PR2 - 18S rRNA sequence database - version 4.11

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Station Biologique de Roscoﬀ UMR7144 - CNRS and Sorbonne Université PR2 release 4.11 Daniel Vaulot [email protected] November 3, 2018

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1 Content What is PR2 ? What is PR2 used for ? History of PR2 PR2 now How is PR2 implemented and maintained ? MySQL database R scripts Access to PR2 What is next ? |

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2 What is PR2 ? |

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3 What is PR2 ? PR2 = Protist Ribosomal Reference database. Open access database of eukaryotic 18S rRNA sequences. |

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3 What is PR2 ? PR2 = Protist Ribosomal Reference database. Open access database of eukaryotic 18S rRNA sequences. All sequences originate from GenBank. |

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3 What is PR2 ? PR2 = Protist Ribosomal Reference database. Open access database of eukaryotic 18S rRNA sequences. All sequences originate from GenBank. Sequences receive a detailed taxonomic assignment (8 levels). Taxonomic annotation for both strain and environmental sequences. |

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4 What is PR2 used for ? |

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5 What is PR2 used for ? Annotation of metabarcoding data |

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5 What is PR2 used for ? Annotation of metabarcoding data Biogeography |

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5 What is PR2 used for ? Annotation of metabarcoding data Biogeography Sequence analysis |

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5 What is PR2 used for ? Annotation of metabarcoding data Biogeography Sequence analysis Links between phylogeny and functional traits |

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5 What is PR2 used for ? Annotation of metabarcoding data Biogeography Sequence analysis Links between phylogeny and functional traits 220 papers citing PR2. |

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6 What is PR2 used for ? Metabarcoding Marine ecosystems |

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6 What is PR2 used for ? Metabarcoding Marine ecosystems Ballast waters |

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6 What is PR2 used for ? Metabarcoding Marine ecosystems Ballast waters River systems |

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6 What is PR2 used for ? Metabarcoding Marine ecosystems Ballast waters River systems Hot Springs |

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6 What is PR2 used for ? Metabarcoding Marine ecosystems Ballast waters River systems Hot Springs Soil |

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6 What is PR2 used for ? Metabarcoding Marine ecosystems Ballast waters River systems Hot Springs Soil Farming systems |

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6 What is PR2 used for ? Metabarcoding Marine ecosystems Ballast waters River systems Hot Springs Soil Farming systems Urban ecology |

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6 What is PR2 used for ? Metabarcoding Marine ecosystems Ballast waters River systems Hot Springs Soil Farming systems Urban ecology Criminology |

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7 What is PR2 used for ? Biogeography Simon, N. et al. 2017. Revision of the Genus Micromonas Manton et Parke (Chlorophyta, Mamiellophyceae), of the Type Species M. pusilla (Butcher) Manton & Parke and of the Species M. commoda van Baren, Bachy and Worden and Description of Two New Species. Protist. 168:612–35. |

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8 What is PR2 used for ? Sequence analysis Primer analysis - On-going work with S. Geisen and D. Bass. |

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9 History of PR2 |

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10 PR2 history 1997 Excel ﬁle created by D. Vaulot during L. Guillou thesis 2000-2003 Access/ARB database maintained by D. Vaulot during PICODIV 2006-2010 KeyDNAtools developed by L. Guillou 2010-2013 Project BioMarks: creation of PR2 by L. Guillou Database maintained by R. Christen : ssu-rrna.org mid-2016 Web site died 2016 D. Vaulot takes over maintenance Raw data deposited to Figshare 2017 Database moved to MySQL Development of R scripts to manage the database Repository on GitHub |

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11 PR2 history PICODIV |

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12 PR2 history PICODIV |

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13 PR2 history Guillou et al. 2013 paper |

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14 PR2 Now |

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15 Statistics Taxonomic distribution |

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16 Statistics Sequence size distribution |

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17 Statistics Geographical distribution |

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18 Recent updates Version Date Who Major group updated 4.11 30/10/2018 D. Vaulot, A. Lopes Chloropicophyceae, Mamiellophyceae EukRef Ciliates 4.9 20/02/2018 S. Mordret, R. Piredda, D. Sarno Dinophyceae 4.7 27/09/2017 C. Bachy, W.-T. Chen Cilates (Sprirotrichea) 4.4 10/11/2016 D. Vaulot Bolidophyceae 4.0 21/10/2015 B. Edvardsen Haptophyta 3.0 31/8/2015 M. Tragin Chlorophyta 2.0 07/02/2015 T. Biard Rhizaria |

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19 Recent updates Dinoﬂagellates |

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20 Recent updates Ciliates - Eukref |

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21 How is PR2 implemented and maintained ? |

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22 Implementation MySQL database |

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22 Implementation MySQL database Processing done with R (tidyr libraries) |

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22 Implementation MySQL database Processing done with R (tidyr libraries) Data available on GitHub (and Figshare - DOI number) |

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23 MySQL database Tables pr2_main : sequences assigned to species |

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23 MySQL database Tables pr2_main : sequences assigned to species pr2_sequence : sequence of each entry |

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23 MySQL database Tables pr2_main : sequences assigned to species pr2_sequence : sequence of each entry pr2_metadata : metadata for each entry |

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23 MySQL database Tables pr2_main : sequences assigned to species pr2_sequence : sequence of each entry pr2_metadata : metadata for each entry pr2_taxonomy : one line per species |

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24 MySQL database Table: pr2_main Each entry has a PR2 accession number (2 entries may correspond to the same Genbank accession number, e.g. for genomes) Sequences are linked to taxonomy by species name Annotation of Chimera (removed when PR2 is exported) |

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25 MySQL database Table: pr2_metadata Genbank annotations (gb_ fields) Some gb fields have been manually edited (e.g. gb_strain and gb_clone) Manually curated annotations (eg. sample_ fields) Fields computed from gb fields such as longitude and latitude Phenotypic information (auto vs. hetero, mixotroph etc. . . ) |

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26 MySQL database Table: pr2_taxonomy 8 taxonomic levels (kingdom -> species) Follows PR2 convention (_X, _XX etc..) Contains 47 000 species Each name is unique (i.e. does not appear in different columns or different lines). Any daughter taxon has a unique mother taxon. |

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27 R scripts R scripts - uses tidyr universe Add new sequences from GenBank Correct taxonomy of existing sequences (EukRef output) Extract metadata from Genbank entries Check sequences problems (short sequences, sequences with ambiguities) Analyze taxonomy Export data to a variety of format (fasta, R data) |

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28 R scripts Sequence processing |

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29 Access to PR2 |

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30 GitHub GitHub https://github.com/vaulot/pr2database Releases - current version 4.11.0 Wiki Issues |

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31 GitHub Wiki |

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32 GitHub Download formats Export formats metabarcode annotation mothur Qiime dada2 USEARCH, VSEARCH BLAST - fasta ﬁles metadata R dataset - new |

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33 GitHub R dataset |

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34 Figshare Figshare https://doi.org/10.6084/m9.ﬁgshare.5913181 PhytoRef (16S plastid) is also on Figshare . |

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35 What is next ? |

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36 Database Coordinate with EukRef |

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36 Database Coordinate with EukRef Reference sequences |

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36 Database Coordinate with EukRef Reference sequences Chimeras |

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36 Database Coordinate with EukRef Reference sequences Chimeras Reannotate environmental sequences (Wang/DECIPHER) |

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36 Database Coordinate with EukRef Reference sequences Chimeras Reannotate environmental sequences (Wang/DECIPHER) Import more recent GenBank sequences |

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36 Database Coordinate with EukRef Reference sequences Chimeras Reannotate environmental sequences (Wang/DECIPHER) Import more recent GenBank sequences Incorporate new metadata types (e.g. mixotrophs) |

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37 Web site In the coming years, we will try to provide users with new functionalities. However this already can be done easily using R and the pr2database library. Speciﬁc datasets |

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37 Web site In the coming years, we will try to provide users with new functionalities. However this already can be done easily using R and the pr2database library. Speciﬁc datasets Reference sequences (e.g.for alignements) Chimeras Taxonomic groups (e.g. diatoms . . . ) BLAST search Automatic metabarcode annotation using Wang classiﬁer/DECIPHER |