Dataset: Links to a microarray and transcriptome for C. finmarchicus in the Gulf of Maine from 2008-2011 (CFINTRANSCRIPT project)

This project focused on developing molecular tools based on relative gene expression to investigate physiological ecology of Calanus finmarchicus (Calanoida: Copepoda) in the Gulf of Maine. For this project, a custom microarray was developed for this species and tested on field and experimental data. Using RNA-seq technology, a de novo transcriptome was obtained from RNA extracted from different developmental stages of C. finmarchicus from embryo to adult female.

Datasets generated through this project were deposited at NCBI (www.ncbi.nlm.nih.gov) in 5 separate NCBI BioProjects:

1. BioProject PRJNA151477 (www.ncbi.nlm.nih.gov/bioproject/PRJNA151477): Microarray platform information and relative expression data for lipid-rich vs. lipid-poor pre-adults (stage CV) and adult females maintained at high- and low-food levels.
2. BioProject PRJNA149523 (www.ncbi.nlm.nih.gov/bioproject/PRJNA1495230): Microarray platform information and relative expression data for pre-adults (stage CV) and adult females collected from depth (130-170 m) and from surface waters (0-30 m).
3. BioProject PRJNA236528 (www.ncbi.nlm.nih.gov/bioproject/PRJNA236528): RNA-Seq data. Data includes biosample description, raw sequence data for each sample, and transcriptome shotgun assembly of sequences. Calanus finmarchicus transcriptome from 6 developmental stages (embryo, early nauplius, late nauplius, early copepodite, late copepodite and adult females).
4. BioProject PRJNA312028 (http://www.ncbi.nlm.nih.gov/bioproject/PRJNA312028): RNA-Seq data. Data includes biosample description, raw sequence data for each sample, and transcriptome shotgun assembly of sequences. Calanus finmarchicus adult female transcriptome of Alexandrium fundyense response.
5. Bioproject: PRJNA356331(http://www.ncbi.nlm.nih.gov/bioproject/PRJNA356331): RNA-Seq data. Data includes biosample description, raw sequence data for each sample, and transcriptome shotgun assembly of sequences Calanus finmarchicus late nauplii (NV-NVI) transcriptome of Alexandrium fundyense response.

Dataset Related References:

Lenz, P.H., Roncalli, V., Hassett, R.P., Wu, L.-S., Cieslak, M.C., Hartline, D.K. and Christie, A.E. (2014) De novo assembly of a transcriptome for Calanus finmarchicus (Crustacea, Copepoda) – the dominant zooplankter of the North Atlantic Ocean. Plos One 9: e885389 DOI: 10.1371/journal.pone.0088589)

Roncalli, V., Cieslak, M.C., Lenz, P.H. Transcriptomic responses of the calanoid copepod Calanus finmarchicus to the saxitoxin producing dinoflagellate Alexandrium fundyense. Scientific Reports 6, Article number: 25708 (2016) doi:10.1038/srep25708.

Roncalli V., Cieslak M.C., Lenz P.H. (2016) Data from: Transcriptomic responses of the calanoid copepod Calanus finmarchicus to the saxitoxin producing dinoflagellate Alexandrium fundyense. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.11978

Roncalli, V., Jungbluth, M.J., Lenz, P.H. (2016). Glutathione S-transferase regulation in Calanus finmarchicus feeding on the toxic dinoflagellate Alexandrium fundyense. PloS One, 11(7): e0159563.

Roncalli, V., Turner, J.T., Kulis, D., Anderson, D.M., Lenz, P.H. (2016). The effect of the toxic dinoflagellate Alexandrium fundyense on the fitness of the calanoid copepod Calanus finmarchicus. Harmful Algae, 51: 56-66

Roncalli, V., Lenz, P.H., Cieslak, M.C., Hartline, D.K. (2017). Complementary mechanisms for neurotoxin resistance in a copepod. Scientific Reports, 2017; 7: 14201, doi: 10.1038/s41598-017-14545-z

Methodology References:

Microarray

Lenz, P.H., Unal, E., Hassett, R.P., Smith, C.M., Bucklin, A., Christie, A.E. and Towle, D.W. (2012) Functional genomics resources for the North Atlantic copepod, Calanus finmarchicus: EST database and physiological microarray. Comparative Biochemistry Physiology Part D, Genomics & Proteomics, 7:110-123

Unal, E., Bucklin, A., Lenz, P.H. and Towle, D.W. (2013) Gene expression of the marine copepod Calanus finmarchicus: Responses to small-scale environmental variation in the Gulf of Maine (NW Atlantic Ocean). Journal of Experimental and Marine Biology and Ecology, 446:76-85

Gene discovery studies using C. finmarchicus transcriptome:

Christie, A.E., Fontanilla, T.M., Nesbit, K.T. and Lenz, P.H. (2013) Prediction of the protein components of a putative Calanus finmarchicus (Crustacea, Copepoda) circadian signaling system using a de novo assembled transcriptome. Comparative Biochemistry and Physiology Part D, Genomics & Proteomics, 8:165-193

Christie, A.E., Roncalli, V., Wu, L.-S., Garrote, C.L., Doak, T. and Lenz, P.H. (2013) Peptidergic signaling in Calanus finmarchicus (Crustacea: Copepoda): in silico identification of putative peptide hormones and their receptors using a de novo assembled transcriptome. General and Comparative Endocrinology, 187:117-135

Christie, A.E., Roncalli, V., Batta Lona, P., McCoole, M.D., King, B.L., Bucklin, A., Hartline, D.K. and Lenz, P.H. (2013) In silico characterization of the insect diapause-associated protein couch potato (CPO) in Calanus finmarchicus (Crustacea: Copepoda). Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics, 8:45-57.

Christie, A.E., Fontanilla, T.M., Roncalli, V., Cieslak, M.C. and Lenz, P.H. (2014) Diffusible gas transmitter signaling in the copepod crustacean Calanus finmarchicus: Identification of the biosynthetic enzymes of nitric oxide (NO), carbon monoxide (CO) and hydrogen sulfide (H2S) using a de novo assembled transcriptome. General and Comparative Endocrinology 202: 76-86

Christie, A.E., Fontanilla, T.M., Roncalli, V., Cieslak, M.C. and Lenz, P.H. (2014) Identification and developmental expression of the enzymes responsible for dopamine, histamine, octopamine and serotonin biosynthesis in the copepod crustacean Calanus finmarchicus. General and Comparative Endocrinology 195: 28-39.

Roncalli, V., Cieslak, M.C., Passamaneck, Y., Christie, A.E., & Lenz, P.H. (2015). Glutathione S-Transferase (GST) Gene diversity in the crustacean Calanus finmarchicus - contributors to cellular detoxification. PloS One, 10(5): e012332.