Stéphane Audic
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View article: PR2_V9, a SSU V9 rDNA reference database with functional annotations.
PR2_V9, a SSU V9 rDNA reference database with functional annotations. Open
The present data set provides a tab separated text file compressed in a gzip archive. The file includes 63,401 18S V9 rDNA reference sequences for 44,084 unique eukaryotic taxa and 9,759 16S V9 rDNA references sequences for 9,661 unique pr…
View article: PR2_V9, a SSU V9 rDNA reference database with functional annotations.
PR2_V9, a SSU V9 rDNA reference database with functional annotations. Open
The present data set provides a tab separated text file compressed in a gzip archive. The file includes 63,401 18S V9 rDNA reference sequences for 44,084 unique eukaryotic taxa and 9,759 16S V9 rDNA references sequences for 9,661 unique pr…
View article: Total V9 rDNA information organized at the OTU level for the Tara Oceans Expedition (2009-2013), including the Tara Polar Circle Expedition (2013).
Total V9 rDNA information organized at the OTU level for the Tara Oceans Expedition (2009-2013), including the Tara Polar Circle Expedition (2013). Open
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) sequ…
View article: PHYTOPK28-D1D2: A curated database of 28S rRNA gene D1-D2 domains from eukaryotic organisms dedicated to metabarcoding analyses of marine phytoplankton samples
PHYTOPK28-D1D2: A curated database of 28S rRNA gene D1-D2 domains from eukaryotic organisms dedicated to metabarcoding analyses of marine phytoplankton samples Open
The PHYTOPK28-D1D2 database comprises accession numbers, taxonomic classification and 28S rDNA (D1-D2 domains) sequences that are available in public DNA databases. The sequences, listed in FASTA format, are identified by the accession num…
View article: <i>UniEuk</i>: Time to Speak a Common Language in Protistology!
<i>UniEuk</i>: Time to Speak a Common Language in Protistology! Open
Universal taxonomic frameworks have been critical tools to structure the fields of botany, zoology, mycology, and bacteriology as well as their large research communities. Animals, plants, and fungi have relatively solid, stable morpho‐tax…
View article: Biogeography and diversity of Collodaria (Radiolaria) in the global ocean
Biogeography and diversity of Collodaria (Radiolaria) in the global ocean Open
Collodaria are heterotrophic marine protists that exist either as large colonies composed of hundreds of cells or as large solitary cells. All described species so far harbour intracellular microalgae as photosymbionts. Although recent env…
View article: Benthic protists: the under-charted majority
Benthic protists: the under-charted majority Open
Marine protist diversity inventories have largely focused on planktonic environments, while benthic protists have received relatively little attention. We therefore hypothesize that current diversity surveys have only skimmed the surface o…
View article: Diversity and oceanic distribution of the Parmales (Bolidophyceae), a picoplanktonic group closely related to diatoms
Diversity and oceanic distribution of the Parmales (Bolidophyceae), a picoplanktonic group closely related to diatoms Open
Bolidomonas is a genus of picoplanktonic flagellated algae that is closely related to diatoms. Triparma laevis, a species belonging to the Parmales, which are small cells with a siliceous covering, has been shown to form a monophyletic gro…
View article: Insights into global diatom distribution and diversity in the world’s ocean
Insights into global diatom distribution and diversity in the world’s ocean Open
Significance Diatoms, considered one of the most diverse and ecologically important phytoplanktonic groups, contribute around 20% of global primary productivity. They are particularly abundant in nutrient-rich coastal ecosystems and at hig…
View article: The symbiotic life of<i>Symbiodinium</i>in the open ocean within a new species of calcifying ciliate (<i>Tiarina</i>sp.)
The symbiotic life of<i>Symbiodinium</i>in the open ocean within a new species of calcifying ciliate (<i>Tiarina</i>sp.) Open
Symbiotic partnerships between heterotrophic hosts and intracellular microalgae are common in tropical and subtropical oligotrophic waters of benthic and pelagic marine habitats. The iconic example is the photosynthetic dinoflagellate genu…
View article: Deep sequencing of amplified <scp> <i>P</i> </scp> <i>rasinovirus</i> and host green algal genes from an <scp>I</scp> ndian <scp>O</scp> cean transect reveals interacting trophic dependencies and new genotypes
Deep sequencing of amplified <span> <i>P</i> </span> <i>rasinovirus</i> and host green algal genes from an <span>I</span> ndian <span>O</span> cean transect reveals interacting trophic dependencies and new genotypes Open
Summary High‐throughput sequencing of P rasinovirus DNA polymerase and host green algal ( M amiellophyceae) ribosomal RNA genes was used to analyse the diversity and distribution of these taxa over a ∼10 000 km latitudinal section of the I…
View article: Global distribution and vertical patterns of a prymnesiophyte–cyanobacteria obligate symbiosis
Global distribution and vertical patterns of a prymnesiophyte–cyanobacteria obligate symbiosis Open
A marine symbiosis has been recently discovered between prymnesiophyte species and the unicellular diazotrophic cyanobacterium UCYN-A. At least two different UCYN-A phylotypes exist, the clade UCYN-A1 in symbiosis with an uncultured small …
View article: Marine protist diversity in <scp>E</scp> uropean coastal waters and sediments as revealed by high‐throughput sequencing
Marine protist diversity in <span>E</span> uropean coastal waters and sediments as revealed by high‐throughput sequencing Open
Summary Although protists are critical components of marine ecosystems, they are still poorly characterized. Here we analysed the taxonomic diversity of planktonic and benthic protist communities collected in six distant E uropean coastal …
View article: Determinants of community structure in the global plankton interactome
Determinants of community structure in the global plankton interactome Open
Species interaction networks are shaped by abiotic and biotic factors. Here, as part of the Tara Oceans project, we studied the photic zone interactome using environmental factors and organismal abundance profiles and found that environmen…
View article: Eukaryotic plankton diversity in the sunlit ocean
Eukaryotic plankton diversity in the sunlit ocean Open
Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity fr…
View article: First Tara Oceans V9 Rdna Metabarcoding Dataset.
First Tara Oceans V9 Rdna Metabarcoding Dataset. Open
Accompanying material, text, data and figures for the article de Vargas et al., 'Eukaryotic plankton diversity in the sunlit ocean', Science 348, 1261605 (2015), doi: 10.1126/science.1261605
View article: Environmental characteristics of Agulhas rings affect interocean plankton transport
Environmental characteristics of Agulhas rings affect interocean plankton transport Open
Agulhas rings provide the principal route for ocean waters to circulate from the Indo-Pacific to the Atlantic basin. Their influence on global ocean circulation is well known, but their role in plankton transport is largely unexplored. We …
View article: PFR<sup>2</sup>: a curated database of planktonic foraminifera 18S ribosomal <scp>DNA</scp> as a resource for studies of plankton ecology, biogeography and evolution
PFR<sup>2</sup>: a curated database of planktonic foraminifera 18S ribosomal <span>DNA</span> as a resource for studies of plankton ecology, biogeography and evolution Open
Planktonic foraminifera (Rhizaria) are ubiquitous marine pelagic protists producing calcareous shells with conspicuous morphology. They play an important role in the marine carbon cycle, and their exceptional fossil record serves as the ba…
View article: Phyto<scp>REF</scp>: a reference database of the plastidial 16S <scp>rRNA</scp> gene of photosynthetic eukaryotes with curated taxonomy
Phyto<span>REF</span>: a reference database of the plastidial 16S <span>rRNA</span> gene of photosynthetic eukaryotes with curated taxonomy Open
Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organism…
View article: MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution
MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution Open
Microbial rhodopsins are a diverse group of photoactive transmembrane proteins found in all three domains of life and in viruses. Today, microbial rhodopsin research is a flourishing research field in which new understandings of rhodopsin …
View article: Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms (file : readme_Forster_et_al_BMC)
Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms (file : readme_Forster_et_al_BMC) Open
file : readme_Forster_et_al_BMC Background: High-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but in silico analyses of the resulting millions of …
View article: details_V4ciliates_Biomarks.tab
details_V4ciliates_Biomarks.tab Open
Background: High-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but in silico analyses of the resulting millions of short amplicons remain a major b…
View article: V4dataset.fna
V4dataset.fna Open
Background: High-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but in silico analyses of the resulting millions of short amplicons remain a major b…
View article: Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms (file : network_output.tab.zip)
Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms (file : network_output.tab.zip) Open
file : network_output.tab.zip Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms (file : readme_Forster_et_al_BMC) http://dx.doi.org/10.60…