Dataset: Symbiodiniaceae communities (via ITS-2 rDNA amplicon sequencing) in reef-associated fish feces, corals, water and sediments

Name: Symbiodiniaceae communities (via ITS-2 rDNA amplicon sequencing) in reef-associated fish feces, corals, water and sediments
Published: 2021-03-09
Keywords: oceans

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Cite This Dataset

Temporal Extent: 2019-01-01

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)

Contact:

Carsten Grupstra (Rice University)

BCO-DMO Data Manager:

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

Version:

Version Date:

2021-03-09

Restricted:

Validated:

Current State:

Preliminary and in progress

Symbiodiniaceae communities (via ITS-2 rDNA amplicon sequencing) in reef-associated fish feces, corals, water and sediments

Abstract:

SRA accessions and collection information for ITS-2 rDNA amplicon data from fish feces, corals, water and sediments sampled from Mo’orea, French Polynesia in August 2019. Sequences will be made available at the National Center for Biotechnology Information (NCBI).

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Methods & Sampling

Methodology summary:

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

Sampling and analytical procedures:

Samples were preserved in DNA/RNA shield (Zymo Research, CA) and stored at -20℃ until further processing. DNA was extracted using the ZymoBIOMICs DNA/RNA Miniprep kit (Zymo Research, CA) from 20-200 mg of feces, small coral tissue sections (~5 mm2), 250 ml sediments and ~1890 ml water using a ZymoBIOMICs DNA/RNA Miniprep kit (Zymo Research, CA).

Sample subject list with aphiaIDs for taxonomic names:

Acropora, 205469
Amanses scopas, 212242
Chaetodon citrinellus, 218744
Chaetodon lunulatus, 398549
Chaetodon ornatissimus, 273352
Chaetodon pelewensis, 273353
Chaetodon reticulatus, 273359
Chlorurus spilurus, 712772
Ctenochaetus flavicauda, 277560
Ctenochaetus striatus, 219659
Pocillopora, 206938
Porites, 206485
Sediment
Water

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Data Processing Description

The sequencing data were processed using Symportal (Hume et al., 2019). Samples with <1,000 reads were discarded and sequencing depth was assessed using rarefaction curves. ITS2-profiles were reduced to number of reads per Symbiodiniaceae genus and expressed as percentages. All data were analysed using R version 3.6.1 (R Core Team, 2019).

BCO-DMO data manager processing notes:
* Data submitted in Excel file "Correa Grupstra 121620 metadata.xlsx" extracted to csv.
* Taxonomic names verified using the World Register or Marine Species taxa match tool. All names matched exactly to accepted taxonomic names (as of 2021-03-09).

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1635913
NSF Division of Ocean Sciences	OCE-1635798

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: Illumina MiSeq platform

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.

Parameters

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Database

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Dataset: Symbiodiniaceae communities (via ITS-2 rDNA amplicon sequencing) in reef-associated fish feces, corals, water and sediments