Meeting Abstract
109.5 Tuesday, Jan. 7 09:00 Transcriptomic response of juvenile red king crab, Paralithodes camtschaticus, to the interactive effects of ocean acidification and warming FAY, S; AHMAD, M; SWINEY, K; FOY, R; STILLMAN, JH*; Univ. of California, Berkeley; Univ. of California, Berkeley; National Marine Fisheries Service; National Marine Fisheries Service; Univ. of California, Berkeley stillmaj@sfsu.edu
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: 11ºC (ambient), 13ºC, 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: massively parallel, quantitative, whole-transcriptome sequencing. After quality filtering the data and joining overlapping read pairs, we de-novo assembled a RKC transcriptome using Trinity. We annotated the RKC transcriptome by best BLAST hit, gene ontology, and Pfam transmembrane and signal peptide domains using a Trinotate pipeline. Rfam was used to search for non-coding RNA family homologies. To estimate gene-wise expression levels, sequence reads were mapped to the de-novo transcriptome as a reference using bowtie2, samtools and eXpress. Significantly differentially expressed genes were found using EdgeR. Genes were clustered by similar change in expression over treatments and grouped within by functional category. 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.
