Transcriptomic Response of Juvenile Red King Crab, Paralithodes camtschaticus, to the Interactive Effects of Ocean Acidification and Warming

Impacts of elevated carbon dioxide on marine ecosystems depend on physiological responses to consequential decreased pH and increased temperature.  Responses to these environmental factors vary among species and life stages, and interactive effects can be significant.  To study effects of decreased pH and increased temperature on juvenile red king crab (RKC, Paralithodes camtschaticus) we exposed individuals to three levels of temperature: 11°C (ambient), 13°C, and 14°C, crossed with three levels of pH: 8.0, 7.8 and 7.5, for a total of nine treatments.  To better understand the effect of these environmental changes at the level of genome regulation, we analyzed total RNA of whole crabs using Illumina-based RNA-seq whole-transcriptome sequencing.  We assembled a RKC transcriptome using Trinity, annotated the transcriptome using Trinotate, and estimated expression levels using bowtie2, samtools and eXpress.  Differentially expressed genes were identified using EdgeR.  Genes were clustered by expression patterns.  Interactive effects were determined by comparing sets of differentially expressed genes using three statistical models to examine the effect of temperature, the effect of pH, and the interaction between temperature and pH in EdgeR.  The largest set of differentially expressed genes encoded proteins involved in regulation of extracellular and cuticular structures, including chitin-binding and calcification related proteins.