Where have all the codfish gone?
Dr. R. Patrick Hassett, Associate Professor of Biological Sciences, is a co-author on a paper assessing the impact of global warming on the North Atlantic food chain. The researchers are using a new technique to acquire data on a tiny crustacean that is a food source for cod.
“The mega-decline in cod and other fisheries across the North Atlantic Ocean threatens the livelihood of fishermen and communities in New England and Atlantic Canada. One suspect in the disappearance of cod and other groundfish is the food source for their young: a planktonic copepod crustacean, no larger than a grain of rice. Recent changes in local copepod populations have co-occurred with declines in fisheries elsewhere, such as the collapse of the cod fishery in Europe’s North Sea,” reports Phys.org.
Because of the copepod’s small size and its vast ocean habitat, it is a poor subject for conventional physiological studies. New molecular techniques have opened doors for an alternative approach. Known as transcriptomics, this technique makes a catalog of all the messages (“transcripts”) produced by the cells that control the animal’s physiology. With this tool, biologists are now able to listen in on the instructions being sent out to direct an organism’s response to its changing environment. With respect to copepods, the challenge is to identify and understand each message, in order to track down the causes of population changes.
The first transcriptome for the key North Atlantic copepod Calanus finmarchicus has now been published and made available for scientists everywhere. Appearing in a February 2014 issue of the journal PLOS ONE, it is the work of a team of scientists from the Pacific Biosciences Research Center at UH Mānoa, Ohio University and Indiana University’s National Center for Genome Analysis Support. Mount Desert Island Biological Laboratory in Salisbury Cove, Maine provided access to the biological samples. The transcriptome was sequenced by the University of Georgia Genomics Facility in Athens, Georgia.
This publication provides the first publicly accessible, large-scale molecular resource for investigating the physiological ecology of Calanus.
Abstract: Assessing the impact of global warming on the food web of the North Atlantic will require difficult-to-obtain physiological data on a key copepod crustacean, Calanus finmarchicus. The de novo transcriptome presented here represents a new resource for acquiring such data. It was produced from multiplexed gene libraries using RNA collected from six developmental stages: embryo, early nauplius (NI-II), late nauplius (NV-VI), early copepodite (CI-II), late copepodite (CV) and adult (CVI) female. Over 400,000,000 paired-end reads (100 base-pairs long) were sequenced on an Illumina instrument, and assembled into 206,041 contigs using Trinity software. Coverage was estimated to be at least 65%. A reference transcriptome comprising 96,090 unique components (“comps”) was annotated using Blast2GO. 40% of the comps had significant blast hits. 11% of the comps were successfully annotated with gene ontology (GO) terms. Expression of many comps was found to be near zero in one or more developmental stages suggesting that 35 to 48% of the transcriptome is “silent” at any given life stage. Transcripts involved in lipid biosynthesis pathways, critical for the C. finmarchicus life cycle, were identified and their expression pattern during development was examined. Relative expression of three transcripts suggests wax ester biosynthesis in late copepodites, but triacylglyceride biosynthesis in adult females. Two of these transcripts may be involved in the preparatory phase of diapause. A key environmental challenge for C. finmarchicus is the seasonal exposure to the dinoflagellate Alexandrium fundyense with high concentrations of saxitoxins, neurotoxins that block voltage-gated sodium channels. Multiple contigs encoding putative voltage-gated sodium channels were identified. They appeared to be the result of both alternate splicing and gene duplication. This is the first report of multiple NaV1 genes in a protostome. These data provide new insights into the transcriptome and physiology of this environmentally important zooplankter.
Citation: Lenz PH, Roncalli V, Hassett RP, Wu L-S, Cieslak MC, et al. (2014) De Novo Assembly of a Transcriptome for Calanus finmarchicus (Crustacea, Copepoda) – The Dominant Zooplankter of the North Atlantic Ocean. PLoS ONE 9(2): e88589. doi:10.1371/journal.pone.0088589