Dataset: Gulf of Alaska copepods: annotated transcriptomes
Data Citation:
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.
DOI:10.26008/1912/bco-dmo.908689.1
Spatial Extent: N:60.6667 E:-147.6667 S:59.845 W:-149.4667
Gulf of Alaska
Temporal Extent: 2015-05-10 - 2019-04-30
Project:
Principal Investigator:
Daniel K. Hartline (University of Hawaiʻi at Mānoa, PBRC)
Scientist:
Petra H. Lenz (University of Hawaiʻi at Mānoa, PBRC)
Contact:
Petra H. Lenz (University of Hawaiʻi at Mānoa, PBRC)
Technician:
Matthew C. Cieslak (University of Hawaiʻi at Mānoa, PBRC)
Data Manager:
Matthew C. Cieslak (University of Hawaiʻi at Mānoa, PBRC)
BCO-DMO Data Manager:
Lynne M. Merchant (Woods Hole Oceanographic Institution, WHOI BCO-DMO)
Version:
1
Version Date:
2024-07-02
Restricted:
No
Validated:
Yes
Current State:
Final no updates expected
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
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, Neocalanus cristatus, Eucalanus bungii and Metridia pacifica and three for Neocalanus flemingeri and two for Calanus marshallae. Total RNA from single individuals was used to construct gene libraries that were sequenced on an Illumina Next-Seq platform. Short-sequence reads were assembled with Trinity software and resulting transcripts were annotated using the SwissProt database with additional functional annotation using gene ontology terms and enzyme function. The annotations files are the first ones published for these species. The integrated dataset can be used for quantitative inter- and intra-species comparisons of gene expression patterns across biological processes using the annotations.
These data are further described in the following publications: Hartline, et al. (2023) (DOI: 10.1038/s41597-023-02130-1), Roncalli, et al. (2022) (DOI: 10.1111/mec.16354), and Roncalli, et al. (2019) (DOI: 10.1038/s42003-019-0565-5)