Universal Metabarcodes (16S & 18S) from AMT 29 Cruise (GRUMP-V2)
This metabarcoding dataset is derived from PCR amplification of marine plankton-derived DNA from the AMT 29 cruise in 2019. 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-2.0 (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:doi.org/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.-These data also use internal standards, meaning that the final dataset can be normalized to gene copies/L, these internal standards are notated in SILVA as species "Thermus_thermophilus", "Blautia_producta", and "Deinococcus_radiodurans". The script used to normalize the data can be found at (https://github.com/Nwilliams96/Project-3-515Y-926R-internal-standards)PCR amplification and sequencing:5' master mix was used for DNA amplification with the 515Y (59-GTGYCAGCMGCCGCGGTAA) and 926R (59-CCGYCAATTYMTTTRAGTTT) primers with Illumina adapters and barcodes pre-ligated (as noted here: dx.doi.org/10.17504/protocols.io.vb7e2rn). Sequencing was done at the University of Minnesota using Element Aviti technology (2x300 bp).