Global ocean’s protist metabarcoding Colomban de Vargas, Stéphane Audic, Nicolas Henry, Johan Decelle, Frédéric Mahé, Cédric Berney, Sébastien Colin, Sarah Romac, Daniel Richter, Ian Probert, Raffaele Siano, Gipsi Lima-Mendez, Jeroen Raes, Chris Bowler, Patrick Wincker, Eric Karsenti, & the Tara Oceans Consortium.
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Global ocean’s protist metabarcodingColomban de Vargas, Stéphane Audic, Nicolas Henry, Johan Decelle, Frédéric Mahé, Cédric Berney, Sébastien Colin, Sarah Romac, Daniel Richter, Ian Probert, Raffaele Siano, Gipsi Lima-Mendez, Jeroen Raes, Chris Bowler, Patrick Wincker, Eric Karsenti, & the Tara Oceans Consortium.
43 samples (viral fraction <0.22um) from 26 stations; 2.16 billion Illumina reads (200X larger than the Pacific Ocean Virome).
pelagic upper-ocean viral community sequence space is now well-sampled and approaches a limit of ca. 1 million PCs
Protein Clusters(ORFs)
• 68 stations68 stations 7.2 Tbp DNA data7.2 Tbp DNA data• 3 depths3 depths in the context ofin the context of• 243 samples243 samples the environmentthe environment
A genetic inventory of the ocean:A genetic inventory of the ocean:Ocean Microbial Reference Gene CatalogOcean Microbial Reference Gene Catalog
High sequencing coverageHigh sequencing coverage• only few new genes peradditional sample• 4 x more genes than inhuman gut microbiome
meta-barcoding – V9 rDNA, the microscope of the III millenary
Top-down interactions potentially driving plankton community structure: (1) parasites
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Dinoflagellates infected by syndiniales
Experimental validation of network-predicted interaction (photosymbiosis)
Model for network-driven hypothesis generation
Laser scanning confocal microscopy (LSCM) of acoel flatwormwith endosymbiotic green algae (Tetraselmis)
UniEuk – towards a universal taxonomic frameworkand integrated reference gene databases foreukaryotic biology, ecology, and evolution
A community-based initiative, highly complementary to EukRef
UniEuk organizational scheme
A community-based initiative, highly complementary to EukRef
To address the current deluge of genetic data from environmentalgenetic surveys, meta-barcoding, -transcriptomics, -genomics, single-cell
transcriptomics and genomics, a common taxonomic framework is critical.
Without it, results of different studies using different genesand different reference databases would not be comparable.
common taxonomic framework
gene 1referencedatabase
gene 2referencedatabase
gene 3referencedatabase
gene 4referencedatabase
One taxonomic framework for multiple genetic markers
UniEuk: a pragmatic implementation
gene reference databases
universaltaxonomicframework
existinggenetic datarepositories
UniEuk: a pragmatic implementation
gene reference databases
taxonomytable
sequencetable
markertables
universaltaxonomicframework
existinggenetic datarepositories
UniEuk: a community-based effort
UniEuk webportal
Redmineenvironment
taxonomyimplementer
databaseimplementer
experts / curators
on a web protal, experts/curators have access to the latest version of the framework and databases
experts/curators use a redmine environment to provide feedback, flag issues, make suggestions of changes
the implementers use this feedback to improve the framework/databases and regularly update the web portal
UniEuk Steering Committee
Sina Adl, University of SaskatchewanGuy Cochrane, EMBL-EBIColomban de Vargas, Station Biologique de RoscoffFrank Oliver Glöckner, Max Planck Institute and Jakobs UniversityEunsoo Kim, American Museum of Natural HistoryLaura Wegener-Parfrey, University of British ColumbiaPelin Yilmaz, Max Planck Institute and Jakobs University