RNAseq data from apparently healthy and Stony Coral Tissue Loss Disease-affected Montastraea cavernosa coral collected from St. Thomas, US Virgin Islands in 2020
Project
| Contributors | Affiliation | Role |
|---|---|---|
| Mydlarz, Laura | University of Texas at Arlington (UT Arlington) | Principal Investigator |
| Beavers, Kelsey | University of Texas at Arlington (UT Arlington) | Scientist |
| Merchant, Lynne M. | Woods Hole Oceanographic Institution (WHOI BCO-DMO) | BCO-DMO Data Manager |
Abstract
Golf ball-sized coral fragments were collected by divers on SCUBA with hammers and chisels from two reefs in St. Thomas, United States Virgin Islands (USVI) showing signs of active SCTLD in February of 2020: Buck Island (18.27883˚, –64.89833˚) and Black Point (18.3445˚, –64.98595˚). Black Point, a nearshore reef, first exhibited SCTLD cases between December 2018 and January 2019, as documented in Brandt et al. (2021). Buck Island, situated near an offshore undeveloped island, recorded its first cases of SCTLD in October 2019, also documented in Brandt et al. (2021). Current environments at both sites are similar. SCTLD-affected corals were identified based on displaying acute multifocal lesions consistent with the SCTLD case definition at the time (SCTLD Case Definition, 2018). Lesions were bright white where the skeleton had recently been denuded of tissue, with no visible algal colonization at the skeletal/tissue boundary, indicating actively expanding lesions.
At both sites, one coral fragment was collected from each apparently healthy colony (Buck Island, n=3; Black Point, n=3), termed apparently healthy tissue on an apparently healthy colony (HH). Two fragments were collected from each diseased colony: one immediately adjacent to the SCTLD lesion line (Buck Island, n=3; Black Point, n=5), termed lesion tissue on a diseased colony (LD), and one as far away from the lesion line as possible (approximately 10 cm from the lesion line) (Buck Island, n=3; Black Point, n=5), termed apparently healthy tissue on a diseased colony (HD). The sampling scheme aimed to capture the variability in gene expression across different tissue health states while ensuring consistency in sampling methodology. Coral fragments were placed in individual bags that were sealed and transported to land on ice before being flash-frozen at -80˚C.
Total RNA was extracted from all 22 coral fragments following the protocol outlined in Beavers et al. (2023) using the RNAqueous-4PCR Total RNA Isolation Kit from Invitrogen (Life Technologies AM1914). About one gram of frozen coral tissue was scraped off each fragment into a 2 mL microcentrifuge tube using a sterilized bone cutter. Lysis buffer was added to each microcentrifuge tube followed by mechanical disruption using a refrigerated Qiagen Tissuelyser II at 30 oscillations/s for 60 s. Elution was performed in two 30 µL steps at a time. After combining elutions, contaminating DNA and chromatin were removed using the Ambion DNase I kit from Invitrogen (Life Technologies AM 2222). Resulting total RNA samples were sent to Novogene Co., LTD (Beijing, China) for quality assessment using an Agilent Bioanalyzer 2100. All 22 samples passed quality assessment with RNA integrity (RIN) values ≥ 7 and were preprocessed for mRNA enrichment using polyA tail capture. cDNA libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit from Illumina and sequenced on the Illumina NovaSeq 6000 for 150 bp, paired-end sequencing. Sample and data analysis was performed in January 2024.
The data presented are raw RNAseq reads and have not undergone any processing besides that done at the sequencing facility.
Processed submitted file named BCO-DMO.xlsx with frictionless BCO-DMO Laminar tool.
Removed the duplicate column named Collection_month/year containing the collection month and year because another column named Collection_month_year contains the same information.
Renamed the columns according to BCO-DMO naming conventions where no units are included in the column names. Removed the units from the columns named Reef_depth_m, Disease_Colony_Sample_Distance_cm, Temperature_C, and Salinity_psu.
Converted the date format in the column Collection_month_year from Month name and two digit year to the ISO8601 format of YYYY-MM.
Renamed the column Collection_month_year to Collection_Date.
Checked the Coral Species name "Montastraea cavernosa" with the World Register of Marine Species (WoRMS) website to verify this is the accepted species name.
Saved the dataset to the primary data file named 935630_v1_rna_seq_montastraea_cavernosa.
| Parameter | Description | Units |
| Sample_ID | Sample identifier | unitless |
| NCBI_BioProject_accession | NCBI BioProject accession number | unitless |
| NCBI_BioSample_accession | NCBI BioSample accession number | unitless |
| NCBI_SRA_accession | NCBI SRA accession number | unitless |
| Sample_type | Type of sample collected. Tissue fragment = a golf ball-sized fragment of coral tissue + skeleton that we later extracted RNA from | unitless |
| Coral_species | Species of Coral collected: All samples were collected from Montastraea cavernosa colonies | unitless |
| Reef_Name | The name of the reef that samples were collected from | unitless |
| Reef_type | Indicates the reef type that samples were collected from | unitless |
| Collection_Date | Indicates the month and year of sample collection | unitless |
| Latitude | Sampling location latitude, south is negative | unitless |
| Longitude | Sampling location longitude, west is negative | unitless |
| SCTLD_duration_months | Indicates in months how long SCTLD had been present at that location prior to sampling | unitless |
| Reef_depth | The depth of the sample collected | meters (m) |
| Temperature | The temperature of sample environment | Celcius (degC) |
| Salinity | The salinity of the sample environment | psu |
| pH | The pH of the sample environment | unitless |
| Colony_status | The health status of the colony sampled. (Diseased = SCTLD; Healthy = Apparently healthy) | unitless |
| Frag_condition | The tissue status of the sample (Apparently healthy = apparently healthy (visibly); Lesion = immediately adjacent to the SCTLD lesion) | unitless |
| Tissue_Health_State | The health state identifier of the sample (HH = apparently healthy tissue from an apparently healthy colony; HD = apparently healthy tissue from a SCTLD-affected colony; LD = lesion tissue from a SCTLD-affected colony) | unitless |
| Disease_Colony_Sample_Distance | Indicates how far away the apparently healthy tissue was sampled from the SCTLD lesion (only applies to HD tissue). nd = not collected (HH or LD) | centimeters (cm) |
| Library_strategy | RNA-Seq = samples were prepared for RNA sequencing | unitless |
| Sequencing_Strategy | all RNA samples were prepared for 150 base-pair, paired-end sequencing | unitless |
| Sequencing_Instrument_model | All RNA samples were sequenced on the Illumina NovaSeq 6000 | unitless |
| Sequencing_strategy_details | All RNA samples were processed for polyA-tail enrichment to remove non-eukaryotic reads | unitless |
| RNA_extraction_method | Indicates how the RNA was extracted from each sample. | unitless |
| Dataset-specific Instrument Name | Illumina NovaSeq 6000 |
| Generic Instrument Name | Automated DNA Sequencer |
| Generic Instrument Description | General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. |
| Dataset-specific Instrument Name | Agilent Bioanalyzer 2100 |
| Generic Instrument Name | Bioanalyzer |
| Generic Instrument Description | A Bioanalyzer is a laboratory instrument that provides the sizing and quantification of DNA, RNA, and proteins. One example is the Agilent Bioanalyzer 2100. |
| Dataset-specific Instrument Name | Qiagen TissueLyser II |
| Generic Instrument Name | Qiagen TissueLyser II |
| Generic 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. |
RAPID: Collaborative Research: Predicting the Spread of Multi-Species Coral Disease Using Species Immune Traits (Multi-Species Coral Disease)
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.
| Funding Source | Award |
|---|---|
| NSF Division of Ocean Sciences (NSF OCE) |
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