Dataset: Multiyear RNA-Seq of Neocalanus flemingeri stages CV and Adult Female from the R/V Tiglax and R/V Sikuliaq in the Northern Gulf of Alaska from 2015-2022

ValidatedFinal no updates expectedDOI: 10.26008/1912/bco-dmo.922330.1Version 1 (2024-07-26)Dataset Type:Cruise ResultsDataset Type:experimental

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

Scientist: Vittoria Roncalli (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

High-throughput sequencing study of field-collected Neocalanus flemingeri pre-adults (stage CV) and adult females between 2015 and 2022. Dataset includes information and accession numbers of the raw sequence reads. Zooplankton collections were made in the northern Gulf of Alaska in collaboration with the Seward Long-term Monitoring Program and the northern Gulf of Alaska Long-term Ecological Research Program (LTER). Pre-adults were collected during the spring from multiple stations, sorted from ...

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In collaboration with the Seward Long-Term Observation Program (LTOP) (http://www.sfos.uaf.edu/sewardline/) and the NGA LTER Program (https://nga.lternet.edu/), we obtained Neocalanus flemingeri individuals during the annual April-May and September oceanographic cruises. During the spring cruises stage CV individuals were collected from four to six locations: spanning the inner shelf to outer shelf gradient along the Seward Line in the northern Gulf of Alaska and at least one station in adjoining Prince William Sound. Samples were collected using a CalVET net (53-µm mesh) towed vertically from 100 m depth to surface. Mixed plankton samples were immediately diluted with surface seawater, and maintained at ~5ºC prior to and during sorting. From each station actively swimming (healthy) N. flemingeri CVs were rapidly sorted under the microscope and preserved within 15 minutes to 1hr of the tow in RNALater Stabilization Reagent (QIAGEN). The rapid sorting of live plankton can lead to misidentifications given the presence of closely related congeners, thus species verification is recommended using the RNA-seq data to check the cytochrome c oxidase subunit 1 (mtCOI) sequence. In September, diapausing N. flemingeri adult females were sorted from collections obtained with a Midi Multinet towed vertically. Collections were diluted with seawater upon net retrieval. Individuals were sorted under the microscope from the 300-700 depth collections and either preserved immediately in RNALater or separated into holding containers for incubation experiments. In three years (2015, 2016, 2017) additional adult females were incubated for different lengths of time and preserved after a specified interval as indicated in the sample information. In July, 2019 we participated in a ship of opportunity cruise to the Gulf of Alaska Seamounts (SKQ201916S) and preserved diapausing adult females collected between 1000-2000 meters from two offshore stations (GAK19 and DeepQuinn).

RNA extraction, gene library preparation and RNA-seq

Total RNA was extracted from individual CV from each station using QIAGEN RNeasy Plus Mini Kit (catalog # 74134) in combination with a Qiashredder column (catalog # 79654) following the instructions of the manufacturer and stored at -80ºC. Total RNA concentration and quality were checked using an Agilent Model 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA). For each station, total RNA from three of the ten individuals with high quality RNA yields were selected for RNA-seq and shipped on dry ice to the University of Georgia Genomics Facility (dna.uga.edu). There, double-stranded cDNA libraries were prepared from total RNA extracted using the Kapa Stranded mRNA-seq kit (KK8420) following manufacturer’s instructions. Briefly, RNA samples were first purified with two oligo-dT selection (polyA enrichment using oligodT beds), and then fragmented and reverse transcribed into double-stranded complementary DNA. Each sample was tagged with an indexed adapter and they were simultaneously paired-end sequenced (PE150 or PE75 bp) using an Illumina NextSeq 500 instrument using High-Output Flow Cell. Data in NCBI are the raw sequence reads.


Related Datasets

IsRelatedTo

Dataset: Molecular identification of genetic variants of Neocalanus flemingeri
Relationship Description: This dataset was cited in metadata of dataset (954181) as a related dataset that provides additional information to National Center for Biotechnology Information raw sequences.
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
Relationship Description: This dataset was cited in metadata of dataset (954181) as a related dataset that provides additional information to National Center for Biotechnology Information raw sequences.
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/PRJNA324453
University of Hawaii at Manoa (2016). Neocalanus flemingeri, Neocalanus flemingeri adult females. 2016/06. NCBI:BioProject: PRJNA324453 [Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; Available from: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA324453
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.

Related Publications

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
Results

Roncalli, V., Cieslak, M. C., Hopcroft, R. R., & Lenz, P. H. (2020). Capital Breeding in a Diapausing Copepod: A Transcriptomics Analysis. Frontiers in Marine Science, 7. doi:10.3389/fmars.2020.00056
Results

Roncalli, V., Cieslak, M. C., Sommer, S. A., Hopcroft, R. R., & Lenz, P. H. (2018). De novo transcriptome assembly of the calanoid copepod Neocalanus flemingeri: A new resource for emergence from diapause. Marine Genomics, 37, 114–119. doi:10.1016/j.margen.2017.09.002
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