PhytoREF statistics

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Protocols

PhytoREF specifications

Information


Unique identifier OMICS_19894
Name PhytoREF
Restrictions to use None
Community driven No
Data access File download
User data submission Not allowed
Maintained Yes

Maintainers


  • person_outline Colomban de Vargas
  • person_outline Richard Christen
  • person_outline Johan Decelle
  • person_outline Daniel Vaulot

Publication for PhytoREF

PhytoREF citations

 (4)
library_books

TREE2FASTA: a flexible Perl script for batch extraction of FASTA sequences from exploratory phylogenetic trees

2018
BMC Res Notes
PMCID: 5838971
PMID: 29506565
DOI: 10.1186/s13104-018-3268-y

[…] To document TREE2FASTA’s execution speed, we downloaded two FASTA sequence reference databases of use in phototroph metabarcoding, tufA [, ] and the 16S rDNA PhytoREF [] (Table ). We produced exploratory ML trees (as above) and edited 10 phyletic clades in FigTree with color and with color + annotation (Additional file ). Using an iMac (3.5 GHz Intel Core […]

call_split

Changes in bacterioplankton community structure during early lake ontogeny resulting from the retreat of the Greenland Ice Sheet

2017
PMCID: 5776470
PMID: 29087379
DOI: 10.1038/ismej.2017.191
call_split See protocol

[…] es (12.9% of the initial reads) remained in the rDNA and 43942 (19.8%) sequences remained in the rRNA fraction.16S rRNA genes classified as chloroplasts in the SILVA database were aligned against the PhytoRef database () and classified after removal of potential chimeric sequences. The PhytoRef database contains 6490 plastidial 16S rDNA reference sequences spanning all major photosynthetic lineage […]

call_split

A pivotal role for ocean eddies in the distribution of microbial communities across the Antarctic Circumpolar Current

2017
PLoS One
PMCID: 5565106
PMID: 28827834
DOI: 10.1371/journal.pone.0183400
call_split See protocol

[…] is [] and the results are provided in the supplementary data (). Microphytoplankton diversity was analyzed using the chloroplast OTUs in the sequence datasets. Dominant OTUs were identified using the PhytoREF reference database [] and the results were tabulated (). […]

call_split

Diversity and oceanic distribution of the Parmales (Bolidophyceae), a picoplanktonic group closely related to diatoms

2016
PMCID: 5030691
PMID: 27003244
DOI: 10.1038/ismej.2016.38
call_split See protocol

[…] 1 and ITS (ITS1+5.8S rDNA+ITS2) sequences from Bolidophyceae was compiled. In particular, we retrieved all sequences assigned as ‘Bolidophyceae' in the PR2 database for nuclear 18S rRNA () and in the PhytoRef database for plastid 16S rRNA (). This data set was used to identify similar environmental sequences in the GenBank (release 206.0; February 2015) and CAMERA (http://camera.calit2.net/—note t […]

Citations

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PhytoREF institution(s)
UMR 7144 - Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, Roscoff, France; CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France; Sir Alister Hardy Foundation for Ocean Science, The Laboratory, Plymouth, UK; Marine Biological Association, The Laboratory, Plymouth, UK; Stazione Zoologica Anton Dohrn, Naples, Italy; The AlgaeBase Foundation, c/o Ryan Institute, National University of Ireland, Ireland; CNRS, UMR 7138, Systématique Adaptation Evolution, Parc Valrose, Nice, France; Université de Nice-Sophia Antipolis, UMR 7138, Systématique Adaptation Evolution, Parc Valrose, Nice, France
PhytoREF funding source(s)
Supported by the OCEANOMICS project, the French Government, under the grant agreement ‘Investissements d’Avenir’ ANR-11-BTBR-0008, the European Union programs MicroB3 (UEcontract-287589) and MaCuMBA (FP7-KBBE-2012-6-311975), the French ‘Investissements d’Avenir’ program EMBRC-France, and the HPC and visualization resources of ‘Centre de Calcul Interactif’ hosted by ‘Université Nice Sophia Antipolis’.

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