Universal Metabarcodes (16S & 18S) from the GP13 Cruise (BioGEOTRACES)

This metabarcoding dataset is derived from PCR amplification of marine plankton-derived DNA from the GP13 cruise, from DNA provided by Paul Berube / Stephen Biller (Biller et al., 2018). Metabarcoding reads were generated using a single primer set that simultaneously amplifies both 16S and 18S genes, though users should note that specific bioinformatic procedures are required to recover and analyze 18S sequences (see: https://github.com/jcmcnch/eASV-pipeline-for-515Y-926R).This dataset is part of a larger collaborative project called GRUMP (Global rRNA Universal Metabarcoding of Plankton) which has produced metabarcoding data from worldwide cruises from the same universal primer set (Parada et al., 2016, doi:10.1111/1462-2920.13023) on unfractionated samples (> 0.2 um). This primer set perfectly matches the rRNA of most surface ocean organisms, including eukaryotic and metazoan 18S (McNichol et al., 2021, doi:10.1128/msystems. 00565-21). As a result, the sequences here represent a full-community profile of each water sample with the same denominator and the same primer set (Yeh et al., 2021, doi:10.1111/1462-2920.15553).Notes for data users:- Only limited environmental covariate data has been uploaded with the raw sequences. More data will be made available at the locations specified below.- Final, processed data (16S + 18S relative abundances with taxonomic annotations) will be provided through the Simons Foundation CMAP (Collaborative Marine Atlas Project; https://simonscmap.com/) alongside environmental covariates. If you do not wish to reanalyze these data, we suggest using this data product.- Bioinformatic intermediates, and scripts are stored at OSF in a single umbrella repository (https://osf.io/57dpa/). This is a useful place for those who might wish to analyze only a subset of our data (e.g. 18S or 16S only) or who wish to understand the bioinformatic processing in greater detail.- Additional updates (e.g. linking additional environmental covariates to metabarcoding data) will be provided at our github page (https://github.com/jcmcnch/Global-rRNA-Univeral-Metabarcoding-of-Plankton). This is a good place to check for the latest updates to the GRUMP project.Specific notes for this dataset:This dataset contains relative abundance and taxonomic information for planktonic organisms collected by filtering whole seawater (100 mL) collected at depths ranging from the sea surface to 5601 m onto 0.2 um 25mm polycarbonate filters during GEOTRACES sections GA03 in 2010-2011. Samples were chased with 3 mL of sterile preservation solution (10 mM Tris, pH 8.0; 100 mM EDTA; 0.5 M NaCl) and stored in cryovials at -80 C until analysis. DNA was isolated and purified using a phenol/chloroform-based method by Steven Biller, Paul Berube, Keven Dooley, and Medline Williams (Chisholm lab, MIT) (Biller et al., 2018; doi:10.1038/sdata.2018.17610.1038/sdata.2018.176). This DNA was amplified and sequenced by Jesse McNichol, Yubin Raut, & Bruce Yanpui Chan (Fuhrman Lab, USC) in 2020 and 2021.PCR amplification and sequencing:5' master mix (product 2200400/2200410) was used for DNA amplification with the 515Y (5'-GTGYCAGCMGCCGCGGTAA) and 926R (5'-CCGYCAATTYMTTTRAGTTT) primers with Illumina adapters and barcodes pre-ligated (as noted here: dx.doi.org/10.17504/protocols.io.vb7e2rn). Sequencing was done at Tufts University Medical School using HiSeq Rapid Run technology (2x250 bp).