pr2database/pr2database: PR2 version 4.12.0

Date : 2019-08-08 Contributors Javier del Campo - U of Miami - Apicomplexa Ramon Massana - ICM, Barcelona - Stramenopiles Daniel Vaulot - CNRS Roscoff - Metadata geolocalisation - based on a idea of Margaret Brisbin Johan Decelle - CNRS Grenoble - Plastid sequences (PhytoRef database) Chetan Gaonkar - Naples - Chaetoceros Database structure Table pr2_main - add fields gene - 18S_RNA, 16S_RNA organelle - nucleus, plastid, mitochondria, nucleomorph, apicoplast (left empty for cyanobacteria) Table pr2_metadata - add or modify fields gb_organelle - import the corresponding gb field pr2_sequence_origin - add other possibilities such as genome and metagenome pr2_continent, pr2_country, pr2_country_lat, pr2_country_lon - geographical origin extracted from gb_country field pr2_location, pr2_location_lat, pr2_location_lon - geographical origin extracted from gb_country field. pr2_ocean, pr2_sea, pr2_sea_lat, pr2_sea_lon - extracted from gb_country field and gb_isolation_source Table pr2_sequences - add fields sequence_hash - hash value of the sequence (using R function digest::sha1, see https://cran.r-project.org/web/packages/openssl/vignettes/crypto_hashing.html) Table pr2_taxonomy - add fields taxon_trophic_mode - detailed trophic mode (e.g. "C-fixation constitutive; Mixotroph") Clean up 1692 sequences that had more than 2 consecutive "NN" have been removed Files provided We are now providing separate files for 18S nuclear and 16S plastid sequences for UTAX, dada2, fasta and mothur/Qiime formats. The merged file contains both 18S and 16S sequences. The metadata file is not provided any more since metadata can be found in the merged file. The whole pr2 database is also provided as an SQLite file. It contains the different tables making up pr2. Taxonomy changed Apicomplexa Taxonomy completely revised following del Campo et al. (2019) New sequences: 2619 Updated sequences: 5889+239 Removed sequences: 89 Stramenopiles - Higher ranks changed according to Massana et al. 2014, Derelle et al 2016, and Adl et al. 2019 compiled by R. Massana. Diatoms - Chaetoceros - 196 new sequences have been added from Gaonkar et al. (2019) with help from B. Edvardsen Chlorophyta Mamiellophyceae - Micromonas clades have been updated according to Tragin and Vaulot 2019. Prasinophytes clade IX - Separation between clades IXA and IXB removed waiting for analysis. Cryptophyceae - Cryptomonadales moved from family to order. Cercozoa - Class Chlorarachniophyceae replaces Filosa-Chlorarachnea Plastid 16S sequences and cyanos Data originate from the PhytoRef database (Decelle et al. 2015). Taxonomy has been harmonized with the PR2 taxonomy framework. In particular going from 12 levels to 8 taxonomy levels. This integration of plastid sequences should be helpful to researchers that get metabarcodes for both 16S and 18S rRNA. 16S plastid sequences added: 6049 16S cyanobacteria sequence added: 42 Metadata Sequence geo-localisation : Following up on the very good post of Margaret Brisbin, the geoname server (http://www.geonames.org/export/geonames-search.html) and the fuzzywuzzy Python library has been used to provide information about sequence location origin. Country and/or ocean are now provided for 90,788 GenBank entries with countries/ocean coordinates. References Adl, S.M., Bass, D., Lane, C.E., Lukeš, J., Schoch, C.L., Smirnov, A., Agatha, S. et al. 2019. Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes. J. Eukaryot. Microbiol. 66:4–119. Decelle, J., Romac, S., Stern, R.F., Bendif, E.M., Zingone, A., Audic, S., Guiry, M.D. et al. 2015. PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy. Mol. Ecol. Resour. 15:1435–1445. Derelle, R., López-García, P., Timpano, H. & Moreira, D. 2016. A Phylogenomic Framework to Study the Diversity and Evolution of Stramenopiles (=Heterokonts). Mol. Biol. Evol. 33:2890–8. Gaonkar, C.C., Piredda, R., Minucci, C., Mann, D.G., Montresor, M., Sarno, D. & Kooistra, W.H.C.F. 2018. Annotated 18S and 28S rDNA reference sequences of taxa in the planktonic diatom family Chaetocerotaceae. PLoS One. 13:e0208929. Massana, R., del Campo, J., Sieracki, M.E., Audic, S. & Logares, R. 2014. Exploring the uncultured microeukaryote majority in the oceans: reevaluation of ribogroups within stramenopiles. ISME J. 8:854–66. del Campo J., Heger T., Rodríguez-Martínez R., Worden AZ., Richards TA., Massana R., Keeling PJ. 2018. A new framework for the study of apicomplexan diversity across environments. bioRxiv 1. DOI: 10.1101/494880