10.5281/zenodo.3768510
https://zenodo.org/records/3768510
oai:zenodo.org:3768510
Henry, Nicolas
Nicolas
Henry
0000-0002-7702-1382
Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680 Roscoff, France
de Vargas, Colomban
Colomban
de Vargas
Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680 Roscoff, France
Audic, Stéphane
Stéphane
Audic
Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680 Roscoff, France
Tara Oceans Consortium, Coordinators
Coordinators
Tara Oceans Consortium
Tara Oceans Expedition, Participants
Participants
Tara Oceans Expedition
Total V9 rDNA information organized at the OTU level for the Tara Oceans Expedition (2009-2013), including the Tara Polar Circle Expedition (2013).
Zenodo
2019
metabarcoding
plankton
eukaryotes
18S
Tara Oceans
2019-11-14
10.1016/j.cell.2019.10.008
10.5281/zenodo.3768509
https://zenodo.org/communities/unieuk
https://zenodo.org/communities/taraoceans
Creative Commons Attribution 4.0 International
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)