Reference database structure

From version 4.14.0, a single SSU database is provided which contains sequences for:

  • 18S rRNA from nuclear and nucleomorph
  • 16S rRNA from plastid, apicoplast, chromatophore, mitochondrion
  • 16S rRNA from a small selection of bacteria

The rationale is that the database can now be used to detect bacterial sequences that are amplified with either 18S rRNA or “universal” primers. These sequences can be further assigned with Silva or GTDB.

Taxonomy structure

Version 5.0 and above

  • 9 levels : Domain / Supergroup / Division / Subdivision / Class / Order / Family / Genus / Species
    • Kingdom is replaced by Domain
    • Adding a Subdivision level

Version 4.14.1 and below

  • 8 levels : Kingdom / Supergroup / Division / Class / Order / Family / Genus / Species

Rules for naming taxonomic levels

  • All taxonomy paths are unique. For example for a given Class, all higher levels are similar (Division -> Supergroup -> Domain)
  • No taxon can appear at different levels. For example “Stramenopiles” cannot appear at both the Supergroup and Division levels.
  • No space (use underscore). For example Home_sapiens
  • If species is not known use “Genus_sp.” (note the . after sp). The Genus level can be a level with Xs (see next rule): e.g. “Stramenopiles_XXXX_sp.“,
  • If level i is unknown
    • if level i-1 is known, use level i-1 followed by “_X” , e.g. “Stramenopiles_X” at Division level
    • if level i-1 is unknown, use level i-1 followed by “X” , e.g. “Stramenopiles_XX” at Class level


In order to allow correct assignation with software such as DECIPHER (IDTax) for organelle, the taxonomy is appended with 4 letters corresponding to the organelle

Organelle Taxonomy suffix
nucleomorph :nucl
plastid :plas
apicoplast :apic
chromatophore :chrom
mitochondrion :mito

e.g. a sequence annotated as Neoceratium_horridum:plas will correspond to a plastid sequence of the species Neoceratium horridum

Rules for sequences

  • Minimum length = 500 bp (except for some plastid sequences which are shorter)
  • Maximum number of ambiguities (N) = 20
  • No consecutive Ns (so sequences such as ..ATGNNAT.. are removed)

Construction of PR2 id (pr2_accession)


For example AF530536.1.1695_U

  • AF530536 : GenBank accession number
  • 1 : Start of the 18S rRNA in the GenBank sequence
  • 1695 : End of the 18S rRNA in the GenBank sequence
  • X can take any of the following values:
    • G: genomic sequence containing a described intron (rDNA)
    • R: the previous genomic rRNA sequence, without the intron(s)
    • U: no intron described, but intron(s) may be present
    • UC: introns were detected in silico and removed from the sequence (putative rRNA)

Database structure (tables and fields)

Table Fields Comment
pr2_main pr2_accession, genbank_accession, species, editing hitory
pr2_sequence pr2_accession, , sequence linked to pr2_main by pr2_accession
pr2_metadata metadata from GenBank and from published references linked to pr2_main by genbank_accession
pr2_taxonomy domain -> species, editing history linked to pr2_main by species
pr2_countries geo-information linked to pr2_metadata by pr2_country
pr2_assign_silva assignment of pr2 sequences according to Silva linked to pr2_main by pr2_accession
eukribo_V2 Eukribo version 2 data linked to pr2_main by genbank_accession
pr2_traits Traits from other databases harboring species traits linked to pr2_taxonomy by taxonomy level (e.g. species, genus). This table used a long format.
worms_taxonomy Worms database entries for taxa from PR2

pr2 database structure

History of database structure changes

PR2 version Table Field Action Comment
5.0.0 eukribo_V2 A New table holding Eukribo version 2 data.
pr2_traits A New table for adding traits to PR2 from other databases (e.g. Mixoplankton Database)
worms_taxonomy A New table with Worms database entries for taxa from PR2
4.14.0 pr2_main quarantined_version A quarantined sequences do not appear in the released version but will be re-assigned latter
pr2_metadata gb_references R empty
gb_locus R empty
gb_division A 3-letter code (e.g. PLN, ENV)
4.13.0 pr2_metadata pr2_depth A depth of sample in meter
gb_id A Genbank ID number (big integer)
gb_project_id A Genbank project ID for metagenomes
gb_sequence A original gb_sequence (longtext)
pr2_countries A New table for country information
pr2_assign_silva A New table for Silva assignation of sequences
4.12.0 pr2_main gene A 18S_RNA, 16S_RNA
organelle A nucleus, plastid, mitochondria, nucleomorph, apicoplast (left empty for cyanobacteria)
pr2_metadata gb_organelle A import the corresponding gb field
pr2_sequence_origin M add other possibilities such as genome and metagenome
pr2_continent, pr2_country, pr2_country_lat, pr2_country_lon A geographical origin extracted from gb_country field, gb_isolation_source, eukref_geo_loc_name
pr2_location, pr2_location_lat, pr2_location_lon A geographical origin extracted from gb_country field, gb_isolation_source, eukref_geo_loc_name
pr2_sea, pr2_sea_lat, pr2_sea_lon A geographical origin extracted from gb_country field, gb_isolation_source, eukref_geo_loc_name
pr2_sequence sequence_hash A hash value of the sequence (using R function digest::sha1
pr2_taxonomy taxon_trophic_mode A detailed trophic mode (e.g. “C-fixation constitutive; Mixotroph”) - for future use
4.11.1 pr2_metadata gb_reference A Contains the whole REFERENCE field from GenBank
eukref_publication eukref_authors eukref_journal M Merged into gb_publication, gb_authors, gb_journal
4.11.0 pr2_metadata eukref_publication eukref_authors eukref_journal eukref_notes A Added
4.11.0 pr2_metadata pr2_xxx M fields annotated by Eukref renamed back to eukref_xxx
4.11.0 pr2_main taxo_id R not used anymore since linked is done by species (this will be probably reinstated later on a different form using a different format for the taxonomy table).
4.9 pr2_metadata eukref_xxx M renamed to pr2_xxx to reflect the fact that these fields will also be updated independantly of EukRef
4.9 pr2_main reference_sequence A designate sequences that can be used as reference e.g. for alignment
4.8 pr2_main, taxo xx_date (e.g. edited_date) R redundant with xx_version (e.g. edited_version) fields
4.8 pr2_sequence sequence_length M Minimum length is now 500 bp.

Action : A=Added/R=Removed/M=Modified

Daniel Vaulot
CNRS, France

Focusing on marine (pico)phytoplankton .