Dataset: Viral Consortia in Stony Corals

Name: Viral consortia in Stony Coral Tissue Loss Disease- affected, disease-exposed, and disease-unexposed coral colonies from a transmission experiment conducted on samples collected from Rupert’s Rock in St. Thomas, U.S. Virgin Islands in 2019
Published: 2022-06-29
Keywords: Symbiodiniaceae, stony coral tissue loss disease, alphaflexivirus, +ssRNA virus, biota, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.875283.1

Spatial Extent: N:18.3276666667 E:-64.9259722222 S:18.3276666667 W:-64.9259722222

Temporal Extent: 2019-04-11 - 2019-04-12

Project:

RAPID: Collaborative Research: Predicting the Spread of Multi-Species Coral Disease Using Species Immune Traits (Multi-Species Coral Disease)

Principal Investigator:

Adrienne M.S. Correa (Rice University)

Co-Principal Investigator:

Laura Mydlarz (University of Texas at Arlington, UT Arlington)

Student:

Kelsey Beavers (University of Texas at Arlington, UT Arlington)

Alex J. Veglia (Rice University)

Contact:

Adrienne M.S. Correa (Rice University)

BCO-DMO Data Manager:

Taylor Heyl (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2022-06-29

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Viral consortia in Stony Coral Tissue Loss Disease- affected, disease-exposed, and disease-unexposed coral colonies from a transmission experiment conducted on samples collected from Rupert’s Rock in St. Thomas, U.S. Virgin Islands in 2019

Abstract:

To understand the extent to which (if any) viruses are associated with stony coral tissue loss disease (SCTLD) in stony corals of the U.S. Virgin Islands, we leveraged viral metatranscriptomes generated from SCTLD-affected, SCTLD-exposed, and control (unexposed) coral holobionts sampled during a SCTLD transmission experiment. Sequence data is available in NCBI Genbank under BioProject accession PRJNA788911.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2022-06-29	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.875283.1	2022-11-04

Methods & Sampling

This dataset represents collections of Montastraea cavernosa, Porites astreoides, and Pseudodiploria strigosa colonies, no larger than 25 centimeters (cm) × 25 centimeters (cm), from Rupert’s Rock (18°19′39.6ʺN 64°55′33.5ʺW) in St. Thomas, U.S. Virgin Islands. The corals were collected by divers on SCUBA with hammers and chisels (March 2019) and preserved for analysis in April 2019.

Methodology:
Samples were preprocessed by Novogene Co., Ltd. (Davis, CA, USA) 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.

Sampling and analytical procedures:
Samples were flash frozen in liquid nitrogen and stored at -80 degrees C until further processing. Total RNA was extracted using the RNAqueous-4PCR total RNA isolation kit (Invitrogen, Life Technologies AM1914). Tissues were lysed using a refrigerated Qiagen TissueLyser II microcentrifuge at 30 oscillations per second for 30 seconds. The elution stage consisted of two consecutive 30-milliliter (mL) elutions. Contaminating DNA and chromatin were removed from the total RNA using the Ambion DNase I (RNase-free) kit (Invitrogen, Life Technologies AM2222).

A combination of reads from stony coral tissue loss disease affected, stony coral tissue loss disease exposed and control (unexposed) holobiont metatranscriptomes (Montastraea cavernosa, Porites astreoides and Pseudodiploria strigosa) were generated from the following samples: Mcav_c3, Mcav_c6, Mcav_c7, Mcav_d2, Mcav_d3, Mcav_d4, Mcav_d6, Mcav_d8, Past_c6, Past_d4, Past_d6 and Pstrig_d5 and given the NCBI accession number: OM030231.

A combination of reads from stony coral tissue loss disease affected, stony coral tissue loss disease exposed and control (unexposed) holobiont metatranscriptomes (Montastraea cavernosa, Porites astreoides and Pseudodiploria strigosa) were generated from the following samples: Mcav_c3, Mcav_c6, Mcav_c7, Mcav_d2, Mcav_d3, Mcav_d4, Mcav_d6, Mcav_d8, Past_c6, Past_d4 and Pstrig_d5 and given the NCBI accession number: OM030232.

Sequence data is available in NCBI Genbank under BioProject accession PRJNA788911 and including NCBI SRA run SRR17230316 - SRR17230326.

Data Processing Description

Data Processing:
All bioinformatic tools were run using default parameters unless otherwise specified. BBSplit (BBMap v38.90) was used to map quality-filtered (fastp v0.20.1) reads to coral or Symbiodiniaceae transcriptomes and generate three read files: (i) coral, (ii) Symbiodiniaceae, and (iii) noncoral/non-Symbiodiniaceae. Noncoral/non-Symbiodiniaceae reads were combined and normalized using BBnorm.sh within BBMap. Normalized reads were assembled using the program TransPi. Multiple assemblies were generated using rnaSPADES v3.14.0 (kmer: 75,85,91,107 nucleotides), Trans-ABySS v2.0.1 (kmer: 25,35,55,75,85 nucleotides), SOAPdenovo-Trans v1.03 (kmer: 25,35,55,75,85 nucleotides), Trinity v2.9.1 (kmer: 35 nucleotides), and Velvet v1.2.12/Oases v0.2.09 (kmer: 65,71,81,87,91,97,101 nucleotides). The multiple assemblies were concatenated into a single file, and the EvidentialGene tr2aacds pipeline v2019.05.14 was used to collapse duplicates and remove misassembled contigs from the assembly file. VirSorter2 was used to detect RNA viruses from the nonredundant metatranscriptome-assembly file (minimum length, 300 nucleotides). Viral genomes similar to known members of the Alphaflexiviridae were identified by aligning translated open reading frames (ORFs) to the proteic version of the Reference Virus Database with DIAMOND BLASTx v2.0.11.149 in “ultra-sensitive” mode. Cenote-Taker 2 was used to annotate identified viral genomes with similarity to the Alphaflexiviridae and calculate the genome coverage using the normalized reads. The alphaflexivirus read count per sample library was estimated by mapping nonnormalized reads to the nonredundant assembly using bowtie2 with the align_and_estimate_abundance.pl script.

BCO-DMO Processing:
- Converted dates to format (YYYY-MM-DD)
- Adjusted field/parameter names to comply with BCO-DMO naming conventions
- Missing data identifier ‘NA’ replaced with 'nd' (BCO-DMO's default missing data identifier)
- Added a conventional header with dataset name, PI names, version date
- Latitude and longitude columns were split from the location columns

Data Files

File
viral_consortia.csv (Comma Separated Values (.csv), 1.72 KB) MD5:c4a4a41056eac03c8234c325518ea518 Primary data file for dataset ID 875283

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1928609

Deployments

None available yet

Instruments

Manual Biota Sampler

Supplied Name: Hammer and Chisel

Supplied Description:

Instrument Type

Generic Name: Manual Biota Sampler

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/90/

Generic Description:

"Manual Biota Sampler" indicates that a sample was collected in situ by a person, possibly using a hand-held collection device such as a jar, a net, or their hands. This term could also refer to a simple tool like a hammer, saw, or other hand-held tool.

Qiagen TissueLyser II

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Qiagen TissueLyser II

Generic 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.

Self-Contained Underwater Breathing Apparatus

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Self-Contained Underwater Breathing Apparatus

Acronym: SCUBA

Generic Description:

The self-contained underwater breathing apparatus or scuba diving system is the result of technological developments and innovations that began almost 300 years ago. Scuba diving is the most extensively used system for breathing underwater by recreational divers throughout the world and in various forms is also widely used to perform underwater work for military, scientific, and commercial purposes.

Reference: https://oceanexplorer.noaa.gov/technology/technical/technical.html

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Sample_Name	name of sample	unitless	sample
Preservation_Date	date of preservation of sample in format YYYY-MM-DD Format: %Y-%m-%d	unitless	date
Depth	depth of sample	meters (m)	depth
Location	location of sample site	unitless	site
Latitude	latitude of sample site	decimal degrees	lat
Longitude	longitude of sample site	decimal degrees	lon
Coral_Species	species of coral	unitless	species
Colony_health_status	status of coral colony health	unitless	status
Experimental_bin_ID	experimental bin ID	unitless	exp_id
SRA_Run	SRA Run ID	unitless	SRA_run
Bio_Project	Bio Project ID	unitless	BioProject

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Database

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Dataset: Viral Consortia in Stony Corals