http://lod.bco-dmo.org/id/dataset/922006 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 2024-03-12 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Acropora cervicornis genomic/trancriptomic sequence accessions with associated data on tank exposure to white band disease and survival outcomes with corals collected from Florida, USA and Bocas del Toro, Panama in 2021 2024-03-12 publication 2024-03-12 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2024-03-21 publication https://doi.org/10.26008/1912/bco-dmo.922006.1 Steven V. Vollmer Northeastern University principalInvestigator Charles L. Roesel Northeastern University principalInvestigator Jason D. Selwyn Texas A&M, Corpus Christi 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: Vollmer, S. V., Selwyn, J. D., Roesel, C. L., Douglas, B. (2024) Acropora cervicornis genomic/trancriptomic sequence accessions with associated data on tank exposure to white band disease and survival outcomes with corals collected from Florida, USA and Bocas del Toro, Panama in 2021. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-03-12 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.922006.1 [access date] Dataset Description: &lt;p&gt;Related NCBI BioProjects containing genomic/transcriptomic data from this study (see Supplemental Files for accession metadata):&lt;/p&gt; &lt;p&gt;mRNA sequencing from 48 A. cervicornis colonies differentially exposed to white band disease at multiple time points: NCBI BioProject PRJNA949884 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA949884)&lt;/p&gt; &lt;p&gt;Whole genome sequencing of DNA from 96 A. cervicornis colonies: NCBI BioProject PRJNA950067&amp;nbsp;(https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA950067)&lt;/p&gt; &lt;p&gt;Short and long read data and Genome Assembly for the Coral Restoration Foundation K2 genotype of A. cervicornis: NCBI BioProject PRJNA948411&amp;nbsp;(https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA948411)&lt;/p&gt; Methods and Sampling: &lt;p&gt;Putative genotypes were collected on SCUBA from either the Coral Restoration Foundation nursery habitat (Florida) or from five natural reefs (Panama). Florida sampling took place in June 2021 and Panama sampling occurred in November 2021. At each location, ten replicate fragments from each putative genotype were spread across one of ten 18-liter recirculating tanks held at ambient seawater temperatures at each location’s flow-thru seawater system. Each fragment was experimentally lesioned with a waterpik to facilitate transmission (Gignoux-Wolfsohn et al. 2012). Five tanks were exposed to 50ml of disease slurry produced from 10 WBD infected coral fragments and five tanks were exposed to 50ml of healthy slurry from 10 healthy fragments. Slurries were produced by waterpiking disease or healthy coral tissue off the sampled corals in filtered seawater (FSW) and normalizing the slurry doses to a standard ocular density of 0.6 at 600nm. Exposed coral tanks were censused for disease twice daily at 6am and 6pm (local time, EST) for up to 7 days and disease coral fragments were pulled from tanks at the first signs of disease to prevent amplifying pathogen spread within each tank.&lt;/p&gt; &lt;p&gt;High molecular weight genomic DNA was extracted from all samples using the Zymo Quick-DNA 96 kit. Whole genome sequencing was produced for all putative genotypes using Illumina DNA Prep kit on two 150bp paired-end NovaSeq S4 runs. For the K2 genotype three libraries were prepared using Oxford Nanopore Technologies (ONT) kit SQK-LSK112. Two libraries were not size selected while the third included 20+kb PippenPrep size-selection. All ONT prepared libraries were sequenced separately on three Minion flow cells (FLO-MIN112). High-quality base-calling was performed using Guppy v6.1.7 (Oxford Nanopore Technologies). An additional four Illumina PCR-Free shotgun libraries were constructed using the DISCOVAR protocol to produce libraries with fragments between 400 and 600 bp (Love et al. 2016). KAPA PCR-free library kits were leveraged with the addition of a second round of 0.7x Agencourt AmPure XP SPRI bead cleanup post adapter ligation. Libraries were multiplexed and sequenced on a single rapid-run HiSeq 2500 flowcell with 250 bp paired-end sequencing. Finally, mRNA sequence data was obtained for 48 samples (including the K2 genotype) using NEBs unidirectional mRNA library preparations sequenced on an Illumina NEXTSEQ 550 platform.&lt;br /&gt; &lt;br /&gt; Organism identifier (LSID):&lt;br /&gt; Acropora cervicornis (urn:lsid:marinespecies.org:taxname:206989)&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1924145 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1924145 completed 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 Charles L. Roesel Northeastern University croesel@gmail.com pointOfContact Jason D. Selwyn Texas A&M, Corpus Christi j.selwyn@northeastern.edu pointOfContact asNeeded Dataset Version: 1 Unknown Tank Treatment Location Genotype Day_1_AM Day_1_PM Day_2_AM Day_2_PM Day_3_AM Day_3_PM Day_4_AM Day_4_PM Day_5_AM Day_5_PM Day_6_AM Day_6_PM Day_7_AM NovaSeq S4 Minion flow cells (FLO-MIN112) Illumina HiSeq 2500 Illumina NEXTSEQ 550 theme None, User defined tank treatment sample description flag featureType BCO-DMO Standard Parameters Automated DNA Sequencer Automated DNA Sequencer Automated DNA Sequencer Automated DNA Sequencer DNA Extractor 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. Multi-omic bases of coral disease resistance https://osprey.bco-dmo.org/project/823361 Multi-omic bases of coral disease resistance <p>NSF Award Abstract:</p> <p>Coral disease outbreaks have radically altered the structure and function of tropical coral reefs worldwide. As progress has been made towards understanding the basic cause of many coral diseases, significant gaps remain in our knowledge of how corals respond to and resist disease infection, even as calls are being made for science to assist in coral evolution by selecting thermal or disease tolerant coral species or genotypes - often called "super corals". This project uses the endangered Caribbean staghorn coral Acropora cervicornis and White Band Disease (WBD) as a host-pathogen system to study the genetics of coral disease resistance. WBD epidemics decimated this key shallow-water Caribbean coral and led to its endangered listing. While the recovery of staghorn corals has been slow, data indicate that up to 15% or more of staghorn corals are highly disease resistant. This project uses modern genomic tools to identify genetic markers for staghorn coral disease resistance. The identification of genetic markers for disease resistance (i) provides needed information on the efficacy of "assisted evolution" for coral resiliency (ii) helps predict how well staghorn coral can resist future disease outbreaks, (iii) assists conservation efforts aimed at identifying and selecting corals with high disease resistance, and (iv) spurs the development of molecular assays for coral disease resistance. This research provides graduate and undergraduate training in the STEM fields of microbiology, genetics, and computational biology. The project is as a platform to develop outreach curricula to teach students about coral diseases and reef health, which are disseminated via Northeastern University's K-12 outreach program and the Smithsonian Tropical Research Institute's outreach program in Panama. This project is co-funded by the Biological Oceanography Program in the Division of Ocean Sciences and the Symbiosis, Defense, and Self-recognition Program in the Division of Integrative Organismal Systems.</p> <p>It is increasingly becoming clear that the future of coral reefs depends on the resilience of reef-building corals to adapt or acclimate to their changing environment, which in turn requires that key traits like thermal tolerance and disease resistance are genetically heritable, identifiable, and quantifiable. Using staghorn corals and WBD as a model host-pathogen system, this project identifies the genetic underpinnings of disease resistance in Caribbean staghorn corals using state-of-the-art, multi-omic approaches linking patterns of variation across the staghorn coral genome, transcriptome and proteome. For Aim 1, genome-wide SNP variation from 200 staghorn coral genotypes from two populations [100 Florida; 100 Panama] is used to identify genomic regions associated with disease resistance using genome-wide association (GWA) analyses. For Aim 2, tank-based transmission experiments are used to profile key differences in the transcriptomic (mRNA and miRNA) and proteomic response of resistant versus susceptible staghorn corals during disease exposure. Mulit-omic data are analyzed using: (1) eQTL to link SNPs to mRNA expression, (2) miRNA-mRNA interactions and correlation networks to test for post-transcriptional gene regulation, and (3) network-based approaches. For Aim 3, 16s rDNA amplicon sequencing are used to identify changes in the staghorn coral microbiome due to disease resistance and exposure using microbial DNA from the resistant and susceptible corals used in the tank-based experiment (Aim 2). In addition to identify genetic markers associated with coral disease resistance, this study produces (1) the most complete multi-omic analysis of coral immunity and disease resistance to date, and (2) the first functional analyses of miRNA post-translational gene regulation in a cnidarian host-pathogen system. Data on the genetics of coral disease resistance provide valuable information on the efficacy of "assisted evolution" for coral resiliency. By using nursery raised staghorn corals from Florida, this project directly identifies highly disease resistant corals that can be used in the large-scale out planting efforts.</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> coral disease resistance largerWorkCitation project eng; USA oceans -82.26 -81.04 9.35 24.73 2021-06-19 2021-11-12 Bocas del Toro, Panama and Coral Restoration Nursery, Marathon, Florida, US 0 BCO-DMO catalogue of parameters from Acropora cervicornis genomic/trancriptomic sequence accessions with associated data on tank exposure to white band disease and survival outcomes with corals collected from Florida, USA and Bocas del Toro, Panama in 2021 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/922060.rdf Name: Tank Units: untiless Description: <p>Experimental tank (H1-5 or D1-5)</p> http://lod.bco-dmo.org/id/dataset-parameter/922061.rdf Name: Treatment Units: untiless Description: <p>Experimental exposure (H - healthy exposure, D - disease exposure)</p> http://lod.bco-dmo.org/id/dataset-parameter/922062.rdf Name: Location Units: untiless Description: <p>Region of origin (Florida or Panama)</p> http://lod.bco-dmo.org/id/dataset-parameter/922063.rdf Name: Genotype Units: untiless Description: <p>Putative Genotype</p> http://lod.bco-dmo.org/id/dataset-parameter/922064.rdf Name: Day_1_AM Units: untiless Description: <p>Disease state (healthy = 0, diseased = 1) of the coral colony in the exposure experiment on Day 1 in the AM (Eastern Time Zone).</p> http://lod.bco-dmo.org/id/dataset-parameter/922065.rdf Name: Day_1_PM Units: untiless Description: <p>Disease state (healthy = 0, diseased = 1) of the coral colony in the exposure experiment on Day 1 in the PM (Eastern Time Zone).</p> http://lod.bco-dmo.org/id/dataset-parameter/922066.rdf Name: Day_2_AM Units: untiless Description: <p>Disease state (healthy = 0, diseased = 1) of the coral colony in the exposure experiment on Day 2 in the AM (Eastern Time Zone).</p> http://lod.bco-dmo.org/id/dataset-parameter/922067.rdf Name: Day_2_PM Units: untiless Description: <p>Disease state (healthy = 0, diseased = 1) of the coral colony in the exposure experiment on Day 2 in the PM (Eastern Time Zone).</p> http://lod.bco-dmo.org/id/dataset-parameter/922068.rdf Name: Day_3_AM Units: untiless Description: <p>Disease state (healthy = 0, diseased = 1) of the coral colony in the exposure experiment on Day 3 in the AM (Eastern Time Zone).</p> http://lod.bco-dmo.org/id/dataset-parameter/922069.rdf Name: Day_3_PM Units: untiless Description: <p>Disease state (healthy = 0, diseased = 1) of the coral colony in the exposure experiment on Day 3 in the PM (Eastern Time Zone).</p> http://lod.bco-dmo.org/id/dataset-parameter/922070.rdf Name: Day_4_AM Units: untiless Description: <p>Disease state (healthy = 0, diseased = 1) of the coral colony in the exposure experiment on Day 4 in the AM (Eastern Time Zone).</p> http://lod.bco-dmo.org/id/dataset-parameter/922071.rdf Name: Day_4_PM Units: untiless Description: <p>Disease state (healthy = 0, diseased = 1) of the coral colony in the exposure experiment on Day 4 in the PM (Eastern Time Zone).</p> http://lod.bco-dmo.org/id/dataset-parameter/922072.rdf Name: Day_5_AM Units: untiless Description: <p>Disease state (healthy = 0, diseased = 1) of the coral colony in the exposure experiment on Day 5 in the AM (Eastern Time Zone).</p> http://lod.bco-dmo.org/id/dataset-parameter/922073.rdf Name: Day_5_PM Units: untiless Description: <p>Disease state (healthy = 0, diseased = 1) of the coral colony in the exposure experiment on Day 5 in the PM (Eastern Time Zone).</p> http://lod.bco-dmo.org/id/dataset-parameter/922074.rdf Name: Day_6_AM Units: untiless Description: <p>Disease state (healthy = 0, diseased = 1) of the coral colony in the exposure experiment on Day 6 in the AM (Eastern Time Zone).</p> http://lod.bco-dmo.org/id/dataset-parameter/922075.rdf Name: Day_6_PM Units: untiless Description: <p>Disease state (healthy = 0, diseased = 1) of the coral colony in the exposure experiment on Day 6 in the PM (Eastern Time Zone).</p> http://lod.bco-dmo.org/id/dataset-parameter/922076.rdf Name: Day_7_AM Units: untiless Description: <p>Disease state (healthy = 0, diseased = 1) of the coral colony in the exposure experiment on Day 7 in the AM (Eastern Time Zone).</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 40878 https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/485c4a47-eb66-483a-ac6e-cb8542ac61ba/content download https://doi.org/10.26008/1912/bco-dmo.922006.1 download onLine dataset &lt;p&gt;Putative genotypes were collected on SCUBA from either the Coral Restoration Foundation nursery habitat (Florida) or from five natural reefs (Panama). Florida sampling took place in June 2021 and Panama sampling occurred in November 2021. At each location, ten replicate fragments from each putative genotype were spread across one of ten 18-liter recirculating tanks held at ambient seawater temperatures at each location’s flow-thru seawater system. Each fragment was experimentally lesioned with a waterpik to facilitate transmission (Gignoux-Wolfsohn et al. 2012). Five tanks were exposed to 50ml of disease slurry produced from 10 WBD infected coral fragments and five tanks were exposed to 50ml of healthy slurry from 10 healthy fragments. Slurries were produced by waterpiking disease or healthy coral tissue off the sampled corals in filtered seawater (FSW) and normalizing the slurry doses to a standard ocular density of 0.6 at 600nm. Exposed coral tanks were censused for disease twice daily at 6am and 6pm (local time, EST) for up to 7 days and disease coral fragments were pulled from tanks at the first signs of disease to prevent amplifying pathogen spread within each tank.&lt;/p&gt; &lt;p&gt;High molecular weight genomic DNA was extracted from all samples using the Zymo Quick-DNA 96 kit. Whole genome sequencing was produced for all putative genotypes using Illumina DNA Prep kit on two 150bp paired-end NovaSeq S4 runs. For the K2 genotype three libraries were prepared using Oxford Nanopore Technologies (ONT) kit SQK-LSK112. Two libraries were not size selected while the third included 20+kb PippenPrep size-selection. All ONT prepared libraries were sequenced separately on three Minion flow cells (FLO-MIN112). High-quality base-calling was performed using Guppy v6.1.7 (Oxford Nanopore Technologies). An additional four Illumina PCR-Free shotgun libraries were constructed using the DISCOVAR protocol to produce libraries with fragments between 400 and 600 bp (Love et al. 2016). KAPA PCR-free library kits were leveraged with the addition of a second round of 0.7x Agencourt AmPure XP SPRI bead cleanup post adapter ligation. Libraries were multiplexed and sequenced on a single rapid-run HiSeq 2500 flowcell with 250 bp paired-end sequencing. Finally, mRNA sequence data was obtained for 48 samples (including the K2 genotype) using NEBs unidirectional mRNA library preparations sequenced on an Illumina NEXTSEQ 550 platform.&lt;br /&gt; &lt;br /&gt; Organism identifier (LSID):&lt;br /&gt; Acropora cervicornis (urn:lsid:marinespecies.org:taxname:206989)&lt;/p&gt; Specified by the Principal Investigator(s) * Submitted file &quot;exposure_experiment.csv&quot; was imported into the BCO-DMO data system for this dataset. * Column names adjusted to conform to BCO-DMO naming conventions designed to support broad re-use by a variety of research tools and scripting languages. [Only numbers, letters, and underscores.  Can not start with a number] 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 NovaSeq S4 NovaSeq S4 PI Supplied Instrument Name: NovaSeq S4 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. Minion flow cells (FLO-MIN112) Minion flow cells (FLO-MIN112) PI Supplied Instrument Name: Minion flow cells (FLO-MIN112) 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. Illumina HiSeq 2500 Illumina HiSeq 2500 PI Supplied Instrument Name: Illumina HiSeq 2500 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. Illumina NEXTSEQ 550 Illumina NEXTSEQ 550 PI Supplied Instrument Name: Illumina NEXTSEQ 550 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: PI Supplied Instrument Description:Zymo Quick-DNA 96 kit Oxford Nanopore Technologies (ONT) kit SQK-LSK112 DNA Prep kit KAPA PCR-free library kits Instrument Name: DNA Extractor Instrument Short Name: Instrument Description: A device that is used to isolate and collect DNA for subsequent molecular analysis.