http://lod.bco-dmo.org/id/dataset/875583 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 2022-06-11 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) RNAseq data used to identify Alphaflexivirus genomes in Stony Coral Tissue Loss Disease-affected, disease-exposed, and disease-unexposed coral colonies in the U.S. Virgin Islands (Multi-Species Coral Disease project) 2022-06-11 publication 2022-06-11 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2022-06-14 publication https://doi.org/10.26008/1912/bco-dmo.875583.1 Laura Mydlarz University of Texas at Arlington principalInvestigator Adrienne M.S. Correa Rice 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: Mydlarz, L., Correa, A. M. (2022) RNAseq data used to identify Alphaflexivirus genomes in Stony Coral Tissue Loss Disease-affected, disease-exposed, and disease-unexposed coral colonies in the U.S. Virgin Islands (Multi-Species Coral Disease project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-06-11 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.875583.1 [access date] Alphaflexivirus Genomes in Stony Coral Tissue Loss Disease-Affected, Disease-Exposed, and Disease-Unexposed Coral Colonies in the U.S. Virgin Islands Dataset Description: Methods and Sampling: &lt;p&gt;&lt;strong&gt;Methodology:&amp;nbsp;&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Sampling and analytical procedures: &lt;/strong&gt;&lt;/p&gt; &lt;p&gt;&lt;em&gt;A SCTLD transmission experiment was carried out at the University of the Virgin Islands (UVI) in April of 2019 and is described in Meiling et al. (2021). One fragment from 6 species of stony coral was placed into a control mesocosm equidistant from a central healthy coral colony. Corresponding genet fragments were placed into an experimental mesocosm equidistant from a SCTLD-infected coral colony. This paired design was replicated for a total of 8 genets per species. Experimental coral fragments that developed lesions were removed and stored at -80ºC for RNA sequencing when 30% tissue loss was achieved. Corresponding control coral fragments were removed and stored at the same time. Tissue samples were harvested from the fragments and total RNA was extracted using the RNAqeous-4PCR total RNA isolation kit (Invitrogen, Life Technologies AM1914) as explained in Veglia et al. (2022). Tissues were lysed using a refrigerated Qiagen TissueLyser II micro centrifuge at 30 oscillations per second for 30 s. Contaminating DNA and chromatin were removed from the total RNA using the Ambion DNase I (RNase-free) kit (Invitrogen, Life Technologies AM2222). Samples were preprocessed by Novogene Co., Ltd. for mRNA enrichment using polyA tail capture; the mRNA libraries underwent 150-bp, paired-end sequencing on an Illumina NovaSeq 6000 instrument using the NEBNext Ultra II RNA library prep kit.&lt;/em&gt;&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1928771 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1928771 completed Laura Mydlarz University of Texas at Arlington 817-272-0397 501 S. Nedderman Dr. 337 Life Sciences Building Arlington TX 76013 United States mydlarz@uta.edu pointOfContact Adrienne M.S. Correa Rice University amsc@berkeley.edu pointOfContact asNeeded Dataset Version: 1 Unknown Sample_Name Organism Dive_Site Lat Lon Collection_Date Experiment_Mesocosm Freeze_Date Accession SRA Illumina NovaSeq 6000 theme None, User defined sample identification species scientific name (binomial) site latitude longitude date treatment NCBI BioProject accession NCBI SRA Sample accession (SRS) featureType BCO-DMO Standard Parameters Automated DNA Sequencer Qiagen TissueLyser II 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. RAPID: Collaborative Research: Predicting the Spread of Multi-Species Coral Disease Using Species Immune Traits https://osprey.bco-dmo.org/project/811115 RAPID: Collaborative Research: Predicting the Spread of Multi-Species Coral Disease Using Species Immune Traits <p><em>NSF Award Abstract:</em><br /> Coral reef ecosystems provide substantial economic resources to the societies of the United States Virgin Islands (USVI) and other US locations in the forms of tourism, fishing and coastal protection. However, reefs are among the most threatened marine environments, and coral disease is having a devastating impact on these valued systems. In early 2019, a multi-species rapid tissue loss disease matching the description of stony coral tissue loss disease (SCTLD) was found severely affecting a reef off the southwest coast of St. Thomas in the US Virgin Islands (USVI). SCTLD has been devastating coral reef communities in southeast Florida for the last four years, and was very recently reported from disparate areas around the Caribbean, including Mexico, Jamaica, and St. Martin. Rapid surveys by the investigators at the University of the Virgin Islands believe that a 50 km2 area southwest of St. Thomas is the initial incidence area of the disease, but will likely spread across the USVI, British Virgin Islands, and Puerto Rico. This study performs experiments to understand how this disease affects coral species immune traits and compares the microbiology and physiology of disease samples in the USVI to samples from Florida. It also examines how changing the species composition of a coral community affects the spread and impact of the disease. The overall aim is to produce a model to predict the impact of multi-species disease spread on reefs based on coral species assemblages. The project contributes to the research training of at least 2 undergraduates, 2 M.S. students, and 3 Ph.D. students, who benefit from cross-investigator mentoring. The research team includes representatives to the Coral Disease Advisory Committees for the USVI and Florida, which ensures rapid communication of findings to management bodies in both regions.</p> <p>Coral disease is a significant and increasing threat to Caribbean coral reef systems. Recent results demonstrate that coral species immune traits can predict disease resistance, and thus, forecast impacts to coral community structure, under multi-species coral disease. The onset of this epizootic in the USVI offers an unprecedented opportunity to test hypotheses about the impact of coral resistance, tolerance and immune traits on disease spread during the early stages of an outbreak that could profoundly change the diversity of Caribbean reefs. It is hypothesized that the abundance of highly susceptible species dictates 1) the onset of disease at reef sites downstream of the initial incidence area, and 2) the spread of disease within reef sites. Furthermore, 3) downstream reef sites where highly susceptible species are removed or treated show lower immune responses in all susceptible corals, later onset of disease, and slower within-site disease spread. To test these hypotheses, two experiments directly compare species responses to disease exposure and test the effect of species assemblage on coral immune function and disease spread. Results from these experiments aim to inform a generalizable model to predict the impact of multi-species disease spread on reefs based on coral species assemblages. Results of this project include direct comparison of the USVI disease to Florida SCTLD and a better understanding of how the abundance of highly susceptible host species impacts the spread of disease during the early onset of a multi-species panzootic.</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> Multi-Species Coral Disease largerWorkCitation project eng; USA oceans -64.926 -64.926 18.3277 18.3277 2019-03-01 2019-03-31 St. Thomas, U.S. Virgin Islands 0 BCO-DMO catalogue of parameters from RNAseq data used to identify Alphaflexivirus genomes in Stony Coral Tissue Loss Disease-affected, disease-exposed, and disease-unexposed coral colonies in the U.S. Virgin Islands (Multi-Species Coral Disease 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/875635.rdf Name: Sample_Name Units: unitless Description: <p>Sample ID</p> http://lod.bco-dmo.org/id/dataset-parameter/875636.rdf Name: Organism Units: unitless Description: <p>Coral species</p> http://lod.bco-dmo.org/id/dataset-parameter/875637.rdf Name: Dive_Site Units: unitless Description: <p>Dive site common name</p> http://lod.bco-dmo.org/id/dataset-parameter/875638.rdf Name: Lat Units: decimal degrees Description: <p>Latitude of dive site in decimal degrees, a positive value indicates North</p> http://lod.bco-dmo.org/id/dataset-parameter/875639.rdf Name: Lon Units: decimal degrees Description: <p>Longitude of dive site in decimal degrees, a negative value indicates West</p> http://lod.bco-dmo.org/id/dataset-parameter/875640.rdf Name: Collection_Date Units: unitless Description: <p>Date collected from the reef; %Y-%M</p> http://lod.bco-dmo.org/id/dataset-parameter/875641.rdf Name: Experiment_Mesocosm Units: unitless Description: <p>The mesocosm the coral fragment went in (conrol or disease; bins 1 through 8)</p> http://lod.bco-dmo.org/id/dataset-parameter/875642.rdf Name: Freeze_Date Units: unitless Description: <p>Date the coral was removed from the experiment and flash frozen; %Y-%M-%D</p> http://lod.bco-dmo.org/id/dataset-parameter/875643.rdf Name: Accession Units: units Description: <p>BioProject Accession ID</p> http://lod.bco-dmo.org/id/dataset-parameter/875644.rdf Name: SRA Units: unitless Description: <p>SRA 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 1560 https://darchive.mblwhoilibrary.org/bitstream/1912/29010/1/dataset-875583_rnaseq-data-used-identify-viral-genomes__v1.tsv download https://doi.org/10.26008/1912/bco-dmo.875583.1 download onLine dataset &lt;p&gt;&lt;strong&gt;Methodology:&amp;nbsp;&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Sampling and analytical procedures: &lt;/strong&gt;&lt;/p&gt; &lt;p&gt;&lt;em&gt;A SCTLD transmission experiment was carried out at the University of the Virgin Islands (UVI) in April of 2019 and is described in Meiling et al. (2021). One fragment from 6 species of stony coral was placed into a control mesocosm equidistant from a central healthy coral colony. Corresponding genet fragments were placed into an experimental mesocosm equidistant from a SCTLD-infected coral colony. This paired design was replicated for a total of 8 genets per species. Experimental coral fragments that developed lesions were removed and stored at -80ºC for RNA sequencing when 30% tissue loss was achieved. Corresponding control coral fragments were removed and stored at the same time. Tissue samples were harvested from the fragments and total RNA was extracted using the RNAqeous-4PCR total RNA isolation kit (Invitrogen, Life Technologies AM1914) as explained in Veglia et al. (2022). Tissues were lysed using a refrigerated Qiagen TissueLyser II micro centrifuge at 30 oscillations per second for 30 s. Contaminating DNA and chromatin were removed from the total RNA using the Ambion DNase I (RNase-free) kit (Invitrogen, Life Technologies AM2222). Samples were preprocessed by Novogene Co., Ltd. for mRNA enrichment using polyA tail capture; the mRNA libraries underwent 150-bp, paired-end sequencing on an Illumina NovaSeq 6000 instrument using the NEBNext Ultra II RNA library prep kit.&lt;/em&gt;&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;&lt;strong&gt;Processing notes from&amp;nbsp;researcher:&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;BBSplit was used to map quality-filtered (fast v0.20.1) reads to coral or Symbiodiniaceae transcriptome and generate three read files: (I) coral, (ii) Symbiodiniaceae, and (iii) noncoral/non-Symbiodiniaceae. Noncoral/non-Symbiodiniaceae reads were uploaded to NCBI.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;BCO-DMO processing description:&lt;/strong&gt;&lt;/p&gt; &lt;ul&gt; &lt;li&gt;Converted dates to YYYY-MM-DD or YYYY-MM formats where appropriate&lt;/li&gt; &lt;li&gt;Removed apostrophes (') from Dive_Site column&lt;/li&gt; &lt;li&gt;Replaced spaces (&quot; &quot;) with underscores (_) in column headers&lt;/li&gt; &lt;li&gt;Converted lat and long from degrees, hours, seconds to decimal degrees format (64˚55'33.5&quot;W → -64.925972)&lt;/li&gt; &lt;/ul&gt; 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 Illumina NovaSeq 6000 Illumina NovaSeq 6000 PI Supplied Instrument Name: Illumina NovaSeq 6000 PI Supplied Instrument Description:An Illumina NovaSeq 6000 was used for 150-bp, pared-end mRNA sequencing 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. PI Supplied Instrument Name: Instrument Name: Qiagen TissueLyser II Instrument Short Name: Instrument Description: The Qiagen TissueLyser II is a tissue processor designed to disrupt biological samples through high-speed shaking in plastic tubes with stainless steel, tungsten carbide, or glass beads. It is used for high-throughput disruption of human, animal, and plant tissues, bacteria, and yeast to access biological information for genomics, transcriptomics, and proteomics applications. It automates the purification of DNA, RNA, and protein from 1 to 96 samples. Disruption and homogenization are achieved through the beating and grinding effect of beads on the sample material as they are shaken together in the grinding vessels. Using the appropriate adapter set, up to 48 or 192 samples can be processed at the same time. Alternatively, a grinding jar set can be used to process large samples. A range of beads, bead dispensers, and collection microtubes and caps are also available. It can be programmed to provide variable speeds from 3 to 30 Hz (180-1800 oscillations per minute) and run times from 10 seconds to 99 minutes.