http://lod.bco-dmo.org/id/dataset/991343
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
2026-01-13
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Annotated genome of Nucella lapillus (Atlantic dog whelk) collected from Nahant, MA in May 2024
2026-03-23
publication
2026-03-23
revision
Woods Hole Oceanographic Institution (WHOI BCO-DMO)
2026-03-27
publication
https://doi.org/10.26008/1912/bco-dmo.991343.1
Geoffrey C. Trussell
Northeastern University
principalInvestigator
Steven V. Vollmer
Northeastern University
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: Ford, M., Vollmer, S. V., Trussell, G. C. (2026) Annotated genome of Nucella lapillus (Atlantic dog whelk) collected from Nahant, MA in May 2024. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-03-23 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.991343.1 [access date]
Atlantic dog whelk (Nucella lapillus) genome Dataset Description: <p><em>Nucella lapillus</em> is an important player in rocky shore food chains and has been a focal organism of ecological and evolutionary studies for decades. Despite poor dispersal, they have a broad geographic range, which makes them an ideal species to examine isolation by distance and selection across environmental gradients. &nbsp;A fully annotated genome of <em>N. lapillus</em> generated with Oxford Nanopore Technology (ONT) sequencing at ∼37× coverage was described in detail in the following publication:</p>
<p>Ford, M. R., Vollmer, S. V., &amp; Trussell, G. C. (2025). Annotated genome of the Atlantic dog whelk, Nucella lapillus. G3: Genes, Genomes, Genetics, 15(10). https://doi.org/10.1093/g3journal/jkaf182</p>
<p>This dataset provides information on the study and includes links to the genetic dataset at the National Center for Biotechnology Information (NCBI) BioProject PRJNA1238877.</p> Methods and Sampling: <p><strong>Sample collection and DNA extraction</strong><br />
An adult <em>Nucella lapillus</em> individual was collected in May 2024 from Nahant, MA (42.419732, −70.902171). The foot tissue was used for DNA extraction and isolation.&nbsp;</p>
<p>High molecular weight (HMW) DNA was extracted from the foot via the CTAB method (1.4 M NaCl&nbsp;and 2% CTAB), followed by three chloroform reactions. The complete&nbsp;extraction protocol is available on the project GitHub repository (https://github.com/meghanclownfish/Nucella-lapillus-genome/tree/main/1_extraction). The HMW DNA was precipitated in ethanol (EtOH) and resuspended in Tris-EDTA buffer. The sample was further purified using a Genomic DNA Clean and Concentrator kit (gDCC-10, ZYMO Research, Irvine, CA, USA) per manufacturer’s instructions. Sample quality and concentration were assessed by running 2 μL of the sample on NanoDrop (Thermo Fisher Scientific, Singapore). A sample was deemed ready for sequencing if the&nbsp;260/280 ratio was ∼1.9 and the&nbsp;260/230 ratio fell between 2.0 and 2.2, following Sun et al. 2020.<br />
<br />
<strong>Library prep and sequencing</strong><br />
<em>N. lapillus</em> long reads were sequenced using ONT platforms and libraries were prepared with the ONT Ligation sequencing kit (SQK-LSK114, ONT, Oxford, UK) and NEBNext Companion Module (E7180S NEB). Standard manufacturer's protocol was implemented with a few exceptions (see Ford et al., 2025 for details). Sequencing was done on a PromethION. Six flow cells in total were used to generate 103,553,219,099 bp raw data. PromethION flow cells (FLO-PRO114M) were primed and loaded per the standard manufacturer's protocol. To increase the yield of each flow cell, runs were paused and flushed using the EXP-WSH004 (ONT) kit and reloaded. High quality base calling was performed with Dorado 0.7.1 (ONT).</p>
<p><strong>Genome size and heterozygosity</strong><br />
Genome size was estimated using JELLYFISH v2.2.10 to count canonical 41-mers from high quality ONT reads (min quality: 5) and computed a histogram of k-mer occurrence (Marcais and Kingsford 2011). The histogram was used to estimate heterozygosity with GenomeScope (Ranallo-Benavidez et al. 2020).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2017626 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2017626
completed
Geoffrey C. Trussell
Northeastern University
781-581-7370 (ext. 300)
Marine Science Center 430 Nahant Road
Nahant
MA
01908
USA
g.trussell@northeastern.edu
pointOfContact
Steven V. Vollmer
Northeastern University
781-581-7370 ext. 312
Marine Science Center 430 Nahant Road
Nahant
MA
01908
USA
steve.vollmer@gmail.com
pointOfContact
asNeeded
Dataset Version: 1
Unknown
BioProject
Sampling_Date
Latitude
Longitude
Habitat
Specimen_type
Species
Taxon_IDs
Tissue_type
GenBank_Assembly
Isolate
Accession
Begin
End
Orientation
Gene_ID
Gene_Type
Protein_accession
Protein_length
Locus_tag
PromethION (Oxford Nanopore Technologies)
NanoDrop spectrophotometer (ThermoFisher Scientific, Singapore)
theme
None, User defined
NCBI BioProject accession
date
latitude
longitude
site description
sample description
species scientific name (binomial)
taxon
accession number
Start position
End position
Chromosome strand
gene identification
gene
length
NCBI locus tag
featureType
BCO-DMO Standard Parameters
Oxford Nanopore Technologies PromethION sequencer
Thermo Scientific NanoDrop spectrophotometer
instrument
BCO-DMO Standard Instruments
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.
Local adaptation and the evolution of plasticity under predator invasion and warming seas: consequences for individuals, populations and communities
https://osprey.bco-dmo.org/project/816470
Local adaptation and the evolution of plasticity under predator invasion and warming seas: consequences for individuals, populations and communities
<p><em>NSF Award Abstract:</em><br />
Over the past two decades, the Gulf of Maine has experienced unprecedented warming that, among other things, has further enabled the invasive green crab to expand its range in rocky shore habitats. The adverse ecological impacts of this invasive predator have been documented worldwide. This study examines how geographic variation in the capacity of two common prey species to respond to the combination of this predator and warming ocean temperatures can shape prey feeding and performance and impact community structure and dynamics. Hence, this research enhances understanding of the evolution of phenotypes, their plasticity, and the nature of adaptation and its role in eco-evolutionary dynamics. More broadly, it informs understanding of how organisms and marine communities may respond to future environmental change. In addition, this project makes contributions to the STEM pipeline by providing middle and high school, undergraduate, and graduate students with cross-disciplinary training in evolutionary and community ecology. In collaboration with an institutional outreach program, the investigator is also developing web-based multimedia projects and teacher resource materials based on this research.</p>
<p>A central principle in ecology is that species residing in the middle of food chains must balance the benefits of eating with the risk of being eaten by their predators. Solving this foraging-predation risk trade-off often involves plasticity in prey traits with consequences for the evolution of adaptation and species interactions that drive community-level processes. Hence, the foraging-predation risk trade-off provides a powerful conceptual framework that links evolutionary and community ecology. Yet at the same time, other environmental stressors like temperature can shape this trade-off, adding complexity that makes it difficult to predict the capacity of organisms to adapt to environmental change and the consequences for communities. The investigator is conducting this study in rocky shore habitats of the Gulf of Maine (GOM) which have long been influenced by strong latitudinal temperature gradients and non-native species invasions. The overarching hypothesis is that predation risk and temperature are factors shaping geographic variation in plasticity and adaptation, with consequences for individuals, populations, and communities. First, the investigator is conducting field experiments to document geographic variation in the trait plasticity of two common prey species in the green crab's diet. Second, he is using reciprocal transplant experiments to examine trait plasticity in response to risk and water temperature, generating data to compare with similar experiments conducted in the late 90s prior to recent ocean warming and expansion in range of green crabs. Third, he is conducting a laboratory common garden experiment to evaluate the effects of risk and water temperature on trait plasticity. Finally, he is using reciprocal transplant experiments in the field to understand the interactive effects of risk and water temperature on prey foraging rates and the abundance of a species that plays an important role in intertidal community structure and dynamics.</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>
evolution of plasticity
largerWorkCitation
project
eng; USA
biota
oceans
-70.902171
-70.902171
42.419732
42.419732
2024-05-01
2024-05-31
0
BCO-DMO catalogue of parameters from Annotated genome of Nucella lapillus (Atlantic dog whelk) collected from Nahant, MA in May 2024
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/995339.rdf
Name: BioProject
Units: unitless
Description: <p>NCBI BioProject</p>
http://lod.bco-dmo.org/id/dataset-parameter/995340.rdf
Name: Sampling_Date
Units: unitless
Description: <p>Date of sampling for whelk specimen</p>
http://lod.bco-dmo.org/id/dataset-parameter/995341.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/995342.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/995343.rdf
Name: Habitat
Units: unitless
Description: <p>Site description of specimen location</p>
http://lod.bco-dmo.org/id/dataset-parameter/995344.rdf
Name: Specimen_type
Units: unitless
Description: <p>Specimen description with life stage and environment</p>
http://lod.bco-dmo.org/id/dataset-parameter/995345.rdf
Name: Species
Units: unitless
Description: <p>Species</p>
http://lod.bco-dmo.org/id/dataset-parameter/995346.rdf
Name: Taxon_IDs
Units: unitless
Description: <p>NCBI and Aphia ID taxon identifiers</p>
http://lod.bco-dmo.org/id/dataset-parameter/995347.rdf
Name: Tissue_type
Units: unitless
Description: <p>Tissue used for analyses</p>
http://lod.bco-dmo.org/id/dataset-parameter/995348.rdf
Name: GenBank_Assembly
Units: unitless
Description: <p>The GenBank assembly accession identifier corresponding to the genome assembly from which the annotation was derived</p>
http://lod.bco-dmo.org/id/dataset-parameter/995349.rdf
Name: Isolate
Units: unitless
Description: <p>The specific biological sample or individual organism from which the genome was obtained.</p>
http://lod.bco-dmo.org/id/dataset-parameter/995350.rdf
Name: Accession
Units: unitless
Description: <p>A unique identifier generated by NCBI for each contig (continuous sequence) in the genome</p>
http://lod.bco-dmo.org/id/dataset-parameter/995351.rdf
Name: Begin
Units: base pair (bp)
Description: <p>The starting genomic coordinate of the annotated feature on the sequence</p>
http://lod.bco-dmo.org/id/dataset-parameter/995352.rdf
Name: End
Units: base pair (bp)
Description: <p>The ending genomic coordinate of the annotated feature on the sequence.</p>
http://lod.bco-dmo.org/id/dataset-parameter/995354.rdf
Name: Orientation
Units: unitless
Description: <p>The strand on which the feature is encoded (plus = forward, minus = reverse)</p>
http://lod.bco-dmo.org/id/dataset-parameter/995357.rdf
Name: Gene_ID
Units: unitless
Description: <p>A unique identifier assigned to the gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/995358.rdf
Name: Gene_Type
Units: unitless
Description: <p>Classification of the gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/995360.rdf
Name: Protein_accession
Units: unitless
Description: <p>Accession number for the translated protein product(s) associated with the gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/995361.rdf
Name: Protein_length
Units: amino acids (aa)
Description: <p>Length of the predicted protein sequence</p>
http://lod.bco-dmo.org/id/dataset-parameter/995362.rdf
Name: Locus_tag
Units: unitless
Description: <p>A systematic, unique identifier assigned to each gene within the genome annotation</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
https://doi.org/10.26008/1912/bco-dmo.991343.1
download
onLine
dataset
<p><strong>Sample collection and DNA extraction</strong><br />
An adult <em>Nucella lapillus</em> individual was collected in May 2024 from Nahant, MA (42.419732, −70.902171). The foot tissue was used for DNA extraction and isolation.&nbsp;</p>
<p>High molecular weight (HMW) DNA was extracted from the foot via the CTAB method (1.4 M NaCl&nbsp;and 2% CTAB), followed by three chloroform reactions. The complete&nbsp;extraction protocol is available on the project GitHub repository (https://github.com/meghanclownfish/Nucella-lapillus-genome/tree/main/1_extraction). The HMW DNA was precipitated in ethanol (EtOH) and resuspended in Tris-EDTA buffer. The sample was further purified using a Genomic DNA Clean and Concentrator kit (gDCC-10, ZYMO Research, Irvine, CA, USA) per manufacturer’s instructions. Sample quality and concentration were assessed by running 2 μL of the sample on NanoDrop (Thermo Fisher Scientific, Singapore). A sample was deemed ready for sequencing if the&nbsp;260/280 ratio was ∼1.9 and the&nbsp;260/230 ratio fell between 2.0 and 2.2, following Sun et al. 2020.<br />
<br />
<strong>Library prep and sequencing</strong><br />
<em>N. lapillus</em> long reads were sequenced using ONT platforms and libraries were prepared with the ONT Ligation sequencing kit (SQK-LSK114, ONT, Oxford, UK) and NEBNext Companion Module (E7180S NEB). Standard manufacturer's protocol was implemented with a few exceptions (see Ford et al., 2025 for details). Sequencing was done on a PromethION. Six flow cells in total were used to generate 103,553,219,099 bp raw data. PromethION flow cells (FLO-PRO114M) were primed and loaded per the standard manufacturer's protocol. To increase the yield of each flow cell, runs were paused and flushed using the EXP-WSH004 (ONT) kit and reloaded. High quality base calling was performed with Dorado 0.7.1 (ONT).</p>
<p><strong>Genome size and heterozygosity</strong><br />
Genome size was estimated using JELLYFISH v2.2.10 to count canonical 41-mers from high quality ONT reads (min quality: 5) and computed a histogram of k-mer occurrence (Marcais and Kingsford 2011). The histogram was used to estimate heterozygosity with GenomeScope (Ranallo-Benavidez et al. 2020).</p>
Specified by the Principal Investigator(s)
<p><strong>Assembly and annotation</strong><br />
Briefly, we assembled the genome using all reads of 2kb in length or greater with &nbsp;Hifiasm (0.25.0-r726). &nbsp;BlobTools2 (v4.4.0, Challis et al. 2020) was used to visually assess the assembly and filter contigs. RepeatModeler (v2.0.6, Flynn et al. 2020) and RepeatMasker (Smit et al.) &nbsp;identified and soft-masked repetitive regions in the genome. RNASeq data was mapped to the soft-masked genome with HISAT2. This information, along with a custom protein database, was supplied as evidence for Braker3. TSEBRA was used to merge Braker outputs. Functional annotation was carried out with InterProScan and Funannotate. For full details, please see Ford et al. (2025) paper.</p>
Specified by the Principal Investigator(s)
- Loaded source files "ncbi_dataset.tsv" (annotated genome) and "Nucleotide_Accessions_2525.xlsx" that had been downloaded from NCBI BioProject PRJNA1238877
- Added fields for Latitude, Longitude, Habitat, Tissue_type, Sampling_Date, and Specimen_type to both tables
- Added fields/columns for taxon_IDs, isolate, species, and GenBank_assembly for the annotated genome table
- Renamed fields/column headings to conform with BCO-DMO naming conventions and improve interoperability.
- Exported two CSV files: 991343_v1_nucella_lapillus_annotated_genome.csv and 991343_v1_nucella_lapillus_nucleotides.csv
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
PromethION (Oxford Nanopore Technologies)
PromethION (Oxford Nanopore Technologies)
PI Supplied Instrument Name: PromethION (Oxford Nanopore Technologies) PI Supplied Instrument Description:Sequencing was done on a PromethION Instrument Name: Oxford Nanopore Technologies PromethION sequencer Instrument Short Name:ONT PromethION Instrument Description: A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. The ONT PromethION is a high-throughput, high-sample number benchtop sequencing machine developed by Oxford Nanopore Technologies.
NanoDrop spectrophotometer (ThermoFisher Scientific, Singapore)
NanoDrop spectrophotometer (ThermoFisher Scientific, Singapore)
PI Supplied Instrument Name: NanoDrop spectrophotometer (ThermoFisher Scientific, Singapore) PI Supplied Instrument Description:Sample quality and concentration were assessed by running 2 μL of the sample on NanoDrop (Thermo Fisher Scientific, Singapore). Instrument Name: Thermo Scientific NanoDrop spectrophotometer Instrument Short Name:NanoDrop spectrophotometer Instrument Description: Thermo Scientific NanoDrop spectrophotometers provide microvolume quantification and purity assessments of DNA, RNA, and protein samples. NanoDrop spectrophotometers work on the principle of ultraviolet-visible spectrum (UV-Vis) absorbance. The range consists of the NanoDrop One/OneC UV-Vis Spectrophotometers, NanoDrop Eight UV-Vis Spectrophotometer and NanoDrop Lite Plus UV Spectrophotometer.