Abstract:

Specimen collection information and genetics data (tufA database, annotated OTUs for Phototrophs, GenBank accession numbers, and raw Illumina sequences) supporting the publication Sauvage, T., Schmidt, W. E., Suda, S., and Fredericq, S. (2016). A metabarcoding framework for facilitated survey of coral reef and rhodolith endolithic communities with tufA. BMC Ecology, 16(1).

Suggested Citation:

Fredericq, Suzanne. 2017. Dataset for: A metabarcoding framework for facilitated survey of coral reef and rhodolith endolithic communities with tufA. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N71Z42G0

Publications:

Sauvage, T., Schmidt, W. E., Suda, S., & Fredericq, S. (2016). A metabarcoding framework for facilitated survey of endolithic phototrophs with tufA. BMC Ecology, 16(1). doi:10.1186/s12898-016-0068-x

Purpose:

The development of a metabarcoding framework for the elongation factor EF-Ttu (tufA) and testing on four Illumina-sequenced marine CaCO3 microfloras for the characterization of their endolithic phototrophs, especially the abundant bioeroding Ostreobium spp. (Ulvophyceae). The framework consists of novel tufA degenerate primers and a comprehensive database enabling Operational Taxonomic Unit (OTU) identification at multiple taxonomic ranks.

Data Parameters and Units:

File: R1.x139.000-0002_Barcoded Ulvophyceae_sub1.txt: Collection information for Ulvophyceae specimens newly sequenced for tufA: GenBank (GenBank Accession number); Genbank Identifier (taxa identifiers); Collection #; taxonomic classifications (Order, Suborder, Family); Cult. (cultured); Geographical origin; Year; Coll (Collector initials, DP = D. Pence, HS = H. Spalding, JR = J. Richards, KI = K. Ikemoto, MDR = M. Diaz-Ruiz, MS = M. Star, NP = N. Pyron, TS = T. Sauvage, WES = W.E. Schmidt, ZM = Z. McCorkhill ); GPS Coordinates; Habitat (CaCO 3 =open reef substratum, Corall. =Florideophycean crusts of the order Corallinales, Peyss. =Florideophycean crusts of the order Peyssonneliales, LPS =large polyp coral species (e.g. Galaxea sp., Favia sp., Shell Oyster shell (primarily) or other bivalve, SP S =small polyp coral species (e.g. Porites sp., Montipora sp., na epilithic, epiphytic, or not recorded). File: R1.x139.000-0002_Barcoded Florideo-Phaeophyceae_sub1.txt: Collection information for specimens of the Florideophyceae and Phaeophyceae sequenced for tufA in the present study (as well as a miscellaneous Prasinophyceae): GenBank (GenBank Accession number); Genbank Identifier (taxa identifiers); Collection #; taxonomic classifications (Class, Order, Family); Geographical origin; Year; Coll (Collector initials, CP = C. Pueschel, CS = C. Stoude, DG = D. Gabriel, DK = D. Krayesky, DWF = D.W. Freshwater, EC = E. Coppejans, ED = E. Deslandes, JC = J. Cabioch, JH = J. Hughey, JR = J. Richards, JRu = J. Rueness, JZ = J. Zertuche, MG = M. Guiry, MHH = M. H. Hommersand, MJW = M. J. Wynne, MY = M. Yoshizaki, OC = O. Camacho, SF = S. Fredericq.); GPS Coordinates. File: R1.x139.000-0002_OTUs_phototrophs_sub1.txt: Parameter Descriptions: OTU number, Domain, Phylum, Class, Order, Family and Genus. File: R1.x139.000-0002_tufA database_sub1.txt: Genbank Accession, Category (Phototroph, Heterotroph), Domain, Phylum, Class, Order, Family and Genus. File: R1.x139.000-0002_SraRunTable_sub1.txt: Run identifier, Biosample identifier, Sample Name, Library Name, MBases, Mbytes, Experiment, Collection Date, geo loc name, Isolation source, latitude, longitude. File: R1.x139.000-0002_GenBank KU362151-KU362236.txt: Parameter Descriptions: Accession number and gene sequences for various species of Coral Reef Endoliths; elongation factor tu gene, partial cds chloroplast

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