Title: Influence of ocean acidification on DNA methylation patterns in geoduck
Meeting information: The Plant and Animal Genome XXVII Conference (PAG) Town and Country San Diego, CA January 11-15, 2020
Aquaculture Workshop Saturday, January 11 8:00 AM - 18:10 PM
Bio: Shelly Trigg is a postdoctoral research associate at the School of Aquatic and Fishery Sciences at the University of Washington in the lab of Steven Roberts. Dr. Trigg received her Ph.D. in Biology at the University of California San Diego in 2018. Her main research interest is the response of aquatic species to environmental change with a focus on molecular networks and physiology.
Abstract: To investigate acclimatization to ocean acidification through epigenetic mechanisms we examined genome-wide DNA methylation in early-stage juvenile geoduck clams that underwent a series of exposure experiments. Compared to ambient conditions, juvenile geoduck displayed decreased shell size in two low pH conditions (pH ~7.4 and pH ~7.0). When returned to ambient conditions for several months, the initial exposure to low pH resulted in compensatory growth with juveniles from the two initial low pH treatments being larger compared to those from the initial ambient pH condition. Interestingly, juvenile clams retained treatment specific regions of differential methylation after 125 days being removed from the initial low pH treatment. This is one of the first indications that DNA methylation could serve as a persistent epigenetic mark with a potential to influence subsequent response to environmental stress. Differentially methylated regions within specific genes and transposable elements shed light on putative functional roles of DNA methylation and mechanisms of intragenerational acclimatization. Taken together these data suggests that acclimatization to ocean acidification can result in benefits to geoduck growth, with exposure memory providing a mechanism for environmental hardening.
- 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: https://osf.io/yem8n/
- Geoduck transcriptome assembly generated using RNAseq data from ctenidia, gonad, heart tissues, whole larval and juvenile animals: https://osf.io/tb5kz/
- Proteins predicted by TransDecoder from the transcriptome assembly: https://osf.io/c6mub/