Plankton Planet Pilot Project rDNA 18S V9 OTU tables

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 P2_TO_18SV9_otu_table.tsv.gz, each OTU, one per row, is described by the following fields: amplicon = identifier of the representative (most abundant) sequence of the swarm; total = total number of reads in the entire dataset; cloud =  number of unique sequences constituting the OTU; length = length of the representative sequence; spread = number of samples in which the OTU has been found; quality = minimum expected error observed for the representative sequence, divided by sequence length; sequence = nucleic acid sequence of the representative sequence; identity = percentage of identity of the representative sequence to the closest reference sequence from PR2_V9 (https://doi.org/10.5281/zenodo.3768951); references = best hit reference sequence(s); taxonomy = taxonomic path assigned to the representative sequence; taxogroup = high-taxonomic level assignation of the representative barcode; chloroplast = yes: presence of permanent chloroplast / no: absence of permanent chloroplast / NA: undetermined; symb_small = parasite: the species is a parasite / commensal: the species is a commensal / mutualist: the species is a mutualist symbiont, most often a microalgal taxa involved in photosymbiosis / no: the species is not involved in a symbiosis as small partner / NA: undetermined; symbiont_host = photo: the host species relies on a mutualistic microalgal photosymbiont to survive (obligatory photosymbiosis) / photo_falc: same as photo, but facultative relationship / photo_klep: the host species maintains chloroplasts from microalgal prey(s) to survive / photo_klep_falc: same as photo_klep, but facultative / Nfix = the host species must interact with a mutualistic symbiont providing N2 fixation to survive / Nfix_falc = same as Nfix, but facultative / no: the species is not involved in any mutualistic symbioses; NA: undetermined; silicification = yes: the species has a silicified skeleton / no: it does not / NA: undetermined; calcification = yes: the species has a calcified skeleton / no: it does not / NA: undetermined; strontification = yes: the species has a skeleton made of strontium / no: it does not / NA: undetermined; PPXXX = number of reads in each of the 214 Plankton Planet samples; TARA_XXXXXXXXXX = number of reads in each of the 386 Tara Oceans samples.

The file P2_TO_18SV9_otu_table_raref_313539.tsv.gz 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 P2_TO_18SV9_context.tsv.gz, each sample is described by the following fields: sample = identifier of the sample; lower_size_fraction = lower limit of the size fraction in µm; upper_size_fraction = lower limit of the size fraction in µm; event_date = date (year-month-day); event_latitude = geographic position (latitude in DD); event_longitude = geographic position (longitude in DD); depth = depth in meters; temperature = sea water temperature in °C