Meeting Abstract

P2.20  Saturday, Jan. 5  De novo assembly of the Paralithodes camtschaticus (Red King Crab) transcriptome to inform its response to ocean acidification FAY, SA*; SWINEY, K; FOY, R; STILLMAN, JH; University of California, Berkeley; National Marine Fisheries Service, Kodiak, AK; National Marine Fisheries Service, Kodiak, AK; University of California, Berkeley scott.a.fay@gmail.com

The Red King Crab, Paralithodes camtschaticus, is an economically important fishery species in Alaska. Experimental results have shown decreased survival and changes in calcification rates in P. camtschaticus exposed to lower pH. The direct effects of climate warming and ocean acidification are highly variable among species, and the underlying molecular mechanisms that allow for acclimation and adaptation to these changes are likewise variable and poorly understood. RNA-seq, using Illumina sequencing of mRNA, allows the direct study of transcriptome-wide gene expression and holds promise to rapidly reveal the molecular underpinnings of biological processes in non-model species. To study differential gene expression a reference database of transcripts is necessary for mapping sequence reads. For species such as P. camtschaticus without existing genomic information, a reference transcriptome can to be built from the sequence reads themselves through de novo assembly. We sequenced the P. camtschaticus transcriptome in larvae that had been exposed to different pH conditions, and used the resulting sequence reads to compare two popular de novo transcriptome assemblers, Trinity and OASES. Trinity ran more than an order of magnitude faster than OASES, and yielded more transcripts with longer average transcript length, suggesting that Trinity is performs better as a de novo assembler. We anticipate that an annotated transcriptome coupled with differential gene expression studies from ongoing temperature and pH experiments will help us identify fine-scale molecular responses of P. camtschaticus to future ocean conditions.