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Exploring the tolerance of Pacific geoduck to low pH through comparative physiology, genomics, and DNA methylation

Meeting information:
The Society for Integrative and Comparative Biology (SICB)
2021 Virtual Annual Meeting
January 3-February 28, 2021

Session information:
Complementary to S2: Genomic Perspectives in Comparative Physiology of Mollusks: Integration Across Disciplines

Virtual presentation:

Slide deck:

Shelly is a Postdoctoral Fellow in the lab of Steven Roberts at the University of Washington. She studies how the environment impacts marine animals at the physiological and molecular systems level by simulating various ocean conditions and using -omics approaches and physiological assays to measure animal response. She loves the ocean and forests.

The Pacific geoduck clam is important in Native American culture, to ecosystems as biofilters and prey, and to the U.S. economy as a valuable fishery that provides revenue and jobs. To gain insight into how this species might fare with future ocean acidification, and if stress conditioning might be beneficial in aquaculture practices, we explored the effects of low static and variable pH exposure on juveniles and adults. We found that juveniles were able to overcome a developmental delay resulting from an initial low pH exposure, growing larger over time and when under a secondary low pH exposure. Genome characteristics and methylation variation supported these phenotypes, with altered DNA methylation occurring mainly within genes associated with specific biological processes. We found that adults experienced decreased survival and delayed reproductive development under static, but not variable low pH exposure. Offspring of adults exposed to variable low pH initially showed delayed larval development, but were able to compensate as juveniles and grew larger under variable low pH conditions while maintaining a lower, less variable metabolic rate. Taken together, stress exposure duration, intensity, and variation, and the developmental stage of the animal produce different phenotypes. These experiments show short-term rather than long-term and variable rather than static stress exposure give rise to beneficial phenotypes (e.g. less metabolic activity to achieve the same or greater size), and that DNA methylation is a mechanism by which these phenotypes can be expressed.

Genomic Resources:

  • Genome sequence reads are available on the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under the following accession numbers SRX5775746-SRX5775753
  • Genome annotation resources:
  • Geoduck transcriptome assembly generated using RNAseq data from ctenidia, gonad, heart tissues, whole larval and juvenile animals:
  • Proteins predicted by TransDecoder from


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