vaulot/pr2database: PR2 version 4.11.0

Annotators : Daniel Vaulot, Adriana Lopes dos Santos, Vittorio Boscaro (Eukref)
Date : 30 October 2018

• Database is now available as a R datafile and
• Remove sequences shorter than 500 bp - 173 sequences affected

• 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

• 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

• 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

• 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.