Dataset: Acropora cervicornis white band exposure experiment survival outcomes

Name: 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
Published: 2024-03-12
Keywords: white band disease, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.922006.1

Spatial Extent: N:24.73 E:-81.04 S:9.35 W:-82.26

Florida samples collected from the Coral Restoration Foundation Nursery in the Florida Keys (24.73 N, 81.04 W). Panama samples collected from near the Smithsonian Tropical Research Institute Station in Bocas del Toro, Panama (9.35 N, 82.26 W).

Temporal Extent: 2021-06-19 - 2021-11-12

Project:

Multi-omic bases of coral disease resistance (coral disease resistance)

Principal Investigator:

Steven V. Vollmer (Northeastern University)

Scientist:

Charles L. Roesel (Northeastern University)

Jason D. Selwyn (Texas A&M, Corpus Christi, TAMU-CC)

Student:

Brecia Douglas (Northeastern University)

Contact:

Steven V. Vollmer (Northeastern University)

Technician:

Charles L. Roesel (Northeastern University)

Data Manager:

Jason D. Selwyn (Texas A&M, Corpus Christi, TAMU-CC)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2024-03-12

Restricted:

Validated:

Yes

Current State:

Final no updates expected

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

Abstract:

Genomic data was collected from 96 Acropora cervicornis samples, 48 of which were collected from the Coral restoration foundation nursery in Florida in June 2021 and the other 48 were collected from Bocas del Toro Panama in November 2021. All samples were sequenced using illumina short read sequencing to create whole genome sequencing profiles of the DNA with one of the Florida samples, the K2 genotype, being sequenced using additional Nanopore long reads to assemble and annotate an A. cervicornis genome. All genotypes were used in a disease exposure assay to assess individual genotype disease resistance with a further, 16 colonies from Florida being sequenced at two timepoints across disease exposed and healthy colonies (total 48 sequences) using RNAseq to identify patterns in differential gene expression based on disease resistance. This dataset includes sample metadata, treatment information, and disease state for corals in the exposure experiment. Sample metadata and accession identifiers for sequences at The National Center for Biotechnology Information (NCBI) are included as a supplemental file.

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2024-03-12	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.922006.1	2024-03-21

Description

Related NCBI BioProjects containing genomic/transcriptomic data from this study (see Supplemental Files for accession metadata):

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)

Whole genome sequencing of DNA from 96 A. cervicornis colonies: NCBI BioProject PRJNA950067 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA950067)

Short and long read data and Genome Assembly for the Coral Restoration Foundation K2 genotype of A. cervicornis: NCBI BioProject PRJNA948411 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA948411)

Methods & Sampling

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.

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.

Organism identifier (LSID):
Acropora cervicornis (urn:lsid:marinespecies.org:taxname:206989)

Problems/Issues

Samples from the experimental tanks H1 in Panama, and H2 and H3 in Florida were removed due to complete colony collapse independent of experimental treatment.

BCO-DMO Processing

* Submitted file "exposure_experiment.csv" 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]

Data Files

File
922006_v1_whiteband-exposure-survival.csv (Comma Separated Values (.csv), 39.92 KB) MD5:db4a7e5b4fb7a2574db5110193b53fc9 Primary data file for dataset ID 922006, version 1. This table includes the disease state for corals in the exposure experiment. See related Supplemental File (sample_metadata.csv) which contains additional metadata and sequence accessions at NCBI.

Supplemental Files

File

Metadata & accession numbers for sequences at NCBI
filename: sample_metadata.csv

(Comma Separated Values (.csv), 8.16 KB)
MD5:d67ab4b1a670bb25aee4f9363725d6d2

Metadata & accession numbers for sequences at The National Center for Biotechnology Information (NCBI) under BioProject PRJNA950067.

Columns in this data table are:

ID, Fully descriptive colony ID
genotype, Putative Genotype
location, Region of origin (Florida or Panama)
reef, Reef of origin (of initial genotype in Florida)
lat,  Latitude,  decimal degrees
lon, Longitude,  decimal degrees
longread_accession, NCBI Accession number for long reads used in genome assembly
WGS_accession, NCBI Accession number for short reads used in whole genome sequencing
T[37]_[HD]_RNA_accession, NCBI Accession number for RNAseq reads from Time point 3 or 7 (T3/T7) in either health (H) or disease (D) exposed treatments.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1924145

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: Minion flow cells (FLO-MIN112)

Supplied Description:

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic 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.

Automated DNA Sequencer

Supplied Name: Illumina HiSeq 2500

Supplied Description:

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

Automated DNA Sequencer

Supplied Name: Illumina NEXTSEQ 550

Supplied Description:

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

Automated DNA Sequencer

Supplied Name: NovaSeq S4

Supplied Description:

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

DNA Extractor

Supplied Name:

Supplied Description:

Zymo Quick-DNA 96 kit
Oxford Nanopore Technologies (ONT) kit SQK-LSK112
DNA Prep kit
KAPA PCR-free library kits

Instrument Type

Generic Name: DNA Extractor

Generic Description:

A device that is used to isolate and collect DNA for subsequent molecular analysis.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Tank	Experimental tank (H1-5 or D1-5)	untiless	tank
Treatment	Experimental exposure (H - healthy exposure, D - disease exposure)	untiless	treatment
Location	Region of origin (Florida or Panama)	untiless	sample_descrip
Genotype	Putative Genotype	untiless	sample_descrip
Day_1_AM	Disease state (healthy = 0, diseased = 1) of the coral colony in the exposure experiment on Day 1 in the AM (Eastern Time Zone).	untiless	flag
Day_1_PM	Disease state (healthy = 0, diseased = 1) of the coral colony in the exposure experiment on Day 1 in the PM (Eastern Time Zone).	untiless	flag
Day_2_AM	Disease state (healthy = 0, diseased = 1) of the coral colony in the exposure experiment on Day 2 in the AM (Eastern Time Zone).	untiless	flag
Day_2_PM	Disease state (healthy = 0, diseased = 1) of the coral colony in the exposure experiment on Day 2 in the PM (Eastern Time Zone).	untiless	flag
Day_3_AM	Disease state (healthy = 0, diseased = 1) of the coral colony in the exposure experiment on Day 3 in the AM (Eastern Time Zone).	untiless	flag
Day_3_PM	Disease state (healthy = 0, diseased = 1) of the coral colony in the exposure experiment on Day 3 in the PM (Eastern Time Zone).	untiless	flag
Day_4_AM	Disease state (healthy = 0, diseased = 1) of the coral colony in the exposure experiment on Day 4 in the AM (Eastern Time Zone).	untiless	flag
Day_4_PM	Disease state (healthy = 0, diseased = 1) of the coral colony in the exposure experiment on Day 4 in the PM (Eastern Time Zone).	untiless	flag
Day_5_AM	Disease state (healthy = 0, diseased = 1) of the coral colony in the exposure experiment on Day 5 in the AM (Eastern Time Zone).	untiless	flag
Day_5_PM	Disease state (healthy = 0, diseased = 1) of the coral colony in the exposure experiment on Day 5 in the PM (Eastern Time Zone).	untiless	flag
Day_6_AM	Disease state (healthy = 0, diseased = 1) of the coral colony in the exposure experiment on Day 6 in the AM (Eastern Time Zone).	untiless	flag
Day_6_PM	Disease state (healthy = 0, diseased = 1) of the coral colony in the exposure experiment on Day 6 in the PM (Eastern Time Zone).	untiless	flag
Day_7_AM	Disease state (healthy = 0, diseased = 1) of the coral colony in the exposure experiment on Day 7 in the AM (Eastern Time Zone).	untiless	flag

Database

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Dataset: Acropora cervicornis white band exposure experiment survival outcomes