http://lod.bco-dmo.org/id/dataset/945292
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
2024-12-04
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Full genome and transcriptome sequence assembly of the non-model organism Kellet’s whelk, Kelletia kelletii
2024-12-04
publication
2024-12-04
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-12-24
publication
https://doi.org/10.26008/1912/bco-dmo.945292.1
Crow White
Cal Poly San Luis Obispo
principalInvestigator
Mark Christie
Purdue University
principalInvestigator
Jean Davidson
Cal Poly San Luis Obispo
principalInvestigator
Robert J. Toonen
University of Hawaiʻi at Mānoa
principalInvestigator
Paul Anderson
Cal Poly San Luis Obispo
principalInvestigator
Benjamin Daniels
Cal Poly San Luis Obispo
principalInvestigator
Andy Lee
Purdue University
principalInvestigator
Cataixa López
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: White, C., Toonen, R. J., Christie, M., Davidson, J., Anderson, P., Daniels, B., Lee, A., López, C. (2024) Full genome and transcriptome sequence assembly of the non-model organism Kellet’s whelk, Kelletia kelletii. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-12-04 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.945292.1 [access date]
Kelletia kelletii: DNA and RNA sequence Dataset Description: <p>Description of linked resources for this dataset, all links can be found in the related dataset section.</p>
<ul>
<li>All codes and parameters used for the bioinformatic analyses carried out are available at https://github.com/bndaniel/Kellets-whelk-genome-assembly and are archived at Zenodo, doi:10.5281/zenodo.13274364</li>
<li>The Kelletia kelletii genome and transcriptome produced by this study have been deposited in Dryad, doi:10.5061/dryad.w0vt4b8zn</li>
<li>All raw sequence data, including the PacBio sequel 2, Nanopore MinION, and Illumina NovaSeq DNA sequencing, as well as the Illumina NovaSeq RNA sequencing, are deposited in the NCBI Sequence Read Archive (SRA) under PRJNA999368 and PRJNA1000198</li>
<li>VCF files for the all-SNPs and DEG-SNPs data sets are deposited in Dryad, doi:10.5061/dryad.qbzkh18s3</li>
<li>The scripts used in this project are hosted in the public repository <a class="OWAAutoLink" href="https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FChristieLab%2Fkellets_whelk_rnaseq&amp;data=05%7C02%7Cadyork%40whoi.edu%7Cc1b676d5d2004ed3100108dd04f0793e%7Cd44c5cc6d18c46cc8abd4fdf5b6e5944%7C0%7C0%7C638672153067844580%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&amp;sdata=%2FB%2FMmba0T8gh8%2FUec91D%2F0JMn5uI5eyvd1Sd1FvXCMg%3D&amp;reserved=0" id="OWAdf30ddcd-0f16-9d4e-99c0-ef54a2461129" rel="noopener noreferrer" target="_blank" title="//github.com/ChristieLab/kellets_whelk_rnaseq. Click or tap if you trust this link.">https://github.com/ChristieLab/kellets_whelk_rnaseq</a> and archived at Zenodo, doi:10.5281/zenodo.14187737</li>
</ul> Methods and Sampling: <p>gDNA was extracted using HMW Circulomics Standard TissueRuptor Protocol. DNA was further cleaned and concentrated using the DNeasy PowerClean Pro Cleanup Kit. Libraries were prepared using the PacBio HiFi SMARTbell from Ultra-low DNA input procedures. Libraries were prepared for sequencing using the Binding kit 2.2.</p>
<p>RNA was extracted using Trizol and RNA phase separation. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non-directional library preparation. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. Libraries were prepared using end repair, A-tailing, adapter ligation, size selection, amplification, and purification.</p>
<p>Detailed methods in Daniels et al., (2023), see related publications</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1924537 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1924537
completed
Crow White
Cal Poly San Luis Obispo
805-756-2954
California Polytechnic State University 1 Grand Avenue
San Luis Obispo
CA
93407
US
cwhite31@calpoly.edu
pointOfContact
Mark Christie
Purdue University
christ99@purdue.edu
pointOfContact
Jean Davidson
Cal Poly San Luis Obispo
jdavid06@calpoly.edu
pointOfContact
Robert J. Toonen
University of Hawaiʻi at Mānoa
808-236-7401
Hawaii Institute of Marine Biology 46-007 Lilipuna Rd
Kaneohe
HI
96744
USA
rjtoonen@gmail.com
pointOfContact
Paul Anderson
Cal Poly San Luis Obispo
pander14@calpoly.edu
pointOfContact
Benjamin Daniels
Cal Poly San Luis Obispo
ben.daniels255@gmail.com
pointOfContact
Andy Lee
Purdue University
lee3617@purdue.edu
pointOfContact
Cataixa López
University of Hawaiʻi at Mānoa
clopezba@ull.edu.es
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Run
Assay_Type
AvgSpotLen
Bases
BioProject
BioSample
BioSampleModel
Bytes
Center_Name
Collection_Date
Consent
DATASTORE_filetype
DATASTORE_provider
DATASTORE_region
Ecotype
env_broad_scale
env_local_scale
env_medium
Experiment
geo_loc_name_country
geo_loc_name_country_continent
geo_loc_name
Instrument
isol_growth_condt
latitude
longitude
Library_Name
LibraryLayout
LibrarySelection
LibrarySource
Organism
Platform
ReleaseDate
create_date
version
Sample_Name
source_material_id
SRA_Study
ILLUMINA
Nanopore MinION
PacBio sequel 2
theme
None, User defined
NCBI SRA run accession (SRR)
seq_descrip
NCBI BioProject accession
NCBI BioSample accession
file_size
date
No BCO-DMO term
sample description
NCBI SRA experiment accession (SRX)
region
instrument
latitude
longitude
sample identification
species scientific name (binomial)
NCBI SRA study accession (SRP)
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Automated DNA Sequencer
Automated DNA Sequencer
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.
Collaborative Research: RUI: Combined spatial and temporal analyses of population connectivity during a northern range expansion
https://osprey.bco-dmo.org/project/851109
Collaborative Research: RUI: Combined spatial and temporal analyses of population connectivity during a northern range expansion
<p><em>NSF Award Abstract:</em><br />
Where do young marine fish and shellfish come from? This project aims to improve our understanding of how coastal marine populations are connected in space and time. Coastal populations are replenished through the arrival of minuscule larvae that have been dispersed for weeks to months in the open ocean after spawning at remote sites. The combination of the long dispersal period of marine fish and shellfish larvae and the varying ocean currents results in complex patterns of "connectivity" among populations near and far. Identifying these patterns of connectivity is fundamental to marine science and critical for effective fisheries management and conservation, yet it remains an unresolved component of marine ecology. The study species is currently expanding its biogeographic range up the U.S. west coast. By genetically analyzing individuals from across the species' range, including offspring spawned in the laboratory by experimentally-crossed individuals collected in the field from throughout the species historical and expanded range, certain genes can serve to differentiate populations along the coast. The team leverages the statistical power of these geographically-informative genes to assign thousands of young collected in the field to the source populations that spawned them (across the species' range and over multiple years). The team then quantifies patterns of connectivity over multiple years, and tests fundamental hypotheses on the spatial scale, temporal variability, biogeographic patterns, and biophysical drivers of population connectivity. The project trains approximately two dozen U.S. university students in molecular ecology and marine science, as well as creating intellectual linkages among Ph.D.-granting and non-Ph.D.-granting universities. The project also supports further development of a K-12 education program that uses SCUBA diving and videography to teach elementary school students Next Generation Science Standards and train them for careers in science, technology, engineering and mathematics.</p>
<p>Using a kelp forest gastropod and fisheries species (Kellet's whelk, Kelletia kelletii), this project combines genome-wide Restriction site Associated DNA (RAD) loci with transcriptomic loci identified from common-garden laboratory crosses of individuals from the species' historical and expanded range to identify geographically-informative loci that maximize power for individual assignment testing. Leveraging the combined power of these loci, genetic assignment of approximately three thousand recruit samples to 20 putative source populations allows the team to construct three independent years of connectivity matrices and test some of the most fundamental questions in marine ecology, including: 1) Are marine populations open or closed and at what scales? 2) To what degree is the evolutionary pattern of gene flow represented by single versus multiple generations of connectivity events? And, 3) How spatially heterogeneous and temporally variable is population connectivity? Can one year of connectivity data predict anything about the next? Additionally, by focusing on a range-expanding species with common life history traits, the team addresses a number of questions with broad applicability and significant ecological and societal implications: 4) How much is population connectivity influenced by post-recruitment demographic and evolutionary processes? 5) How well-connected are historic- and expanded-range populations? And, of particular relevance to climate change, 6) Are El Nino oceanographic conditions, which are predicted to increase in frequency and intensity this century, driving the poleward range expansion of this coastal marine species? By coupling common-garden experimental crosses to identify maximally-informative transcriptomic loci with genomic RAD analysis of field samples, this project aims to accurately and precisely quantify marine population connectivity in high gene flow species with large population sizes.</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>
KW connectivity
largerWorkCitation
project
eng; USA
oceans
-120.75
-119.57
34.25
35.17
2019-08-28
2020-07-08
California, USA and Baja, Mexico coast
0
BCO-DMO catalogue of parameters from Full genome and transcriptome sequence assembly of the non-model organism Kellet’s whelk, Kelletia kelletii
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/945438.rdf
Name: Run
Units: unitless
Description: <p>NCBI SRA run accession ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/945439.rdf
Name: Assay_Type
Units: unitless
Description: <p>Type of sequencing assay performed: WGS or RNA-Seq</p>
http://lod.bco-dmo.org/id/dataset-parameter/945440.rdf
Name: AvgSpotLen
Units: unitless
Description: <p>The average length of the spots (reads) in the run</p>
http://lod.bco-dmo.org/id/dataset-parameter/945441.rdf
Name: Bases
Units: unitless
Description: <p>The total number of bases sequenced</p>
http://lod.bco-dmo.org/id/dataset-parameter/945442.rdf
Name: BioProject
Units: unitless
Description: <p>NCBI Bioproject accession ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/945443.rdf
Name: BioSample
Units: unitless
Description: <p>NCBI Biosample accession ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/945444.rdf
Name: BioSampleModel
Units: unitless
Description: <p>NCBI BioSample package representing type of biosample and required attributes</p>
http://lod.bco-dmo.org/id/dataset-parameter/945445.rdf
Name: Bytes
Units: unitless
Description: <p>Filesize in bytes for datastore file</p>
http://lod.bco-dmo.org/id/dataset-parameter/945446.rdf
Name: Center_Name
Units: unitless
Description: <p>The name of the sequencing center</p>
http://lod.bco-dmo.org/id/dataset-parameter/945447.rdf
Name: Collection_Date
Units: unitless
Description: <p>Collection date of organism</p>
http://lod.bco-dmo.org/id/dataset-parameter/945448.rdf
Name: Consent
Units: unitless
Description: <p>Information on the consent for data usage</p>
http://lod.bco-dmo.org/id/dataset-parameter/945449.rdf
Name: DATASTORE_filetype
Units: unitless
Description: <p>The file type stored in the NCBI DataStore (e.g., FASTQ, BAM)</p>
http://lod.bco-dmo.org/id/dataset-parameter/945450.rdf
Name: DATASTORE_provider
Units: unitless
Description: <p>The provider of the DataStore where files are kept</p>
http://lod.bco-dmo.org/id/dataset-parameter/945451.rdf
Name: DATASTORE_region
Units: unitless
Description: <p>The geographical region of the DataStore</p>
http://lod.bco-dmo.org/id/dataset-parameter/945452.rdf
Name: Ecotype
Units: unitless
Description: <p>A population within a given species displaying genetically based, phenotypic traits that reflect adaptation to a local habitat, e.g., Columbia</p>
http://lod.bco-dmo.org/id/dataset-parameter/945453.rdf
Name: env_broad_scale
Units: unitless
Description: <p>Broad-scale environmental context</p>
http://lod.bco-dmo.org/id/dataset-parameter/945454.rdf
Name: env_local_scale
Units: unitless
Description: <p>Local-scale environmental context</p>
http://lod.bco-dmo.org/id/dataset-parameter/945455.rdf
Name: env_medium
Units: unitless
Description: <p>Material displaced by the entity at time of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/945456.rdf
Name: Experiment
Units: unitless
Description: <p>The NCBI identifier for the sequencing experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/945457.rdf
Name: geo_loc_name_country
Units: unitless
Description: <p>Geographic location of the origin of the sample: country = USA</p>
http://lod.bco-dmo.org/id/dataset-parameter/945458.rdf
Name: geo_loc_name_country_continent
Units: unitless
Description: <p>Geographic location of the origin of the sample: continent = North America</p>
http://lod.bco-dmo.org/id/dataset-parameter/945459.rdf
Name: geo_loc_name
Units: unitless
Description: <p>Geographic location of the origin of the sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/945460.rdf
Name: Instrument
Units: unitless
Description: <p>The sequencing instrument used (e.g., Illumina MiSeq)</p>
http://lod.bco-dmo.org/id/dataset-parameter/945461.rdf
Name: isol_growth_condt
Units: unitless
Description: <p>Isolation and growth condition specifications</p>
http://lod.bco-dmo.org/id/dataset-parameter/945462.rdf
Name: latitude
Units: decimal degrees
Description: <p>Latitude of sampling location, south is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/945463.rdf
Name: longitude
Units: decimal degrees
Description: <p>Longitude of sampling location, west is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/945464.rdf
Name: Library_Name
Units: unitless
Description: <p>Unique identifier for the sequencing library (can be the sample name repeated)</p>
http://lod.bco-dmo.org/id/dataset-parameter/945465.rdf
Name: LibraryLayout
Units: unitless
Description: <p>Single or paired end sequencing reads</p>
http://lod.bco-dmo.org/id/dataset-parameter/945466.rdf
Name: LibrarySelection
Units: unitless
Description: <p>Selection used for sequencing library</p>
http://lod.bco-dmo.org/id/dataset-parameter/945467.rdf
Name: LibrarySource
Units: unitless
Description: <p>Source material of sequencing library</p>
http://lod.bco-dmo.org/id/dataset-parameter/945468.rdf
Name: Organism
Units: unitless
Description: <p>Name of organism from which the sample was taken: Kelletia kelletii</p>
http://lod.bco-dmo.org/id/dataset-parameter/945469.rdf
Name: Platform
Units: unitless
Description: <p>Sequencing platform manufacturer</p>
http://lod.bco-dmo.org/id/dataset-parameter/945470.rdf
Name: ReleaseDate
Units: unitless
Description: <p>Date of release of NCBI data to the public</p>
http://lod.bco-dmo.org/id/dataset-parameter/945471.rdf
Name: create_date
Units: unitless
Description: <p>Date of creation of NCBI submission</p>
http://lod.bco-dmo.org/id/dataset-parameter/945472.rdf
Name: version
Units: unitless
Description: <p>The version of the NCBI submission: 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/945473.rdf
Name: Sample_Name
Units: unitless
Description: <p>Unique sample name</p>
http://lod.bco-dmo.org/id/dataset-parameter/945474.rdf
Name: source_material_id
Units: unitless
Description: <p>Unique identifier assigned to the sequenced material</p>
http://lod.bco-dmo.org/id/dataset-parameter/945475.rdf
Name: SRA_Study
Units: unitless
Description: <p>NCBI SRA study accession ID</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
47341
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/fb83d5ca-ece6-4b15-be75-e996e70e4128/content
download
https://doi.org/10.26008/1912/bco-dmo.945292.1
download
onLine
dataset
<p>gDNA was extracted using HMW Circulomics Standard TissueRuptor Protocol. DNA was further cleaned and concentrated using the DNeasy PowerClean Pro Cleanup Kit. Libraries were prepared using the PacBio HiFi SMARTbell from Ultra-low DNA input procedures. Libraries were prepared for sequencing using the Binding kit 2.2.</p>
<p>RNA was extracted using Trizol and RNA phase separation. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non-directional library preparation. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. Libraries were prepared using end repair, A-tailing, adapter ligation, size selection, amplification, and purification.</p>
<p>Detailed methods in Daniels et al., (2023), see related publications</p>
Specified by the Principal Investigator(s)
* Merged RNA and DNA sequence files
* Split lat_lon column into latitude and longitude column
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
ILLUMINA
PI Supplied Instrument Name: ILLUMINA 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.
Nanopore MinION
Nanopore MinION
PI Supplied Instrument Name: Nanopore MinION 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.
PacBio sequel 2
PacBio sequel 2
PI Supplied Instrument Name: PacBio sequel 2 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.