Dataset: A custom ARB database of SSU rRNA gene sequences from corals, as well representative cultivated and environmental sequences from public sources (Coral Microbial Relationships project)

ValidatedFinal no updates expectedVersion 2 (2021-06-10)Dataset Type:experimental

Principal Investigator, Contact: Amy Apprill (Woods Hole Oceanographic Institution)

Scientist: Megan Huggett (University of Newcastle)

BCO-DMO Data Manager: Amber D. York (Woods Hole Oceanographic Institution)

Project: Fundamental Coral-Microbial Associations (Coral Microbial Relationships)

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A custom ARB database of SSU rRNA gene sequences from corals, as well representative cultivated and environmental sequences from public sources. These data are described in Huggett and Apprill (in press).

Metadata for the database is available in the primary dataset file coral_microb_suppl.csv.  The database is also available for download as an ARB file ​coralmicrobiome_database.arb.

ARB software (version arb-6.06) is available from http://www.arb-home.de/downloads.html

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Related Publications

Methods
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403–410. doi:10.1016/s0022-2836(05)80360-2
Methods
Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., & Wheeler, D. L. (2007). GenBank. Nucleic Acids Research, 36(Database), D25–D30. doi:10.1093/nar/gkm929
Methods
Huggett, M. J., & Apprill, A. (2018). Coral microbiome database: Integration of sequences reveals high diversity and relatedness of coral‐associated microbes. Environmental Microbiology Reports, 11(3), 372–385. doi:10.1111/1758-2229.12686
Methods
Ludwig, W. (2004). ARB: a software environment for sequence data. Nucleic Acids Research, 32(4), 1363–1371. doi:10.1093/nar/gkh293
Methods
Pruesse, E., Quast, C., Knittel, K., Fuchs, B. M., Ludwig, W., Peplies, J., & Glockner, F. O. (2007). SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Research, 35(21), 7188–7196. doi:10.1093/nar/gkm864

Apprill, A., Huggett, M. (2021). A custom ARB database of SSU rRNA gene sequences from corals, as well representative cultivated and environmental sequences from public sources (Coral Microbial Relationships project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2) Version Date 2021-06-10 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/724355 [access date]

Terms of Use

This dataset is licensed under Creative Commons Attribution 4.0.


If you wish to use this dataset, it is highly recommended that you contact the original principal investigators (PI). Should the relevant PI be unavailable, please contact BCO-DMO (info@bco-dmo.org) for additional guidance. For general guidance please see the BCO-DMO Terms of Use document.

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Funded by the U.S. National Science Foundation