Dataset: Symbiodiniaceae communities in corals with ITS-2 rDNA amplicon sequencing

Name: An investigation of Symbiodiniaceae communities via ITS-2 rDNA amplicon sequencing in Acropora millepora corals from the Great Barrier Reef following exposure to stressors in October 2014
Published: 2021-03-31
Keywords: Acropora millepora, alpha diversity, beta diversity, climate change, Coral, Symbiodiniaceae, biota, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.844431.1

Spatial Extent: N:-18.4815 E:147.38 S:-18.8125 W:146.4331

Temporal Extent: 2014-10-01 - 2014-10-08

Project:

Collaborative Research: Viral Reefscapes: The Role of Viruses in Coral Reef Health, Disease, and Biogeochemical Cycling (Moorea Virus Project)

Principal Investigator:

Adrienne M.S. Correa (Rice University)

Student:

Lauren I. Howe-Kerr (Rice University)

BCO-DMO Data Manager:

Dana Stuart Gerlach (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

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

Version:

Version Date:

2021-03-31

Restricted:

Validated:

Yes

Current State:

Final no updates expected

An investigation of Symbiodiniaceae communities via ITS-2 rDNA amplicon sequencing in Acropora millepora corals from the Great Barrier Reef following exposure to stressors in October 2014

Abstract:

Symbiodiniaceae communities were investigated at three locations on the Great Barrier Reef in October 2014. Acropora millepora samples from Davies Reef lagoon (18°30′3.96′′S, 147°22′48′′E), Rib Reef (18°28′53.4′′S, 146°52′24.96′′E), and Pandora Island (18°48′45′′S, 146°25′59.16′′E), were exposed to various stressors including pCO2, heat, bacteria, all of these, or none of these (control). This dataset lists accessions and collection information for ITS-2 rDNA amplicon data that are available at the National Center for Biotechnology Information (NCBI) under BioProject PRJNA596498.

Expand/Collapse All

Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2021-03-31	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.844431.1	2022-02-09

Methods & Sampling

Symbiodiniaceae communities from Acropora millepora corals were investigated at three locations on the Great Barrier Reef between October 1st and 8th, 2014. Samples from Davies Reef lagoon, Rib Reef, and Pandora Island were collected and snap frozen in liquid nitrogen and stored at -20℃ until further processing. DNA was extracted using Wayne's Method (Wilson et al., 2002; Lundgren et al., 2013) from tissue slurry prepared following the method of Wright et al. (2019).

This dataset lists accessions and collection information for ITS-2 rDNA amplicon data from Acropora millepora corals following exposure to various stressors. Stressors included pCO2, heat, bacteria, all of these, or none of these (control). ITS-2 rDNA Symbiodiniaceae community libraries were prepared and PE 300bp reads were generated using Illumina MiSeq platform. BioSamples and SRA accessions are available at the National Center for Biotechnology Information (NCBI) under BioProject PRJNA596498 (https://www.ncbi.nlm.nih.gov/search/all/?term=PRJNA596498)

Data Processing Description

Demultiplexed fastq files were generated with Illumina's BaseSpaceFS (version 1.5.964) and reads were processed in RStudio (version 1.1.456) through the DADA2 pipeline (version 1.11.0; Callahan et al., 2016) with modifications for the Symbiodiniaceae ITS-2 region. The DADA2 pipeline generated a table of amplicon sequence variants (ASVs). Samples with fewer than 10,000 reads (n = 2) were removed from the dataset.

To identify biologically relevant entities from Symbiodiniaceae ITS-2 sequence data, we applied a post-DADA2 clustering curation using the LULU pipeline (Frøslev et al., 2017). LULU uses co-occurrence patterns and sequence similarity to collapse ITS-2 sequences that likely represent intragenomic variants; we applied thresholds of 95% and 84%, respectively, in this study. Symbiodiniaceae ITS-2 types were then assigned based on BLAST results to a local Symbiodiniaceae ITS-2 database (Cunning et al., 2017).

BCO-DMO processing description:
- Converted latitude and longitude values from DMS to decimal degrees
- Created columns for DD latitude and longitudes for the three sites
- Separated Collection Location into Region and Site
- Added columns for Year and Month of sampling
- Adjusted field/parameter names to comply with database requirements
- Added a conventional header with dataset name, PI names, version date

Data Files

File
coral_accessions.csv (Comma Separated Values (.csv), 12.71 KB) MD5:ed7a4a7017903946aee34741f6961907 Primary data file for dataset ID 844431

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1635798

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: Illumina MiSeq platform

Supplied Description:

ITS-2 rDNA Symbiodiniaceae community libraries were prepared and PE 300bp reads were generated using Illumina MiSeq platform

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.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Year	Year of collection	unitless	year
Month	Month of collection	unitless	month
Region	Geographical area of sampling	unitless	region
Site	Site of sampling	unitless	site
Latitude	Latitude of sampling	decimal degrees	lat
Longitude	Longitude of sampling	decimal degrees	lon
Sample_Name	Sample name	unitless	sample
Genotype_ID	Genotype identifier	unitless	sample
Treatment	Stressor exposure treatment	unitless	treatment
Host_Species	Host species	unitless	species
SRA_Run	NCBI Sequence Read Archive Run identifier	unitless	accession_number
BioSample_Accession	NCBI BioSample Accession identifier	unitless	accession_number

Status message

Database

Contribute Data

Dataset: Symbiodiniaceae communities in corals with ITS-2 rDNA amplicon sequencing