Universal Metabarcodes (16S & 18S) from the P16N Cruise (GO-SHIP)

This metabarcoding dataset is derived from PCR amplification of marine plankton-derived DNA from the P16N GO-SHIP cruise, from samples provided by the Carlson Lab, UCSB. 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 (2L P16N) collected at various depths onto 0.2 um 25mm Supor filter filters during a latitudinal transects of the Pacific Ocean P16N in 2006. Samples were collected at sea by Elisa Halewood and Meredith Meyers (Carlson Lab, UCSB) as part of the GO-SHIP repeat hydrography program (then known as CLIVAR). Samples were stored as partially extracted lysates in sucrose lysis buffer at -80C until analysis. DNA was isolated, purified, 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).