Dataset: Molecular identification of genetic variants of Neocalanus flemingeri in the Gulf of Alaska from samples collected from 2015 to 2023

Name: Molecular identification of genetic variants of Neocalanus flemingeri in the Gulf of Alaska from samples collected from 2015 to 2023
Published: 2025-02-21
Keywords: mtCOI, Neocalanus flemingeri, Gulf of Alaska, genetic variants, oceans

ValidatedRelease Date:2025-03-31Final no updates expectedDOI: 10.26008/1912/bco-dmo.954181.1Version 1 (2025-02-21)Dataset Type:Cruise Results

Principal Investigator: Petra H. Lenz (University of Hawaiʻi at Mānoa)

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

Scientist: Vittoria Roncalli (University of Hawaiʻi at Mānoa)

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

BCO-DMO Data Manager: Amber D. York (Woods Hole Oceanographic Institution)

Project: Collaborative Research: Zooplankton restarts in a high-latitude marine ecosystem: species-specific recruitment and development in early spring (Zooplankton recruitment)

Abstract

The subarctic Pacific is inhabit by three copepod congeners in the genus Neocalanus with an overlapping biogeographic range that includes the open ocean, marginal seas and fjord systems. Two distinct genetic variants of Neocalanus flemingeri have been reported from the western Pacific: the “small form” with an annual life cycle is found throughout the region, while the “large form” population with a 2-year life cycle is centered in the Sea of Okhotsk. Using a molecular approach, this study exami...

Cite Dataset

Spatial Extent: N:59.84 E:-145.42 S:56.23 W:-149.48
Temporal Extent: 2015-05-01 - 2023-03-24
Gulf of Alaska, sub-arctic Pacific

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Data File(s)	Type	Description	Action
954181_v1_bowtie-mapping-results.csv (19.69 KB)	Comma Separated Values (.csv)	Mapping results for RNA-Seq data showing short-sequence read counts aligned to mtCOI sequences from six different species. This is the primary data table of this BCO-DMO dataset (953181 version 1).	954181_v1_bowtie-mapping-results.csv View Table What is ERDDAP? SUBSET DATA VIEW TABLE CSV TSV MATLAB netCDF

Supplemental File(s)	Type	Description	Action
collections_regional_map.png (192.85 KB)	Portable Network Graphics (.png)	A regional map of the eastern Pacific and locates the collection area. These locations were previously published as part of Figure 1 of Pinchuk, et al. (2008).	collections_regional_map.png
species_list_copepods.csv (687.00 B)	Comma Separated Values (.csv)	Copepod ScientificNames and taxnomic identifiers. Columns: Name_in_Dataset, Category name as it appears in 954181_v1_copepod_species_filter.csv column "Species" ScientificName, The scientific name within "Species" column. AphiaID, World Register of Marine Species identifier (AphiaID) for the ScientificName LSID, Life Science Identifier (LSID) for the ScientificName	species_list_copepods.csv View Table
954181_v1_sra-run-table.csv (238.83 KB)	Comma Separated Values (.csv)	Supplemental table containing additional information related to the SRA accessions and BioSamples referenced in this dataset. These tables are the results of the NCBI SRA Run Selector for each of the BioProjects referenced in this dataset (PRJNA324453, PRJNA662858, PRJNA496596, PRJNA807352). See https://www.ncbi.nlm.nih.gov/Traces/study/#	954181_v1_sra-run-table.csv View Table
954181_v1_suitos-blast-data.csv (6.84 KB)	Comma Separated Values (.csv)	Search results and identification to genetic variant of mtCOI sequences obtained from a ca. 600 bp amplicon from DNA extracted from individual Neocalanus flemingeri. Column (parameter) information Station,GAK = numbering on Seward Line; PWS & KIP2 = Prince William Sound,Unitless, Sample,Sample sequence number; gaps in numbering due to failed sequencing reaction,Unitless, Date,Collection date,Da... Show more	954181_v1_suitos-blast-data.csv View Table
954181_v1_copepod_species_filter.csv (12.34 KB)	Comma Separated Values (.csv)	Reference mtCOI sequences and their source used in the species identification using Bowtie mapping. Sequences are provided in FASTA format. Column (parameter) information: Identifier,COI sequence identifier description ,Unitless, NCBI Accession,NCBI Accession number available at the National Center for Biotechnology Information,Unitless, COI location,The location of the reference sequence in ... Show more	954181_v1_copepod_species_filter.csv View Table

Files

Filename: 954181_v1_bowtie-mapping-results.csv (19.69 KB)
Type: Comma Separated Values (.csv)

Description:

Mapping results for RNA-Seq data showing short-sequence read counts aligned to mtCOI sequences from six different species. This is the primary data table of this BCO-DMO dataset (953181 version 1).

954181_v1_bowtie-mapping-results.csv View Table

Supplemental Files

Filename: collections_regional_map.png (192.85 KB)
Type: Portable Network Graphics (.png)

Description:

A regional map of the eastern Pacific and locates the collection area. These locations were previously published as part of Figure 1 of Pinchuk, et al. (2008).

collections_regional_map.png

Filename: species_list_copepods.csv (687.00 B)
Type: Comma Separated Values (.csv)

Description:

Copepod ScientificNames and taxnomic identifiers. Columns: Name_in_Dataset, Category name as it appears in 954181_v1_copepod_species_filter.csv column "Species" ScientificName, The scientific name within "Species" column. AphiaID, World Register of ...

species_list_copepods.csv View Table

Filename: 954181_v1_sra-run-table.csv (238.83 KB)
Type: Comma Separated Values (.csv)

Description:

Supplemental table containing additional information related to the SRA accessions and BioSamples referenced in this dataset. These tables are the results of the NCBI SRA Run Selector for each of the BioProjects referenced in this dataset (PRJNA3244...

954181_v1_sra-run-table.csv View Table

Filename: 954181_v1_suitos-blast-data.csv (6.84 KB)
Type: Comma Separated Values (.csv)

Description:

Search results and identification to genetic variant of mtCOI sequences obtained from a ca. 600 bp amplicon from DNA extracted from individual Neocalanus flemingeri. Column (parameter) information Station,GAK = numbering on Seward Line; PWS & KIP2 ...

954181_v1_suitos-blast-data.csv View Table

Filename: 954181_v1_copepod_species_filter.csv (12.34 KB)
Type: Comma Separated Values (.csv)

Description:

Reference mtCOI sequences and their source used in the species identification using Bowtie mapping. Sequences are provided in FASTA format. Column (parameter) information: Identifier,COI sequence identifier description ,Unitless, NCBI Accession,...

954181_v1_copepod_species_filter.csv View Table

The raw sequence data are available through the National Center for Biotechnology Information (NCBI):
RNA-Seq data: BioProjects: PRJNA324453, PRJNA662858, PRJNA496596, PRJNA807352
* Supplemental file "954181_v1_sra-run-table.csv" for SRA accession and BioSample collection information for the four bioprojects.

Related Datasets

IsDerivedFrom

Dataset: https://metazoogene.org/database/

MetaZooGene & O'Brien, T. (2023). MetaZooGene Atlas & Database (mzgdb): A collaborative product of SCOR WG157 (MetaZooGene) and Todd O'Brien. https://metazoogene.org/ accessed July 14, 2023.

IsDerivedFrom

Dataset: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA324453

University of Hawaii at Manoa (2016). Neocalanus flemingeri adult females. NCBI:BioProject: PRJNA324453. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; Available from: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA324453

IsDerivedFrom

Dataset: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA496596

University of Hawaii at Manoa (2018). Neocalanus flemingeri pre adult (CV). 2018/10. In: NCBI:BioProject: PRJNA496596[Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; Available from: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA496596

IsDerivedFrom

Dataset: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA662858

University of Hawaii at Manoa (2020). Neocalanus plumchrus, Neocalanus cristatus, Calanus marshallae, Eucalanus bungii, Metridia pacifica. NCBI:BioProject: PRJNA662858. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; Available from: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA662858

IsDerivedFrom

Dataset: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA807352

University of Hawaii at Manoa (2022). Neocalanus flemingeri, Response to food availability in pre-adult Neocalanus flemingeri. 2022/02. In: NCBI:BioProject: PRJNA807352 [Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; Available from: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA807352

Related Publications

Results

Block, L. N. (2024). Evaluating Species-Specific Naupliar Recruitment During the Winter-to-Spring Transition in the Northern Gulf of Alaska Using Molecular Tools (Master's thesis, University of Hawai'i at Manoa). Available from https://hdl.handle.net/10125/108679

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

Lenz, P. H., Block, L. N., Cieslak, M. C., Suitos, J., Roncalli, R., Castelfranco, A. M., and Hartline, D. K. (n.d.) Genetic divergence in a marine copepod associated with marginal habitats across the subarctic Pacific. Marine Ecology Progress Series, in review

Results

Roncalli, V., Cieslak, M. C., Castelfranco, A. M., Hopcroft, R. R., Hartline, D. K., & Lenz, P. H. (2021). Post-diapause transcriptomic restarts: insight from a high-latitude copepod. BMC Genomics, 22(1). https://doi.org/10.1186/s12864-021-07557-7

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

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Dataset: Molecular identification of genetic variants of Neocalanus flemingeri in the Gulf of Alaska from samples collected from 2015 to 2023

ValidatedRelease Date:2025-03-31Final no updates expectedDOI: 10.26008/1912/bco-dmo.954181.1Version 1 (2025-02-21)Dataset Type:Cruise Results

Principal Investigator: Petra H. Lenz (University of Hawaiʻi at Mānoa)

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

Scientist: Vittoria Roncalli (University of Hawaiʻi at Mānoa)

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

BCO-DMO Data Manager: Amber D. York (Woods Hole Oceanographic Institution)