19:I[42426,["/_next/static/immutable/chunks/1xctgzqre-wsy.js","/_next/static/immutable/chunks/06_-wz6pdtp2b.js","/_next/static/immutable/chunks/30e52g49hg40p.js","/_next/static/immutable/chunks/02yq6tul2z-oh.js","/_next/static/immutable/chunks/10bx_ec2vj7n_.js","/_next/static/immutable/chunks/33bfn03fo8xnt.js","/_next/static/immutable/chunks/0tfjf78scu61b.js","/_next/static/immutable/chunks/31xnvej4n1bi9.js"],"default"] 1a:T5ec,

Methodology:

Sampling and analytical procedures:

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.

1b:Te2a,NSF Award Abstract: 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. 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. 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.6:["$","$L19",null,{"dataset":{"_id":"875583","description":"","problem":"","acquisition":"$1a","processing":"

Processing notes from researcher:

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.

BCO-DMO processing description:

Converted dates to YYYY-MM-DD or YYYY-MM formats where appropriate
Removed apostrophes (') from Dive_Site column
Replaced spaces (\" \") with underscores (_) in column headers
Converted lat and long from degrees, hours, seconds to decimal degrees format (64˚55'33.5\"W → -64.925972)

\n","bcodmoProcessing":"","title":"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)","nickname":"RNAseq data used to identify viral genomes","dataUrl":"","currentState":"Final no updates expected","currentStateId":"7","validated":true,"restricted":false,"version":"1","version_date":"2022-06-11T04:00:00.000Z","abstract":"RNA-seq data from healthy, SCTLD-exposed, and SCTLD-infected coral samples taken from a transmission experiment carried out in the US Virgin Islands. ","citation":"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]","citationParts":{"identifier":"doi:10.26008/1912/bco-dmo.875583.1","versionDate":"2022-06-11","versionId":"1","year":"2022","title":"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)","authors":"Mydlarz, L., Correa, A. 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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.","type_acronym":""}],"parameters":[{"_id":"875635","name":"Sample_Name","format":"","frictionlessType":"string","description":"

Sample ID

","units":{"_id":"","name":"unitless"},"type":{"_id":"960","name":"sample","description":"

unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent

"}},{"_id":"875636","name":"Organism","format":"","frictionlessType":"string","description":"

Coral species

","units":{"_id":"","name":"unitless"},"type":{"_id":"976","name":"species","description":"

a taxonomic binomial that consists of a genus name followed by the species name of an organism

"}},{"_id":"875637","name":"Dive_Site","format":"","frictionlessType":"string","description":"

Dive site common name

","units":{"_id":"","name":"unitless"},"type":{"_id":"1124","name":"site","description":"

Sampling site identification.

"}},{"_id":"875638","name":"Lat","format":"","frictionlessType":"number","description":"

Latitude of dive site in decimal degrees, a positive value indicates North

","units":{"_id":"","name":"decimal degrees"},"type":{"_id":"730","name":"latitude","description":"

latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes

"}},{"_id":"875639","name":"Lon","format":"","frictionlessType":"number","description":"

Longitude of dive site in decimal degrees, a negative value indicates West

","units":{"_id":"","name":"decimal degrees"},"type":{"_id":"731","name":"longitude","description":"

longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datasets as degrees, minutes

"}},{"_id":"875640","name":"Collection_Date","format":"%Y-%m","frictionlessType":"date","description":"

Date collected from the reef; %Y-%M

","units":{"_id":"","name":"unitless"},"type":{"_id":"1070","name":"date","description":"

date; generally reported in GMT as YYYYMMDD (year; month; day); also as MMDD (month; day); EqPac dates are local Hawaii time. ISO_Date format is YYYY-MM-DD (http://www.iso.org/iso/home/standards/iso8601.htm)

"}},{"_id":"875641","name":"Experiment_Mesocosm","format":"","frictionlessType":"string","description":"

The mesocosm the coral fragment went in (conrol or disease; bins 1 through 8)

","units":{"_id":"","name":"unitless"},"type":{"_id":"489066","name":"treatment","description":"

Experimental conditions applied to experimental units. In comparative experiments, members of the complementary group, the control group, receive either no treatment or a standard treatment.

"}},{"_id":"875642","name":"Freeze_Date","format":"%Y-%m-%d","frictionlessType":"date","description":"

Date the coral was removed from the experiment and flash frozen; %Y-%M-%D

","units":{"_id":"","name":"unitless"},"type":{"_id":"1070","name":"date","description":"

"}},{"_id":"875643","name":"Accession","format":"","frictionlessType":"string","description":"

BioProject Accession ID

","units":{"_id":"","name":"units"},"type":{"_id":"854958","name":"BioProject","description":"

The National Center for Biotechnology Information (NCBI) BioProject identifier.

A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project.

"}},{"_id":"875644","name":"SRA","format":"","frictionlessType":"string","description":"

SRA ID

","units":{"_id":"","name":"unitless"},"type":{"_id":"857016","name":"SRA_sample","description":"

The National Center for Biotechnology Information (NCBI) Sample accession number in the Sequence Read Archive (SRA).

A Sample in the SRA is an object that contains the metadata describing the physical sample upon which a sequencing experiment was performed. Imported from BioSample.

An experiment targets one or more samples. Results are expressed in terms of individual samples or bundles of samples as defined by the experiment.

The identifier usually begins with SRS

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