http://lod.bco-dmo.org/id/dataset/514202
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
2014-04-28
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Diatom ribosomal DNA sequence accession numbers from samples collected from the Eastern and Western Pacific and from the Western Atlantic between 2007 and 2009 (Diatom Gene Flow project)
2014-04-28
publication
2014-04-28
revision
BCO-DMO Linked Data URI
2014-04-28
creation
http://lod.bco-dmo.org/id/dataset/514202
Tatiana A. Rynearson
University of Rhode Island
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: Rynearson, T. A. (2014) Diatom ribosomal DNA sequence accession numbers from samples collected from the Eastern and Western Pacific and from the Western Atlantic between 2007 and 2009 (Diatom Gene Flow project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 28 April 2014) Version Date 2014-04-28 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/514202 [access date]
Diatom ribosomal DNA sequence accession numbers. Dataset Description: <p>GenBank accession numbers for ribosomal DNA sequences from the diatoms <em>Ditylum brightwellii</em>, <em>Thalassiosira rotula</em>, and <em>Thalassiosira gravida</em>.</p> Methods and Sampling: <p><strong>Summary of methods: <em>Thalassiosira rotula</em> and <em>Thalassiosira gravida</em></strong><br />
See Whittaker et al. (2012) for more information. Cells of the diatom <em>Thalassiosira rotula/gravida</em> were collected from the Eastern and Western Pacific and from the Western Atlantic between 2007 and 2009. Cultured isolates were also obtained (refer to Table 1 of Whittaker et al. (2012)). Three regions of the ribosomal DNA (rDNA) were sequenced: the small subunit (18S), the D1 hypervariable region of the large subunit (28S), and the internal transcribed spacer region I (ITS1). ITS1 was amplified from 106 isolates by polymerase chain reaction (PCR) using a newly-designed primer specific to <em>T. rotula</em> and <em>T. gravida </em>and primer 1645F. The 18S was amplified from 16 isolates using universal 18SA and 18SB primers. The D1 region of the 28S was also amplified from those 16 isolates using the forward primer 28SF and a reverse primer. Sequencing was performed on an ABI 3130xl (Applied Biosystems). SeqMan II 3.61 (DNASTAR, Inc.) was used to assemble sequences and they were aligned using Clustal W in Mega4. Boundaries of the ITS1 were determined through alignment with Genbank accession EF208798.</p>
<p><strong>Refer to Rynearson et al. (2009) for the <em>Ditylum brightwellii </em>methodology.</strong></p>
<p><strong>References:</strong><br />
Rynearson, T.A., E.O. Lin and E.V. Armbrust. 2009. Metapopulation structure in the planktonic diatom <em>Ditylum brightwellii </em>(Bacillariophyceae)<em>. Protist</em>, 160(1):111-121. doi:<a href="http://dx.doi.org/10.1016/j.protis.2008.10.003" target="_blank">10.1016/j.protis.2008.10.003</a><br />
<br />
Whittaker, K., Rignanese, D., Olson, R., Rynearson, T., 2012. Molecular subdivision of the marine diatom <em>Thalassiosira rotula</em> in relation to geographic distribution, genome size, and physiology. <em>BMC Evolutionary Biology,</em> 12:209. doi:<a href="http://dx.doi.org/10.1186/1471-2148-12-209" target="_blank">10.1186/1471-2148-12-209</a></p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0727227 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0727227
completed
Tatiana A. Rynearson
University of Rhode Island
401-874-6022
Graduate School of Oceanography, University of Rhode Island 215 South Ferry Rd.
Narragansett
RI
02882
USA
rynearson@uri.edu
pointOfContact
asNeeded
Dataset Version: 28 April 2014
Unknown
species
description
accession_number
accession_number_link
ABI 3130xL (Applied Biosystems)
Thermocycler
theme
None, User defined
species scientific name (binomial)
brief description
accession number
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
lab_Rynearson_diatoms
service
Deployment Activity
Narragansett, RI
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.
Connecting local, regional and global scales of gene flow in planktonic marine diatoms
https://osprey.bco-dmo.org/project/511708
Connecting local, regional and global scales of gene flow in planktonic marine diatoms
<p><em>Description from NSF award abstract:</em><br />
Diatoms are ubiquitous, unicellular, eukaryotes that generate about 40% of the organic carbon fixed annually in the sea. Interpretation of diatom species distributions and abundances in relation to environmental conditions has relied on two assumptions: (1) cells with identical morphologies represent the same species and (2) high potentials for dispersal and gene flow in passively drifting diatoms prevent local adaptation. Recent studies have challenged both assumptions, suggesting diatoms possess rich patterns of genetic and physiological variation both within and between species. Although there is emerging evidence of intra-specific population differentiation on local scales (~100km), it is commonly assumed that planktonic microbes are homogenously distributed on global scales (e.g. Fenchel and Finlay 2004). There is currently no data on diatoms to support this assumption. Aside from intriguing data on local scales, nothing is known about regional and global-scale population genetics and biogeography of diatoms.</p>
<p>The research proposed here will focus on the essential questions of if and how populations of planktonic diatoms are connected at local, regional and global scales. Connectivity among populations can influence a species'' ecology, adaptive potential, evolutionary longevity and ultimately speciation potential. The proposed research will examine how local populations are connected to each other on regional scales and how regional dynamics connect to global-scale biogeographies using two model diatom species. rDNA sequence variation will be used to test whether broad species distributions observed in diatoms result from cryptic speciation. Within species, microsatellite markers will be used to identify genetically distinct populations, determine their relatedness to each other and examine spatial patterns of differentiation. The degree of physiological variation that accompanies genetic differentiation between populations will also be examined. Samples will be collected in a framework of existing oceanography and biodiversity programs, permitting genetic data to be interpreted in the context of larger, often long-term, studies. Because little is known about diatom biogeography, this work will begin to shed light on the connections between local and global population dynamics. Because the proposed research will represent the first large-scale sampling of diatom population genetics, it will also serve to generate many new hypotheses about the mechanisms that regulate ecological processes such as bloom formation over space and time and evolutionary processes such as the development of reproductive isolation and eventual speciation in planktonic organisms.</p>
<p><em>Related publications:</em><br />
Rynearson, T.A., E.O. Lin and E.V. Armbrust. 2009. Metapopulation structure in the planktonic diatom <em>Ditylum brightwellii </em>(Bacillariophyceae)<em>. Protist</em>, 160(1):111-121. doi:<a href="http://dx.doi.org/10.1016/j.protis.2008.10.003" target="_blank">10.1016/j.protis.2008.10.003</a></p>
<p>Whittaker, K., Rignanese, D., Olson, R., Rynearson, T., 2012. Molecular subdivision of the marine diatom <em>Thalassiosira rotula</em> in relation to geographic distribution, genome size, and physiology. <em>BMC Evolutionary Biology,</em> 12:209. doi:<a href="http://dx.doi.org/10.1186/1471-2148-12-209" target="_blank">10.1186/1471-2148-12-209</a></p>
<p>Boyd, P.W., Rynearson, T.A., Armstrong, E.A., Fu, F., Hayashi, K., Hu, Z., Hutchins, D.A., Kudela, R.M., Litchman, E., Mulholland, M.R., Passow, U., Strzepek, R.F., Whittaker, K.A., Yu, E., Thomas, M.K., 2013. Marine Phytoplankton Temperature versus Growth Responses from Polar to Tropical Waters - Outcome of a Scientific Community-Wide Study. <em>PLoS One</em>, 8(5), e63091. doi:<a href="http://dx.doi.org/10.1371/journal.pone.0063091" target="_blank">10.1371/journal.pone.0063091</a></p>
Diatom Gene Flow
largerWorkCitation
project
eng; USA
oceans
Narragansett, RI
2014-04-28
global diatom samples; laboratory-based analyses
0
BCO-DMO catalogue of parameters from Diatom ribosomal DNA sequence accession numbers from samples collected from the Eastern and Western Pacific and from the Western Atlantic between 2007 and 2009 (Diatom Gene Flow 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
http://lod.bco-dmo.org/id/dataset-parameter/514203.rdf
Name: species
Units: text
Description: <p>Name of the species.</p>
http://lod.bco-dmo.org/id/dataset-parameter/514204.rdf
Name: description
Units: text
Description: <p>Brief description of the type of sequence.</p>
http://lod.bco-dmo.org/id/dataset-parameter/514205.rdf
Name: accession_number
Units: alphanumeric
Description: <p>GenBank accession number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/514206.rdf
Name: accession_number_link
Units: alphanumeric hyperlink
Description: <p>Link to GenBank (opens in new window) for the specific accession number.</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
20887
https://datadocs.bco-dmo.org/file/8XXgyjNSPoLqwL/sequence_accessions.csv
sequence_accessions.csv
Primary data file for dataset ID 514202
download
https://osprey.bco-dmo.org/dataset/514202/data/download
download
onLine
dataset
<p><strong>Summary of methods: <em>Thalassiosira rotula</em> and <em>Thalassiosira gravida</em></strong><br />
See Whittaker et al. (2012) for more information. Cells of the diatom <em>Thalassiosira rotula/gravida</em> were collected from the Eastern and Western Pacific and from the Western Atlantic between 2007 and 2009. Cultured isolates were also obtained (refer to Table 1 of Whittaker et al. (2012)). Three regions of the ribosomal DNA (rDNA) were sequenced: the small subunit (18S), the D1 hypervariable region of the large subunit (28S), and the internal transcribed spacer region I (ITS1). ITS1 was amplified from 106 isolates by polymerase chain reaction (PCR) using a newly-designed primer specific to <em>T. rotula</em> and <em>T. gravida </em>and primer 1645F. The 18S was amplified from 16 isolates using universal 18SA and 18SB primers. The D1 region of the 28S was also amplified from those 16 isolates using the forward primer 28SF and a reverse primer. Sequencing was performed on an ABI 3130xl (Applied Biosystems). SeqMan II 3.61 (DNASTAR, Inc.) was used to assemble sequences and they were aligned using Clustal W in Mega4. Boundaries of the ITS1 were determined through alignment with Genbank accession EF208798.</p>
<p><strong>Refer to Rynearson et al. (2009) for the <em>Ditylum brightwellii </em>methodology.</strong></p>
<p><strong>References:</strong><br />
Rynearson, T.A., E.O. Lin and E.V. Armbrust. 2009. Metapopulation structure in the planktonic diatom <em>Ditylum brightwellii </em>(Bacillariophyceae)<em>. Protist</em>, 160(1):111-121. doi:<a href="http://dx.doi.org/10.1016/j.protis.2008.10.003" target="_blank">10.1016/j.protis.2008.10.003</a><br />
<br />
Whittaker, K., Rignanese, D., Olson, R., Rynearson, T., 2012. Molecular subdivision of the marine diatom <em>Thalassiosira rotula</em> in relation to geographic distribution, genome size, and physiology. <em>BMC Evolutionary Biology,</em> 12:209. doi:<a href="http://dx.doi.org/10.1186/1471-2148-12-209" target="_blank">10.1186/1471-2148-12-209</a></p>
Specified by the Principal Investigator(s)
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
ABI 3130xL (Applied Biosystems)
ABI 3130xL (Applied Biosystems)
PI Supplied Instrument Name: ABI 3130xL (Applied Biosystems) PI Supplied Instrument Description:Sequencing was done on an ABI ABI 3130xL (Applied Biosystems) genetic analyzer. 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.
Thermocycler
Thermocycler
PI Supplied Instrument Name: Thermocycler Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
Deployment: lab_Rynearson_diatoms
lab_Rynearson_diatoms
URI-GSO
laboratory
lab_Rynearson_diatoms
Tatiana A. Rynearson
University of Rhode Island
URI-GSO
laboratory