vaulot/pr2database: PR2 version 4.11.0

Annotators : Daniel Vaulot, Adriana Lopes dos Santos, Vittorio Boscaro (Eukref) Date : 30 October 2018 Database changes Database is now available as a R datafile and Remove sequences shorter than 500 bp - 173 sequences affected Bug fixes Correct some Genbank clone information (gb-clone) that were wrongly formatted as dates (e.g. 07-02 was mis-labelled as jul.-02). Correct PR2 accession numbers, start, end and label - 1170 sequences affected GenBank entries with 2 PR2 sequences and different taxonomy: 4 sequences corrected and 2 removed (AF245249, AY706334, FJ848510, JF276416, KM020045, KM020071) R Script - PR2 update 4.11 - Management Chlorophyta Orders Prasinococcales and Palmophyllales incorporated into class Palmophyllophyceae. Prasinophytes clade VII moved to the two newly created classes: Chloropicophyceae and Picocystophycaeae - 198 sequences updated and 104 sequences added (Lopes dos Santos et al. 2018). Mamiellophyceae (Micromonas, Ostreococcus, Mantoniella) - 872 sequences updated and 8 sequences added (Tragin and Vaulot 2018) R Script - PR2 update 4.11 - Chloropicophyceae R Script - PR2 update 4.11 - Mamiellophyceae Ciliates (from Eukref) Follows the publication of Boscaro et al. Sequences annotated by Eukref as either "low quality" (125) or "chimeras" (283) have been annotated and removed from PR2. Sequences with taxonomy updated: 4550 New sequences added: 2478 sequences Sequences removed (will need to be re-examined later) : 652 R Script - PR2 update 4.11 - Ciliophora References Lopes dos Santos, A., Pollina, T., Gourvil, P., Corre, E., Marie, D., Garrido, J.L., Rodríguez, F. et al. 2017. Chloropicophyceae, a new class of picophytoplanktonic prasinophytes. Sci. Rep. 7:14019. Tragin, M. & Vaulot, D. 2018. Novel diversity within marine Mamiellophyceae (Chlorophyta) unveiled by metabarcoding. bioRxiv. Boscaro, V., Santoferrara, L.F., Zhang, Q., Gentekaki, E., Syberg-Olsen, M.J., del Campo, J. & Keeling, P.J. 2018. EukRef-Ciliophora: A manually curated, phylogeny-based database of small subunit rRNA gene sequences of ciliates. Environ. Microbiol