Profiling Spatial & Temporal Gene Expression Responses of a Copepod (Calanus pacificus) from the Northern California Current Using a Novel RNA-Seq Procedure

Copepods are the most abundant metazoans on Earth and play an important role in marine food webs and the carbon cycle. As the dominant group of zooplankton, copepods are crucial secondary producers serving either directly or indirectly as food sources for most commercially important fish species. Through their vertical migrations, copepods indirectly transfer carbon from the atmosphere into the deep sea where it can be stored. In addition, copepods are ecological indicators of climate change, with warming ocean temperatures affecting copepod community structure, abundance, distribution, and seasonal timing. Although they are abundant in the Northern California current during the winter and spring, the copepod species Calanus pacificus has been the subject of very few transcriptome studies. Using a novel RNA-Seq technique, TagSeq, the transcriptomes were sequenced for C. pacificus samples from three locations off Oregon and Northern California in May 2017 and 2018. Bioinformatic techniques were utilized to curate the sequences, assemble them into potential genes, annotate, and analyze for differential gene expression. Thirty-four genes had significantly different expression profiles among years and locations. Various genes related to oxidative phosphorylation and muscle contraction were upregulated and a stress biomarker, ferritin, and a cuticle protein gene were downregulated in 2018 compared to 2017. During this time period there was a significant change in phytoplankton abundance, determined by chlorophyll fluorescence, and water nutrients at all locations. By further investigating gene expression responses of C. pacificus spatially and temporally, the health of the copepods could be determined to then assess the health of the surrounding marine ecosystem.