DOI: 10.5281/zenodo.6778239
title: Plankton Planet Pilot Project rDNA 18S V9 OTU tables

description: This repository contains the rDNA 18S V9 OTU table, its rarefied version, and the related contextual data from Plankton Planet Pilot Project. In the file <strong>P2_TO_18SV9_otu_table.tsv.gz</strong>, each OTU, one per row, is described by the following fields: <strong>amplicon</strong> = identifier of the representative (most abundant) sequence of the swarm; <strong>total</strong> = total number of reads in the entire dataset; <strong>cloud</strong> = number of unique sequences constituting the OTU; <strong>length</strong> = length of the representative sequence; <strong>spread</strong> = number of samples in which the OTU has been found; <strong>quality</strong> = minimum expected error observed for the representative sequence, divided by sequence length; <strong>sequence</strong> = nucleic acid sequence of the representative sequence; <strong>identity</strong> = percentage of identity of the representative sequence to the closest reference sequence from PR2_V9 (https://doi.org/10.5281/zenodo.3768951); <strong>references</strong> = best hit reference sequence(s); <strong>taxonomy</strong> = taxonomic path assigned to the representative sequence; <strong>taxogroup</strong> = high-taxonomic level assignation of the representative barcode; <strong>chloroplast</strong> = <em>yes</em>: presence of permanent chloroplast / <em>no</em>: absence of permanent chloroplast / <em>NA</em>: undetermined; <strong>symb_small</strong> = <em>parasite</em>: the species is a parasite / <em>commensal</em>: the species is a commensal / <em>mutualist</em>: the species is a mutualist symbiont, most often a microalgal taxa involved in photosymbiosis / <em>no</em>: the species is not involved in a symbiosis as small partner / <em>NA</em>: undetermined; <strong>symbiont_host</strong> = <em>photo</em>: the host species relies on a mutualistic microalgal photosymbiont to survive (obligatory photosymbiosis) / <em>photo_falc</em>: same as photo, but facultative relationship / <em>photo_klep</em>: the host species maintains chloroplasts from microalgal prey(s) to survive / <em>photo_klep_falc</em>: same as <em>photo_klep</em>, but facultative / <em>Nfix</em> = the host species must interact with a mutualistic symbiont providing N2 fixation to survive / <em>Nfix_falc</em> = same as Nfix, but facultative / <em>no</em>: the species is not involved in any mutualistic symbioses; <em>NA</em>: undetermined; <strong>silicification</strong> = <em>yes</em>: the species has a silicified skeleton / <em>no</em>: it does not / <em>NA</em>: undetermined; <strong>calcification</strong> = <em>yes</em>: the species has a calcified skeleton / <em>no</em>: it does not / <em>NA</em>: undetermined; <strong>strontification</strong> = <em>yes</em>: the species has a skeleton made of strontium / <em>no</em>: it does not / <em>NA</em>: undetermined; <strong>PPXXX</strong> = number of reads in each of the 214 Plankton Planet samples; <strong>TARA_XXXXXXXXXX</strong> = number of reads in each of the 386 <em>Tara</em> Oceans samples. The file <strong>P2_TO_18SV9_otu_table_raref_313539.tsv.gz</strong> contains the same fields but with number of reads (total and per sample) obtained after random subsampling (313,539 reads per sample). In the file <strong>P2_TO_18SV9_context.tsv.gz</strong>, each sample is described by the following fields: <strong>sample</strong> = identifier of the sample; <strong>lower_size_fraction</strong> = lower limit of the size fraction in µm; <strong>upper_size_fraction</strong> = lower limit of the size fraction in µm; <strong>event_date</strong> = date (year-month-day); <strong>event_latitude</strong> = geographic position (latitude in DD); <strong>event_longitude</strong> = geographic position (longitude in DD); <strong>depth</strong> = depth in meters; <strong>temperature</strong> = sea water temperature in °C