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Dataset Open Access

Total V9 rDNA information organized at the OTU level for the Tara Oceans Expedition (2009-2013), including the Tara Polar Circle Expedition (2013).

Henry, Nicolas; de Vargas, Colomban; Audic, Stéphane; Tara Oceans Consortium, Coordinators; Tara Oceans Expedition, Participants

The present data set provides a tab separated text file compressed in a gzip archive. The file includes metadata for each TaraOceans V9 rDNA OTU including the following fields: md5sum = identifier of the representative (most abundant) sequence of the swarm; cid = identifier of the OTU; ctotab = total abundance of barcodes in this OTU; abundance = total abundance of the representative barcode; sequence = nucleic acid sequence of the representative barcode; pid = percentage identity of the representative barcode to the closest reference sequence from V9_PR2; lineage = taxonomic path assigned to the representative barcode; refs = best hit reference sequence(s) with respect to the representative barcode; taxogroup = high-taxonomic level assignation of the representative barcode; TARA_xxx = number of occurrences of barcodes in this OTU in each of the 1046 samples. The file also includes six categories of functional annotations: (1) chloroplast: yes, presence of permanent chloroplast; no, absence of permanent chloroplast; NA, undetermined. (2) symbiont (small partner): parasite, the species is a parasite; commensal, the species is a commensal; mutualist, the species is a mutualist symbiont, most often a microalgal taxon involved in photosymbiosis; no the species is not involved in a symbiosis as small partner; NA, undetermined. (3) 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. (4) silicification; yes, the species has a silicified skeleton; no, it does not; NA, undetermined. (5) calcification; yes, the species has a calcified skeleton; no, it does not; NA, undetermined. (6) strontification; yes, the species has a skeleton made of strontium; no, it does not; NA, undetermined.

This table has been generated with the same pipeline as for the OTU table in 10.1126/science.1261605 with the following modifications:

  • a more recent version of swarm has been used (v 2.1.1 with fastidious option)
  • vsearch v2.3.1 replace ggsearch36 for the taxonomic assignation with equivalent options
  • An updated version of the reference database has been used (see 10.5281/zenodo.3768951)
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