Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. Environmental metabarcoding is a powerful approach to assess the composition and global distribution of algal communities, in particular the unicellular microalgae that often lack distinctive morphological characters. However, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms.
The PhytoREF database provides an access to plastidial 16S rRNA gene sequences of a large diversity of photosynthetic eukaryotes with curated and normalized taxonomy. PhytoREF has been built using the publicly available sequences and plastidial genomes from GenBank, as well as, new amplicon sequences obtained from numerous cultures of marine phytoplankton. Stringent quality filtering and phylogeny-based taxonomic classification were applied for each single 16S rRNA gene sequence. All the major eukaryotic lineages that perform photosynthesis or keep a relict plastid are represented in PhytoREF, and comprise terrestrial, freshwater and marine taxa (land plants, marine and freshwater macro and microalgae).
PhytoREF is not only a new tool to explore, evaluate and monitor the diversity of photosynthetic eukaryotes in different ecosystems with metabarcoding approaches, but also a genomic resource to annotate new 16S rRNA sequences, and design primers and probes. This new database can be used for many purposes from biomonitoring of photosynthetic eukaryotes in various habitats (e.g. water, sediment, ice), paleoecological studies in past environments, to dietary studies.
The PhytoREF database can be downloaded on this website by different ways: 1) as a single file, 2) according to a search for a given taxonomic level (e.g. Class, Genus etc.) 3) or a search by similarity. Contributions or suggestions are very welcome and can be submitted either to Colomban de Vargas, Johan Decelle or Richard Christen (see contacts).
If you find PhytoREF useful for your research purposes, please cite : Decelle, J., Romac, S., Stern, R. F., Bendif, E. M., Zingone, A., Audic, S., Guiry, M. D., Guillou, L., Tessier, D., Le Gall, F., Gourvil, P., Dos Santos, A. L., Probert, I., Vaulot, D., de Vargas, C. and Christen, R. (2015), PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy. Mol Ecol Resour, 15: 1435-1445. doi:10.1111/1755-0998.12401
This work was supported by the OCEANOMICS project, funded by the French Government and managed by the Agence Nationale de la Recherche, under the grant agreement 'Investissements d'Avenir' ANR-11-BTBR-0008. Financial support for this work was also provided by the European Union programs MicroB3 (UEcontract- 287589) and MaCuMBA (FP7-KBBE-2012-6-311975) and the French 'Investissements d'Avenir' program EMBRC-France.
We are grateful to Ales Horak, Jan Janouskovec, Chris Jackson, Akira Kuwata, Camille Poirier and Daphne Grulois for providing 16S rDNA sequences and microalgal strains.
