Dataset: Annotated de novo transcriptomes generated from six co-occurring species of calanoid copepods from the R/V Tiglax TXF18, TXS19, TXF15, TXF17 in the Gulf of Alaska from 2015-2019

ValidatedFinal no updates expectedDOI: 10.26008/1912/bco-dmo.908689.1Version 1 (2024-07-02)Dataset Type:experimentalDataset Type:Cruise Results

Principal Investigator: Daniel K. Hartline (University of Hawaiʻi at Mānoa)

Scientist, Contact: Petra H. Lenz (University of Hawaiʻi at Mānoa)

Technician, Data Manager: Matthew C. Cieslak (University of Hawaiʻi at Mānoa)

BCO-DMO Data Manager: Lynne M. Merchant (Woods Hole Oceanographic Institution)

Project: Collaborative Proposal: Optimizing Recruitment of Neocalanus copepods through Strategic Timing of Reproduction and Growth in the Gulf of Alaska (Neocalanus Gulf of Alaska)

Project: Collaborative Research: Molecular profiling of the ecophysiology of dormancy induction in calanid copepods of the Northern Gulf of Alaska LTER site (Diapause preparation)

Abstract

The dataset includes the annotation files of nine high-quality de novo transcriptomes generated from shotgun assemblies of short-sequence reads. The species are ecologically-important members of sub-arctic North Pacific marine zooplankton communities. The de novo assemblies included one generated several years ago plus eight new ones generated from six co-occurring species of calanoid copepods in the Gulf of Alaska. The transcriptomes include the first published ones for Neocalanus plumchrus, Ne...

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Cite Dataset

These data are further described in the following publications:

Hartline, D. K., Cieslak, M. C., Castelfranco, A. M., Lieberman, B., Roncalli, V., & Lenz, P. H. (2023). De novo transcriptomes of six calanoid copepods (Crustacea): a resource for the discovery of novel genes. Scientific Data, 10(1). https://doi.org/10.1038/s41597-023-02130-1

Roncalli, V., Niestroy, J., Cieslak, M. C., Castelfranco, A. M., Hopcroft, R. R., & Lenz, P. H. (2022). Physiological acclimatization in high‐latitude zooplankton. Molecular Ecology, 31(6), 1753–1765. Portico. https://doi.org/10.1111/mec.16354

Roncalli, V., Cieslak, M. C., Germano, M., Hopcroft, R. R., & Lenz, P. H. (2019). Regional heterogeneity impacts gene expression in the subarctic zooplankter Neocalanus flemingeri in the northern Gulf of Alaska. Communications Biology, 2(1). https://doi.org/10.1038/s42003-019-0565-5

Related Datasets

IsRelatedTo
Dataset: Molecular identification of genetic variants of Neocalanus flemingeri
Relationship Description: This dataset (908689) was cited in the methods of another dataset (954181) "...The reference consisted of consensus sequences obtained by comparing sequences downloaded from NCBI and from de novo assemblies (Hartline et al., 2023; Hartline et al., 2024 [BCO-DMO dataset 908689]). "
Block, L. N., Lenz, P. H. (2025) Molecular identification of genetic variants of Neocalanus flemingeri in the Gulf of Alaska from samples collected from 2015 to 2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-02-21 http://lod.bco-dmo.org/id/dataset/954181
IsRelatedTo
Dataset: Neocalanus flemingeri incubation experiment: gene expression
Lenz, P. H., Hartline, D. K., Roncalli, V., Block, L. N., Niestroy, J. L., Cieslak, M. C. (2024) Gene expression profiles for Neocalanus flemingeri pre adults (CV) exposed to four different experimental food conditions collected from the M/V Dora in the Gulf of Alaska at station GAK1 from April 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-05-30 doi:10.26008/1912/bco-dmo.914459.1
IsRelatedTo
Dataset: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA496596
University of Hawaii at Manoa (2018). Neocalanus flemingeri, Neocalanus flemingeri pre adult (CV). 2018/10. NCBI:BioProject: PRJNA496596 [Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; Available from: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA496596.
IsRelatedTo
Dataset: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA662858
University of Hawaii at Manoa (2018). Neocalanus plumchrus, Neocalanus cristatus, Calanus marshallae, Eucalanus bungii, Metridia pacifica, Ocean ZOOP-Zooplankton transcriptomes. 2020/09. NCBI:BioProject: PRJNA662858.[Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; Available from: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA662858

Related Publications

Results
Hartline, D. K., Cieslak, M. C., Castelfranco, A. M., Lieberman, B., Roncalli, V., & Lenz, P. H. (2023). De novo transcriptomes of six calanoid copepods (Crustacea): a resource for the discovery of novel genes. Scientific Data, 10(1). https://doi.org/10.1038/s41597-023-02130-1
Results
Roncalli, V., Cieslak, M. C., Germano, M., Hopcroft, R. R., & Lenz, P. H. (2019). Regional heterogeneity impacts gene expression in the subarctic zooplankter Neocalanus flemingeri in the northern Gulf of Alaska. Communications Biology, 2(1). https://doi.org/10.1038/s42003-019-0565-5
Results
Roncalli, V., Niestroy, J., Cieslak, M. C., Castelfranco, A. M., Hopcroft, R. R., & Lenz, P. H. (2022). Physiological acclimatization in high‐latitude zooplankton. Molecular Ecology, 31(6), 1753–1765. Portico. https://doi.org/10.1111/mec.16354
Methods
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., Harris, M. A., Hill, D. P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J. C., Richardson, J. E., Ringwald, M., Rubin, G. M., & Sherlock, G. (2000). Gene Ontology: tool for the unification of biology. Nature Genetics, 25(1), 25–29. https://doi.org/10.1038/75556
Methods
Bateman, A., Martin, M.-J., Orchard, S., Magrane, M., Agivetova, R., Ahmad, S., Alpi, E., Bowler-Barnett, E. H., Britto, R., Bursteinas, B., Bye-A-Jee, H., Coetzee, R., Cukura, A., Da Silva, A., Denny, P., Dogan, T., Ebenezer, T., Fan, J., … Teodoro, D. (2020). UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Research, 49(D1), D480–D489. https://doi.org/10.1093/nar/gkaa1100

Hartline, D. K., Lenz, P. H., Cieslak, M. C. (2024) Annotated de novo transcriptomes generated from six co-occurring species of calanoid copepods from the R/V Tiglax TXF18, TXS19, TXF15, TXF17 in the Gulf of Alaska from 2015-2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-07-02 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.908689.1 [access date]

Terms of Use

This dataset is licensed under Creative Commons Attribution 4.0.


If you wish to use this dataset, it is highly recommended that you contact the original principal investigators (PI). Should the relevant PI be unavailable, please contact BCO-DMO (info@bco-dmo.org) for additional guidance. For general guidance please see the BCO-DMO Terms of Use document.

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Funded by the U.S. National Science Foundation