| Summary: | <p>This project focused on developing molecular tools based on relative gene expression to investigate physiological ecology of <em>Calanus finmarchicus</em> (Calanoida: Copepoda) in the Gulf of Maine. For this project, a <strong>custom microarray</strong> was developed for this species and tested on field and experimental data. Using <em>RNA-seq</em> technology, a <strong><em>de novo</em> transcriptome</strong> was obtained from RNA extracted from different developmental stages of <em>C. finmarchicus </em>from embryo to adult female.</p> <p>Datasets generated through this project were deposited at NCBI (<a href=\"http://www.ncbi.nlm.nih.gov/\">www.ncbi.nlm.nih.gov</a>) in 5 separate NCBI BioProjects:</p> <ol> <li>BioProject PRJNA151477 (<a href=\"http://www.ncbi.nlm.nih.gov/bioproject/PRJNA1495230\" target=\"_blank\">www.ncbi.nlm.nih.gov/bioproject/PRJNA151477</a>): 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.</li> <li>BioProject PRJNA149523 (<a href=\"http://www.ncbi.nlm.nih.gov/bioproject/PRJNA1495230\" target=\"_blank\">www.ncbi.nlm.nih.gov/bioproject/PRJNA1495230</a>): 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).</li> <li>BioProject PRJNA236528 (<a href=\"http://www.ncbi.nlm.nih.gov/bioproject/PRJNA236528\" target=\"_blank\">www.ncbi.nlm.nih.gov/bioproject/PRJNA236528</a>): RNA-Seq data. Data includes biosample description, raw sequence data for each sample, and transcriptome shotgun assembly of sequences. <em>Calanus finmarchicus</em> transcriptome from 6 developmental stages (embryo, early nauplius, late nauplius, early copepodite, late copepodite and adult females).</li> <li>BioProject PRJNA312028 <a href=\"http://www.ncbi.nlm.nih.gov/bioproject/PRJNA312028\" target=\"_blank\">(http://www.ncbi.nlm.nih.gov/bioproject/PRJNA312028</a>): RNA-Seq data. Data includes biosample description, raw sequence data for each sample, and transcriptome shotgun assembly of sequences. <em>Calanus finmarchicus</em> adult female transcriptome of Alexandrium fundyense response.</li> <li>Bioproject: PRJNA356331(<a href=\"http://www.ncbi.nlm.nih.gov/bioproject/PRJNA356331\" target=\"_blank\">http://www.ncbi.nlm.nih.gov/bioproject/PRJNA356331</a>): RNA-Seq data. Data includes biosample description, raw sequence data for each sample, and transcriptome shotgun assembly of sequences <em>Calanus </em><em>finmarchicus</em> late nauplii (NV-NVI) transcriptome of <em>Alexandrium </em><em>fundyense</em> response.</li> </ol> <p><strong>Dataset Related References:</strong></p> <p>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 <em>Calanus </em><em>finmarchicus</em> (Crustacea, Copepoda) – the dominant zooplankter of the North Atlantic Ocean. Plos One 9: e885389 <a href=\"http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0088589\" target=\"_blank\">DOI: 10.1371/journal.pone.0088589</a>)</p> <p>Roncalli, V., Cieslak, M.C., Lenz, P.H. Transcriptomic responses of the calanoid copepod <em>Calanus </em><em>finmarchicus</em> to the saxitoxin producing dinoflagellate Alexandrium fundyense. Scientific Reports 6, Article number: 25708 (2016) <a href=\"http://www.nature.com/articles/srep25708\">doi:10.1038/srep25708</a>.</p> <p>Roncalli V., Cieslak M.C., Lenz P.H. (2016) Data from: Transcriptomic responses of the calanoid copepod <em>Calanus </em><em>finmarchicus</em> to the saxitoxin producing dinoflagellate Alexandrium fundyense. Dryad Digital Repository. <a href=\"http://dx.doi.org/10.5061/dryad.11978\" target=\"_blank\">http://dx.doi.org/10.5061/dryad.11978</a></p> <p>Roncalli, V., Jungbluth, M.J., Lenz, P.H. (2016). Glutathione S-transferase regulation in <em>Calanus </em><em>finmarchicus</em> feeding on the toxic dinoflagellate Alexandrium fundyense. PloS One, 11(7): e0159563.</p> <p>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 <em>Calanus </em><em>finmarchicus</em>. Harmful Algae, 51: 56-66</p> <p>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</p> <p><strong>Methodology References:</strong></p> <p><u>Microarray</u></p> <p>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, <em>Calanus </em><em>finmarchicus</em>: EST database and physiological microarray. Comparative Biochemistry Physiology Part D, Genomics & Proteomics, 7:110-123</p> <p>Unal, E., Bucklin, A., Lenz, P.H. and Towle, D.W. (2013) Gene expression of the marine copepod <em>Calanus finmarchicus</em>: 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</p> <p><strong>Gene discovery studies using <em>C. finmarchicus</em> transcriptome:</strong></p> <p>Christie, A.E., Fontanilla, T.M., Nesbit, K.T. and Lenz, P.H. (2013) Prediction of the protein components of a putative <em>Calanus </em><em>finmarchicus</em> (Crustacea, Copepoda) circadian signaling system using a de novo assembled transcriptome. Comparative Biochemistry and Physiology Part D, Genomics & Proteomics, 8:165-193</p> <p>Christie, A.E., Roncalli, V., Wu, L.-S., Garrote, C.L., Doak, T. and Lenz, P.H. (2013) Peptidergic signaling in <em>Calanus </em><em>finmarchicus</em> (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</p> <p>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 <em>Calanus </em><em>finmarchicus</em> (Crustacea: Copepoda). Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics, 8:45-57.</p> <p>Christie, A.E., Fontanilla, T.M., Roncalli, V., Cieslak, M.C. and Lenz, P.H. (2014) Diffusible gas transmitter signaling in the copepod crustacean <em>Calanus </em><em>finmarchicus</em>: 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</p> <p>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 <em>Calanus </em><em>finmarchicus</em>. General and Comparative Endocrinology 195: 28-39.</p> <p>Roncalli, V., Cieslak, M.C., Passamaneck, Y., Christie, A.E., & Lenz, P.H. (2015). Glutathione S-Transferase (GST) Gene diversity in the crustacean <em>Calanus finmarchicus</em> - contributors to cellular detoxification. PloS One, 10(5): e012332.</p>
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