http://lod.bco-dmo.org/id/dataset/908689
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2023-09-19
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
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
2024-07-02
publication
2024-07-02
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-07-16
publication
https://doi.org/10.26008/1912/bco-dmo.908689.1
Daniel K. Hartline
University of Hawaiʻi at Mānoa
principalInvestigator
Petra H. Lenz
University of Hawaiʻi at Mānoa
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: 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]
The dataset includes the annotation files of nine high-quality de novo transcriptomes generated from shotgun assemblies of short-sequence reads. Dataset Description: <p>These data are further described in the following publications:</p>
<p>Hartline, D. K., Cieslak, M. C., Castelfranco, A. M., Lieberman, B., Roncalli, V., &amp; Lenz, P. H. (2023). De novo transcriptomes of six calanoid copepods (Crustacea): a resource for the discovery of novel genes. <em>Scientific Data</em>, 10(1). https://doi.org/10.1038/s41597-023-02130-1</p>
<p>Roncalli, V., Niestroy, J., Cieslak, M. C., Castelfranco, A. M., Hopcroft, R. R., &amp; Lenz, P. H. (2022). Physiological acclimatization in high‐latitude zooplankton. <em>Molecular Ecology</em>, 31(6), 1753–1765. Portico. https://doi.org/10.1111/mec.16354</p>
<p>Roncalli, V., Cieslak, M. C., Germano, M., Hopcroft, R. R., &amp; Lenz, P. H. (2019). Regional heterogeneity impacts gene expression in the subarctic zooplankter Neocalanus flemingeri in the northern Gulf of Alaska. <em>Communications Biology</em>, 2(1). https://doi.org/10.1038/s42003-019-0565-5</p> Methods and Sampling: <p>Sample collection: Zooplankton were collected from depth (2015, 2017, 2018, and 2019) at two stations in Prince William Sound: “PWS2” (Lat: 60°32′. N, Long: -147°48.2′ W) and “PWS3” (Lat: 60°40.0′ N, Long: -147°40.0′ W,) and the Gulf station “GAK1” (Lat: 59º50.7′ N, Long: -149º28′ W). Collection date, station and depth stratum for each individual are given in Hartline et al. (2023) and Roncalli et al. (2019). Zooplankton collections were made using vertical net tows with either a QuadNet with two 150 µm and two 53 µm mesh nets (April and May collections), or a multiple opening and closing plankton net (0.25 m<sup>2 </sup>cross-sectional area; 150 μm mesh nets; Multinet-Midi, Hydro-Bios; September collections). Zooplankton samples were diluted, and copepods were sorted under a dissection microscope to select individuals from the target species. Briefly, live and undamaged individuals were identified and staged using morphological criteria and preserved in RNALater Stabilization Reagent. Preserved copepods were frozen first in -20ºC during the cruises, and then transferred to −80°C until further processing. Species identification were confirmed through the COI sequence in the assembled transcriptomes.</p>
<p>Total RNA extraction, library construction, RNA sequencing and quality control: For each target species, total RNA was extracted from individuals using QIAGEN RNeasy Plus Mini Kit (catalog # 74134) in combination with a Qiashredder column (catalog # 79654). Selection for sequencing was based on high RNA yields and purity of extraction (RIN&gt;8). The final list included pre-adults (CV) for&nbsp;<em>Neocalanus flemingeri</em>&nbsp;(n=3),&nbsp;<em>Neocalanus&nbsp;cristatus</em>&nbsp;(n=1),&nbsp;<em>Calanus marshallae</em>&nbsp;(n=2),&nbsp;<em>Eucalanus bungii</em>&nbsp;(n=1), an adult male (developmental stage CVI) for&nbsp;<em>Neocalanus plumchrus&nbsp;</em>(n=1) and an adult female for&nbsp;<em>Metridia pacifica</em>&nbsp;(n=1). Total RNA was shipped on dry ice to the Georgia Genomics Bioinformatics Core (https://dna.uga.edu) for RNA-Seq. There, double-stranded cDNA libraries (KAPA Stranded mRNA-Seq Kit, with KAPA mRNA Capture Beads (cat #KK8421]) from each individual were multiplexed and sequenced using an Illumina Next-Seq 500 instrument (High-Output Flow Cell, 150 bp, paired end). Quality of each RNA-Seq library was reviewed with the FastQC software28. From each RNA-Seq library, low quality reads were removed using FASTQ Toolkit (v. 2.2.5 within BaseSpace). Illumina adaptors, reads &lt;50 bp long, reads with an average Phred score &lt;30 and the first 12 bp from each read, were removed from each library. The same workflow was applied to all nine datasets.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1459235 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1459235
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756767 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756767
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756859 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756859
completed
Daniel K. Hartline
University of Hawaiʻi at Mānoa
808-956-8003
Pacific Biosciences Research Center 1993 East-West Rd.
Honolulu
HI
96822
USA
danh@pbrc.hawaii.edu
pointOfContact
Petra H. Lenz
University of Hawaiʻi at Mānoa
808-956-8003
Pacific Biosciences Research Center (PBRC), Bekesy Laboratory of Neurobiology 1993 East-West Road
Honolulu
HI
96822
United States
petra@hawaii.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
seq_id
Genbank_accession
Species
Station
Latitude
Longitude
Collection_date
Depth_range
Life_stage
Sex
Entry
Entry_name
evalue
Protein_names
Gene_names
Organism
Cross_reference_KEGG
Gene_ontology_IDs
Gene_ontology_GO
Gene_ontology_biological_process
Gene_ontology_cellular_component
Gene_ontology_molecular_function
BioProject
TSA_Master_Accession
Study_Accession
Study_Title
Experiement_Accession
Experiment_Title
SRA_Accession
BioSample
Sample_Accession
Illumina Next-Seq 500
Dissection microscope
Multinet-Midi, Hydro-Bios
QuadNet
theme
None, User defined
sequence
NCBI Genbank nucleotide accession
species scientific name (binomial)
station
latitude
longitude
date
depth range
stage
sex
controlled vocabulary term
No BCO-DMO term
protein_ID
NCBI BioProject accession
accession number
NCBI SRA study accession (SRP)
experiment type
NCBI SRA experiment accession (SRX)
NCBI SRA run accession (SRR)
NCBI BioSample accession
NCBI SRA Sample accession (SRS)
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Microscope - Optical
MultiNet
Plankton Net
instrument
BCO-DMO Standard Instruments
TXF18
TXS19
TXF15
TXF17
TXS15
service
Deployment Activity
Northern Gulf of Alaska
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Collaborative Proposal: Optimizing Recruitment of Neocalanus copepods through Strategic Timing of Reproduction and Growth in the Gulf of Alaska
https://osprey.bco-dmo.org/project/542182
Collaborative Proposal: Optimizing Recruitment of Neocalanus copepods through Strategic Timing of Reproduction and Growth in the Gulf of Alaska
<p>NSF abstract:</p>
<p>The Gulf of Alaska supports a diverse and productive marine community that includes many commercially important fishes. Toward the base of this food web are small planktonic crustaceans that serve as the primary food source for many of these fish, as well as seabirds and marine mammals. The copepod Neocalanus flemingeri is one of these crustaceans, and it experiences rapid population growth during each spring's algal, or phytoplankton, bloom. An apparent mismatch between the presence of the youngest stages of the copepod, or nauplii, in early winter and the unpredictable timing of the spring phytoplankton bloom several months later raises important questions about when females reproduce and how this relates to survival and growth of nauplii. Two types of dormancy, diapause in adult females and physiological quiescence in nauplii, may be the key to the success of this copepod species. Timing and duration of the egg-laying period by adult females is linked to emergence from diapause. In addition, nauplii may enter a state of physiological quiescence while food resources are low, resuming growth after phytoplankton levels increase. This research will address a long-standing goal of biological oceanographers to understand dormancy and its role in controlling population cycles in marine copepods. It will use new technologies in molecular biology called transcriptomics to catalog the messages used by the cells to control copepod life processes, in this case those related to dormancy in adults and nauplii. Undergraduate students and a postdoctoral investigator will be trained in interdisciplinary research, and students from Native Hawaiian and Native Alaskan groups will be targeted for participation. Fishing is a major industry in the Gulf of Alaska, and outreach will focus on communicating the role copepods play in marine ecosystems. New content, including images, will be generated for existing websites: the Seward Line long-term observation program, the Alaska Ocean Observing System and the Gulf Watch Alaska Program.</p>
<p>Recruitment to the Neocalanus flemingeri spring population is dependent on successful emergence from diapause followed by reproduction, survival, and growth of the next generation. Individual-based models have made significant progress in predicting population growth in calanoid copepods using food, temperature, and advection as key environmental factors. Few of these models include predictors for naupliar recruitment, however, because little is known about this part of the life cycle given sampling difficulties and the lack of biomarkers to evaluate physiological state. This study will leverage existing monitoring efforts to track the N. flemingeri population during the winter and early spring. The research team will combine laboratory and field approaches to determine duration and synchronization of reproduction in emerging females and strategies for naupliar survival during low food conditions. Zooplankton samples will be processed to enumerate nauplii to species and to determine physiological condition of both nauplii and adult females. Gene expression studies will develop molecular markers for female dormancy and reproductive readiness and for naupliar growth and possible dormancy, which in turn will be used to evaluate field collected individuals. This will be the first comprehensive study to combine molecular and traditional tools to connect diapausing adults, naupliar production, and the resulting spring population of copepodites.</p>
Neocalanus Gulf of Alaska
largerWorkCitation
project
Collaborative Research: Molecular profiling of the ecophysiology of dormancy induction in calanid copepods of the Northern Gulf of Alaska LTER site
https://osprey.bco-dmo.org/project/720280
Collaborative Research: Molecular profiling of the ecophysiology of dormancy induction in calanid copepods of the Northern Gulf of Alaska LTER site
<p>NSF Award Abstract:<br />
The sub-arctic Pacific sustains major fisheries with nearly all commercially important species depending either directly or indirectly on lipid-rich copepods (Neocalanus flemingeri, Neocalanus plumchrus, Neocalanus cristatus and Calanus marshallae). In turn, these species depend on a short-lived spring algal bloom for growth and the accumulation of lipid stores in order to complete an annual life cycle that includes a period of dormancy. The intellectual thrust of this project measures how the timing and magnitude of algal blooms affect preparation for dormancy using a combination of field and experimental observations. The Northern Gulf of Alaska - with four calanid species that experience dormancy, steep environmental gradients, well-described phytoplankton bloom dynamics, and a concurrent NSF-LTER program - provides an unusual opportunity to identify the factors that affect dormancy preparation. Education and outreach plans are integrated with the research. Educational efforts focus on interdisciplinary opportunities for undergraduate, graduate and post-doctoral trainees. The project will generate content for existing graduate and undergraduate courses. U. of Alaska Fairbanks and U. Hawaii at Manoa are Alaska Native and Native Hawaiian Serving Institutions, and students from these groups will be recruited to participate in the project. Because fishing is a major industry in the Gulf of Alaska, outreach will communicate the role copepods play in marine ecosystems using the concept of a dynamic food web tied to production cycles.</p>
<p>Diapause (dormancy) and the accompanying accumulation of lipids in copepods have been identified as key drivers in high latitude ecosystems that support economically important fisheries, including those of the Gulf of Alaska. While the disappearance of lipid-rich copepods has been linked to severe declines in fish stocks, little is known about the environmental conditions that are required for the successful completion of the copepod's life cycle. A physiological profiling approach that measures relative gene expression will be used to test two alternative hypotheses: the lipid accumulation window hypothesis, which holds that individuals enter diapause only after they have accumulated sufficient lipid stores, and the developmental program hypothesis, which holds that once the diapause program is activated, progression occurs independent of lipid accumulation. The specific objectives are: 1) determine the effect of food levels during N. flemingeri copepodite stages on progression towards diapause using multiple physiological and developmental markers; 2) characterize the seasonal changes in the physiological profile of N. flemingeri across environmental gradients and across years; 3) compare physiological profiles across co-occurring calanid species (N. flemingeri, Neocalanus plumchrus, Neocalanus cristatus and Calanus marshallae); and 4) estimate the reproductive potential of the overwintering populations of N. flemingeri. The broader scientific significance includes the acquisition of new genomic data and molecular resources that will be made publicly available through established data repositories, and the development of new tools for routinely obtaining physiological profiles of copepods.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
<p> </p>
<p><strong>NOTE:</strong> Petra Lenz is a former Principal Investigator (PI) and Andrew Christie is a former Co-Principal Investigator (Co-PI) on this project (award #1756767). Daniel Hartline is the PI listed for the award #1756767 and is now a former Co-PI on this project.</p>
Diapause preparation
largerWorkCitation
project
eng; USA
oceans
Northern Gulf of Alaska
-149.4667
-147.6667
59.845
60.6667
2015-05-10
2019-04-30
From projects that focused on the following 2 locations: 1. Gulf of Alaska; Seward Line 2. Northern Gulf of Alaska LTER
0
BCO-DMO catalogue of parameters from 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)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/931703.rdf
Name: seq_id
Units: unitless
Description: <p>The Trinity software names assembled by Trinity software are named hierarchically grouping sequences by similarity</p>
http://lod.bco-dmo.org/id/dataset-parameter/931704.rdf
Name: Genbank_accession
Units: unitless
Description: <p>NCBI (National Center for Biotechnology Information) Accession number for nucleotide sequence in the Transcriptome Shotgun Assembly (TSA) Sequence Database. The accession number is a unique identifier assigned to a record in the sequence database GenBank at NCBI. It is of the format [alphabetical prefix][series of digits].[version]. A change in the record is tracked by an integer extension of the accession number, an Accession.version identifier. The initial version of a sequence has the extension “.1”.</p>
http://lod.bco-dmo.org/id/dataset-parameter/931705.rdf
Name: Species
Units: unitless
Description: <p>A taxonomic binomial that consists of a genus name followed by the species name</p>
http://lod.bco-dmo.org/id/dataset-parameter/931706.rdf
Name: Station
Units: unitless
Description: <p>Station identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/931707.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Sampling location latitude, south is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/931708.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Sampling location longitude, west is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/931709.rdf
Name: Collection_date
Units: unitless
Description: <p>Collection date of organism</p>
http://lod.bco-dmo.org/id/dataset-parameter/931710.rdf
Name: Depth_range
Units: meters (m)
Description: <p>Collection depth range</p>
http://lod.bco-dmo.org/id/dataset-parameter/931711.rdf
Name: Life_stage
Units: unitless
Description: <p>Organism life history stage</p>
http://lod.bco-dmo.org/id/dataset-parameter/931712.rdf
Name: Sex
Units: unitless
Description: <p>sex</p>
http://lod.bco-dmo.org/id/dataset-parameter/931713.rdf
Name: Entry
Units: unitless
Description: <p>Uniprot KB entry identifies the top BLAST (Basic Local Alignment Search Tool) hit sequence to the assembled nucleotide sequence, searches were conducted using the blastx algorithm, #N/A indicates that there was no positive BLAST hit that met the e-value threshold</p>
http://lod.bco-dmo.org/id/dataset-parameter/931714.rdf
Name: Entry_name
Units: unitless
Description: <p>Uniprot entry name for the top hit, #N/A = no hit</p>
http://lod.bco-dmo.org/id/dataset-parameter/931715.rdf
Name: evalue
Units: unitless
Description: <p>Expected probability, e-value is the number of expected hits of similar quality (score) that could be found just by chance, cut-off value used for the annotation: E-value = 10-5, #N/A = no hit</p>
http://lod.bco-dmo.org/id/dataset-parameter/931716.rdf
Name: Protein_names
Units: unitless
Description: <p>Protein names, #N/A = no hit</p>
http://lod.bco-dmo.org/id/dataset-parameter/931717.rdf
Name: Gene_names
Units: unitless
Description: <p>Gene name based on the reference genome of the top hit, #N/A = no hit</p>
http://lod.bco-dmo.org/id/dataset-parameter/931718.rdf
Name: Organism
Units: unitless
Description: <p>Species name of top hit sequence, #N/A = no hit</p>
http://lod.bco-dmo.org/id/dataset-parameter/931719.rdf
Name: Cross_reference_KEGG
Units: unitless
Description: <p>KEGG identification based on the cross-reference of protein annotation and the Kyoto Encyclopedia of Genes and Genomes database, #N/A = no hit</p>
http://lod.bco-dmo.org/id/dataset-parameter/931720.rdf
Name: Gene_ontology_IDs
Units: unitless
Description: <p>GO terms based on cross-reference of protein annotation to the Gene Ontology Resource for functional identification as to Biological Process (BP), Cellular Component (CC) and Molecular Function (MF), proteins are typically involved in multiple processes, #N/A = no hit</p>
http://lod.bco-dmo.org/id/dataset-parameter/931721.rdf
Name: Gene_ontology_GO
Units: unitless
Description: <p>Identification of GO term with a functional description, #N/A = no hit</p>
http://lod.bco-dmo.org/id/dataset-parameter/931722.rdf
Name: Gene_ontology_biological_process
Units: unitless
Description: <p>Gene ontology terms and descriptions associated with Biological Process, #N/A = no hit</p>
http://lod.bco-dmo.org/id/dataset-parameter/931723.rdf
Name: Gene_ontology_cellular_component
Units: unitless
Description: <p>Gene ontology terms and descriptions associated with Cellular Component, #N/A = no hit</p>
http://lod.bco-dmo.org/id/dataset-parameter/931724.rdf
Name: Gene_ontology_molecular_function
Units: unitless
Description: <p>Gene ontology terms and descriptions associated with Molecular Function, #N/A = no hit</p>
http://lod.bco-dmo.org/id/dataset-parameter/931725.rdf
Name: BioProject
Units: unitless
Description: <p>NCBI BioProject accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/931726.rdf
Name: TSA_Master_Accession
Units: unitless
Description: <p>NCBI (National Center for Biotechnology Information) Accession number for the Transcriptome Shotgun Assembly (TSA) master record. The accession number is a unique identifier assigned to a master record in the database GenBank at NCBI. It is of the format [alphabetical prefix][00000000].[version]. A change in the record is tracked by an integer extension of the accession number, an Accession.version identifier. The initial version of a sequence has the extension “.1”.</p>
http://lod.bco-dmo.org/id/dataset-parameter/931727.rdf
Name: Study_Accession
Units: unitless
Description: <p>NCBI SRA study accession (SRP)</p>
http://lod.bco-dmo.org/id/dataset-parameter/931728.rdf
Name: Study_Title
Units: unitless
Description: <p>Title of NCBI SRA study</p>
http://lod.bco-dmo.org/id/dataset-parameter/931729.rdf
Name: Experiement_Accession
Units: unitless
Description: <p>Experiment metadata table (SRX) accession number in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA).</p>
http://lod.bco-dmo.org/id/dataset-parameter/931730.rdf
Name: Experiment_Title
Units: unitless
Description: <p>Title of the the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) experiment metadata table (SRX)</p>
http://lod.bco-dmo.org/id/dataset-parameter/931731.rdf
Name: SRA_Accession
Units: unitless
Description: <p>Run accession in the Sequence Read Archive (SRA) at NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/931732.rdf
Name: BioSample
Units: unitless
Description: <p>NCBI BioSample accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/931733.rdf
Name: Sample_Accession
Units: unitless
Description: <p>NCBI SRA Sample accession (SRS)</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
641460072
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/e5693dc0-ec66-4e19-bc93-440cbb8f03ed/content
download
https://doi.org/10.26008/1912/bco-dmo.908689.1
download
onLine
dataset
<p>Sample collection: Zooplankton were collected from depth (2015, 2017, 2018, and 2019) at two stations in Prince William Sound: “PWS2” (Lat: 60°32′. N, Long: -147°48.2′ W) and “PWS3” (Lat: 60°40.0′ N, Long: -147°40.0′ W,) and the Gulf station “GAK1” (Lat: 59º50.7′ N, Long: -149º28′ W). Collection date, station and depth stratum for each individual are given in Hartline et al. (2023) and Roncalli et al. (2019). Zooplankton collections were made using vertical net tows with either a QuadNet with two 150 µm and two 53 µm mesh nets (April and May collections), or a multiple opening and closing plankton net (0.25 m<sup>2 </sup>cross-sectional area; 150 μm mesh nets; Multinet-Midi, Hydro-Bios; September collections). Zooplankton samples were diluted, and copepods were sorted under a dissection microscope to select individuals from the target species. Briefly, live and undamaged individuals were identified and staged using morphological criteria and preserved in RNALater Stabilization Reagent. Preserved copepods were frozen first in -20ºC during the cruises, and then transferred to −80°C until further processing. Species identification were confirmed through the COI sequence in the assembled transcriptomes.</p>
<p>Total RNA extraction, library construction, RNA sequencing and quality control: For each target species, total RNA was extracted from individuals using QIAGEN RNeasy Plus Mini Kit (catalog # 74134) in combination with a Qiashredder column (catalog # 79654). Selection for sequencing was based on high RNA yields and purity of extraction (RIN&gt;8). The final list included pre-adults (CV) for&nbsp;<em>Neocalanus flemingeri</em>&nbsp;(n=3),&nbsp;<em>Neocalanus&nbsp;cristatus</em>&nbsp;(n=1),&nbsp;<em>Calanus marshallae</em>&nbsp;(n=2),&nbsp;<em>Eucalanus bungii</em>&nbsp;(n=1), an adult male (developmental stage CVI) for&nbsp;<em>Neocalanus plumchrus&nbsp;</em>(n=1) and an adult female for&nbsp;<em>Metridia pacifica</em>&nbsp;(n=1). Total RNA was shipped on dry ice to the Georgia Genomics Bioinformatics Core (https://dna.uga.edu) for RNA-Seq. There, double-stranded cDNA libraries (KAPA Stranded mRNA-Seq Kit, with KAPA mRNA Capture Beads (cat #KK8421]) from each individual were multiplexed and sequenced using an Illumina Next-Seq 500 instrument (High-Output Flow Cell, 150 bp, paired end). Quality of each RNA-Seq library was reviewed with the FastQC software28. From each RNA-Seq library, low quality reads were removed using FASTQ Toolkit (v. 2.2.5 within BaseSpace). Illumina adaptors, reads &lt;50 bp long, reads with an average Phred score &lt;30 and the first 12 bp from each read, were removed from each library. The same workflow was applied to all nine datasets.</p>
Specified by the Principal Investigator(s)
<p>De novo assembly, mapping, core-gene statistics: Individual de novo transcriptomes were generated from each RNA-Seq dataset at the National Center for Genome Analysis Support's (NCGAS; Indiana University, Bloomington, IN, USA) Mason Linux cluster using Trinity software (v. 2.4.0, except&nbsp;<em>N. plumchrus</em>, v. 2.0.6). Initial evaluation involved self-mapping of reads against the respective de novo assembly using Bowtie2 software (v. 2.3.5.1). Completeness of each de novo assembly was evaluated using Benchmarking Universal Single-Copy Orthologs (BUSCO) software31 by searching each assembly for the presence of eukaryote “core” genes using the Arthropoda database as reference (BUSCO version 5.3.2, dataset: arthropoda_odb10 (2020-09-10, 90 genomes, 1,013 BUSCOs). RNA-Seq data and transcriptome shotgun assemblies (TSAs) have been deposited with links to BioProject accession numbers PRJNA496596, and PRJNA662858 in the NCBI (National Center for Biotechnology Information) BioProject database (https://www.ncbi.nlm.nih.gov/bioproject/).</p>
<p>Functional annotation: Assemblies were functionally annotated against the NCBI Swiss-Prot protein and UniProt databases. Initial annotations were obtained by using the BLASTx algorithm on a local BLAST webserver with a Beowulf cluster using the Swiss-Prot protein database (downloaded February 2021) as reference and a threshold E-value of 10-5. Transcripts with BLAST annotations were then searched against the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway databases using UniProt.</p>
Specified by the Principal Investigator(s)
Processing steps for submitted annotated individual transcriptome files and metadata
The following are the submitted annotated transcriptome files that are processed to include metadata information and then concatenated together.
Filename: n-flem_CV2015_GAK1_AccAnnots_multispp_Aug23_q-fix-2.csv
Description: Neocalanus flemingeri 2015 stage CV annotated transcriptome
Filename: Nf2018_CV_Acc&Annot-single-rev_quoted.csv
Description: Neocalanus flemingeri 2018 stage CV annotated transcriptome
Filename: Nf2019_CV-PWS2_Acc&Annot.csv
Description: Neocalanus flemingeri 2019 stage CV annotated transcriptome
Filename: Np2015_maleR1_Acc&Annot.csv
Description: Neocalanus plumchrus 2015 stage Adult Male annotated transcriptome
Filename: Nc2017_CV_Acc&Annot.csv
Description: Neocalanus cristatus 2017 stage CV annotated transcriptome
Filename: Cm2017_CV_Acc&Annot.csv
Description: Calanus marshallae 2017 stage CV annotated transcriptome
Filename: Cm2018_CV_Acc&Annot.csv
Description: Calanus marshallae 2018 stage CV annotated transcriptome
Filename: Eb2017_CV_Acc&Annot.csv
Description: Eucalanus bungii 2017 stage CV annotated transcriptome
Filename: Mp2017_AF_Acc&Annot.csv
Description: Metridia pacifica 2017 stage Adult Female annotated transcriptome
---------------------------------------------------------------------
A metadata table with NCBI accession numbers was created using information from the submitter and by gathering accession numbers from NCBI for each BioProject.
Metadata from Submitter via email:
File Name: Summary Table for the Annotated Transcriptomes in BCO.docx
Title: Summary table from Lenz of metadata for transcriptome annotation files
Table columns
Species, Annot Filename, Stage/Collection information (which includes the Life Stage, Sex if indicated, Collection date, station, and collection depth range in meters), and NCBI TSA#
The accession number GHLB01000000 was changed to GHLB00000000 because the TSA project records accessions begin with a four-letter prefix of the TSA project followed by eight zeroes. A TSA project master accession (GenBank accession value) adds an extension of '.1' which indicates the version.
This explains it further:
See this 2013 article from NCBI on the definition of the TSA master accession number: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531190/
TSA projects will now contain a master record, in addition to records representing each of the assembled contigs. TSA will be using a similar accession number scheme to WGS as well. Like WGS accessions, the new TSA accessions have a four-letter prefix, representing the TSA project, followed by a two-digit version number and a six-digit contig number. For example, GAAA01000020 is contig 20 from the first version of TSA project GAAA. The TSA project master records have accessions that begin with the four-letter prefix followed by eight zeroes (e.g. GAAA00000000) and are indexed in the Nucleotide database.
A metadata table was created including metadata from the submitter:
File name: transcriptome_annotations_metadata_table.csv
Title: DM created metadata table of supporting information for each transcriptome annotation
Station lat and lon values from the 'Methods & Sampling' section of the submission were converted to decimal degrees with 6 digit precision.
A column named TSA_project_accession, with project accession numbers but without the version extension, was included to join the metadata table with the annotated transcriptome files later in processing, and it is removed in the final metadata table.
A column named TSA_Master_Accession which is the TSA_project_accession number with the version extension of '.1'.
From the National Center for Biotechnology Information (NCBI), various accession numbers and titles were added for each annotated transcriptome file.
Table columns:
Species, Station, Latitude, Longitude, Collection_date, Depth_range, Life_stage, Sex, BioProject, TSA_project_accession, TSA_Master_Accession, Study_Accession, Study_Title, Experiment_Accession, Experiment_Title, SRA_Accession, BioSample, Sample_Accession
---------------------------------------------
1) Used the BCO-DMO data processor laminar, to load in the submitted annotated transcriptomes files and the DM created metadata table. The fill value '#N/A' which stands for 'no result found' was kept.
2) Created a new column for each annotated transcriptome file, TSA_project_accession, to join on the metadata table using regular expressions to extract the first 4 letters of each TSA accession number and then concatenate 8 zeros. This is the NCBI format for a TSA project accession number.
3) Joined each annotated transcriptome file with the metadata table on the key TSA_project_accession.
4) Removed the parameter TSA_project_accession, since it was only used for the Join process. The TSA project accession number with the version will be recorded as the parameter TSA_master_accession.
5) Added a suffix ‘.1’ to each TSA accession number to indicate version 1.
6) Renamed Accession# to Genbank_accession which is the TSA accession value with a version extension.
7) Renamed parameters in each annotated transcriptome file by removing commas and parentheses, and replacing spaces with underscores to follow BCO-DMO parameter naming conventions.
8) Reordered the parameters so that experiment metadata parameters are at the beginning of each annotated transcriptome file and most NCBI accession numbers are at the end
9) Using a second laminar processor pipeline, loaded in the individual annotated transcriptomes files that were created by laminar processing above and concatenated all the individual annotated transcriptome files into the primary dataset file.
10) Saved the output of the laminar processing to the supplemental files of the metadata table and the individual transcriptome annotation files.
----------------------------
Created a Species WoRMS taxonomy file species_list.csv by using the WoRMS website to create a table of the species name and their corresponding AphiaID and LSID values.
Checked that all the species names in the transcriptome annotation files matched those found in WoRMS.
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Illumina Next-Seq 500
Illumina Next-Seq 500
PI Supplied Instrument Name: Illumina Next-Seq 500 PI Supplied Instrument Description:Desktop sequencer Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
Dissection microscope
Dissection microscope
PI Supplied Instrument Name: Dissection microscope PI Supplied Instrument Description:An optical microscope variant Instrument Name: Microscope - Optical Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope". Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
Multinet-Midi, Hydro-Bios
Multinet-Midi, Hydro-Bios
PI Supplied Instrument Name: Multinet-Midi, Hydro-Bios PI Supplied Instrument Description:Hydro-Bios Multinet-Midi with a 0.25 m2 cross-sectional area and 150 μm mesh Instrument Name: MultiNet Instrument Short Name:MultiNet Instrument Description: The MultiNet© Multiple Plankton Sampler is designed as a sampling system for horizontal and vertical collections in successive water layers. Equipped with 5 or 9 net bags, the MultiNet© can be delivered in 3 sizes (apertures) : Mini (0.125 m2), Midi (0.25 m2) and Maxi (0.5 m2). The system consists of a shipboard Deck Command Unit and a stainless steel frame to which 5 (or 9) net bags are attached by means of zippers to canvas. The net bags are opened and closed by means of an arrangement of levers that are triggered by a battery powered Motor Unit. The commands for actuation of the net bags are given via single or multi-conductor cable between the Underwater Unit and the Deck Command Unit. Although horizontal collections typically use a mesh size of 300 microns, mesh sizes from 100 to 500 may also be used. Vertical collections are also common. The shipboard Deck Command Unit displays all relevant system data, including the actual operating depth of the net system. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/NETT0099/
QuadNet
QuadNet
PI Supplied Instrument Name: QuadNet PI Supplied Instrument Description:Two 150 µm and two 53 µm mesh nets Instrument Name: Plankton Net Instrument Short Name:Plankton Net Instrument Description: A Plankton Net is a generic term for a sampling net that is used to collect plankton. It is used only when detailed instrument documentation is not available. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/22/
Cruise: TXF18
TXF18
R/V Tiglax
Community Standard Description
International Council for the Exploration of the Sea
R/V Tiglax
vessel
TXF18
Russell R. Hopcroft
University of Alaska Fairbanks
https://nga.lternet.edu/wp-content/uploads/2019/04/Cruise-Report-TXF18.pdf
Report describing TXF18
Cruise: TXS19
TXS19
R/V Tiglax
Community Standard Description
International Council for the Exploration of the Sea
R/V Tiglax
vessel
TXS19
Russell R. Hopcroft
University of Alaska Fairbanks
https://nga.lternet.edu/wp-content/uploads/2019/10/Cruise-Report-TXS19.pdf
Report describing TXS19
Cruise: TXF15
TXF15
R/V Tiglax
Community Standard Description
International Council for the Exploration of the Sea
R/V Tiglax
vessel
TXF15
Russell R. Hopcroft
University of Alaska Fairbanks
https://www.ncei.noaa.gov/access/ocean-carbon-acidification-data-system/oceans/Coastal/seward.html
Report describing TXF15
Cruise: TXF17
TXF17
R/V Tiglax
Community Standard Description
International Council for the Exploration of the Sea
R/V Tiglax
vessel
TXF17
Russell R. Hopcroft
University of Alaska Fairbanks
https://www.ncei.noaa.gov/access/ocean-carbon-acidification-data-system/oceans/Coastal/seward.html
Report describing TXF17
Cruise: TXS15
TXS15
R/V Tiglax
Community Standard Description
International Council for the Exploration of the Sea
R/V Tiglax
vessel
TXS15
Russell R. Hopcroft
https://www.ncei.noaa.gov/access/ocean-carbon-acidification-data-system/oceans/Coastal/seward.html
Report describing TXS15
R/V Tiglax
Community Standard Description
International Council for the Exploration of the Sea
R/V Tiglax
vessel