Ewels et al, 2016). Following quality control, reads were mapped to the P. generosa reference genome (Putnam et al, 2022) using hisat2 (Kim et al, 2015) with a mapping efficiency of ~30%; the majority of unmapped reads aligned to ribosomal rRNAs (i.e., 18S and 28S) in geoduck clams (i.e., Panopea globosa ). stringtie2 (Pertea et al, 2015) was used to quantify reads and assemble a count matrix (using prepDE.py) for analysis in R version 3.5.1 (https://www.r-project.org).…”

“…Raw TagSeq reads were trimmed of Illumina adapters, poly-A sequence and quality filtered with fastp (Chen et al, 2018); quality control for filter optimization was completed using multiqc (Ewels et al, 2016). Following quality control, reads were mapped to the P. generosa reference genome (Putnam et al, 2022) using hisat2 F I G U R E 1 Experimental design for sampling. Line thickness indicates the pCO 2 treatments.…”