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St. Petersburg Coastal and Marine Science Center

Data Release

Cold-water Coral Microbiomes (Astrangia poculata) from Narragansett Bay: Sequence Data

By Dawn B. Goldsmith and Christina A. Kellogg

Summary

The files in this data release are the DNA sequence files referenced in Goldsmith and others (2019), which represent a 16S rRNA gene amplicon survey of Astrangia poculata microbiomes completed using Sanger dideoxy sequencing. The coral samples were collected from Narragansett Bay (Fort Wetherill State Park, Jamestown, Rhode Island) in 2015 and 2016. Sequences were obtained by first extracting DNA from a fragment of each A. poculata sample comprising mucus, tissue, and skeleton. Bacterial DNA was amplified from all samples by polymerase chain reaction (PCR) using primers 8F (5′–AGA GTT TGA TCC TGG CTC AG) and 1492R (5′–GGT TAC CTT GTT ACG ACT T) to target the 16S rDNA gene in bacteria. Archaeal DNA from two of the samples (FW1B8 and FW1W8) was amplified using primers 21F (5′–TTC CGG TTG ATC CYG CCG GA) and 958R (5′–YCC GGC GTT GAM TCC AAT T) to target the 16S rDNA gene from archaea. All amplicons were visualized on an agarose gel, extracted from the gel, quantitated, cloned into a vector, and used to transform competent cells. Inserts in positive transformants were sequenced by the Clemson University Genomics Computational Laboratory (Clemson, South Carolina).

The sequences were processed by trimming vectors and ends, removing sequences less than 50 base pairs, checking for chimeras, classifying taxonomy, and removing unclassified, chloroplast, and mitochondrial sequences. After processing, 806 bacterial operational taxonomic units (OTUs) and 18 archaeal OTUs remained. Sequences representing each OTU have been deposited in the National Center for Biotechnology Information’s (NCBI) GenBank archive and have been assigned accession numbers MK175495 through MK176300 (bacterial sequences) and MH915525 through MH915542 (archaeal sequences). For more information, please see the README file.

Goldsmith, D.B., Pratte, Z.A., Kellogg, C.A., Snader, S.E., and Sharp, K.H., 2019, Stability of temperate coral Astrangia poculata microbiome is reflected across different sequencing methodologies: AIMS Microbiology, 5(1), p. 62–76, https://doi.org/10.3934/microbiol.2019.1.62.


Data

File Name and Description Metadata (XML format) Metadata (text format) Download File
Astrangia_archaeal_seqs_data.zip
Zip file containing archaeal sequences and MIMARKS metadata (FASTA, .csv, .txt, xlsx).
Astrangia_microbiomes_metadata.xml Astrangia_microbiomes_metadata.txt Astrangia_archaeal_seqs_data.zip
(40 KB)
Astrangia_bacterial_seqs_data.zip
Zip file containing bacterial sequences and MIMARKS metadata (FASTA, .csv, .txt, .xlsx).
Same as above Same as above Astrangia_bacterial_seqs_data.zip
(284 KB)
README_Astrangia.txt
Readme file explaining data
Same as above Same as above README_Astrangia.txt
(5 KB)

Location Map
Figure 1. Location of sampling.

Suggested Citation

Goldsmith, D.B., and Kellogg, C.A., 2019, Cold-water coral microbiomes (Astrangia poculata) from Narragansett Bay—sequence data: U.S. Geological Survey data release, https://doi.org/10.5066/P9C2XCQQ.



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