The PFR² database

The database offers access to planktonic Foraminifera 18S ribosomal DNA sequence library with a curated taxonomy at the morphological and molecular level. These sequences have been obtained through single-cell DNA extraction from specimens, identified taxonomically by characters of their calcite shells. The vast majority of the sequences cover the fragment of the gene between the helices 32 and 50. The aim of PFR² is to provide a comprehensive and high quality free resource to study the ecology and biogeography of planktonic foraminifera as a model system for evolution in the pelagic realm. The first version of PFR² combines sequences available on Genbank with new data generated across several laboratories. The compilation was facilitated through the efforts of the SCOR/IGBP Working Group 138 “Modern planktonic foraminifera and ocean changes”. A strict control of the quality of the sequences has been applied and the taxonomy has been curated to achieve full internal consistency. PFR² can be used to annotate environmental sequences and also to design probes and primers.

Download and availability

The first release of PFR² contains 3322 18S ribosomal DNA sequences with curated taxonomy, associated with metadata that locate the specimens from which the sequences were obtained in space and time. All PFR² sequences longer than 200 nt are lodged on Genbank. The database can be downloaded entirely or by taxonomic rank and is searchable by keywords. Several BLAST tools are also available to facilitate identification of unknown sequences. A mapping tool is provided to visualize the distribution of the sequences. A list of publications will be kept up to date to document the various sources of PFR².

Version history

PFR² v. 1: released on 20/01/2015, 3322 18S ribosomal DNA sequences

How to cite

The manuscript presenting the PFR² database is available here.

If you make use of the database in the frame of your research please cite:

Morard, R., Darling, K.F., Mahé, F., Audic, S., Ujiié, Y., Weiner, A.K.M., André, A., Seears, H. a., Wade, C.M., Quillévéré, F., Douady, C.J., Escarguel, G., de Garidel-Thoron, T., Siccha, M., Kucera, M., de Vargas, C., 2015. PFR² : a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution. Molecular Ecology Resources. 15, 1472–1485. doi:10.1111/1755-0998.12410


PFR² would like to thank: MARUM, SCOR, OCEANOMICS.