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Preliminary release information: SILVA 138

Release information of the SILVA SSU and LSU databases 138 as of Sep 3, 2019

SSU 138 LSU 138
Parc 9,470,435 (+ 3,397,254) 1,312,673 (+ 405,291)
Ref 4,945,070 (+ 2,854,402) 357,845 (+ 159,002)
Ref NR 99 659,046 (- 36,125) 123,524 (new)


Since release 115, for SSU only SSU Ref NR 99 contains a guide tree. Since release 138, for LSU only LSU Ref NR 99 contains a guide tree.

Former statistics:

Opens internal link in current windowSILVA 95, Silva 96, SILVA 98, SILVA 100, SILVA 102,
SILVA 104, Opens internal link in current windowSILVA 106, Opens internal link in current windowSILVA 108, Opens internal link in current windowSILVA 111, Opens internal link in current windowSILVA 115,
Opens internal link in current windowSILVA 119, Opens internal link in current windowSILVA 123, Opens internal link in current windowSILVA 128, Opens internal link in current windowSILVA 132

Small Subunit rRNA Database

SSU Parc (Web database only) contains all aligned sequences with an alignment identity value equal and above 50, an alignment quality value equal and above 40 as well as an basepair score or sequence quality equal and above 30. All sequences with a Pintail value < 50 or an alignment quality value < 75 have been assigned to color group 1 in ARB (red). All Living Tree Project or StrainInfo typestrains have been assigned to color group 2 in ARB (light blue). No further sequence curation has been applied.

To create SSU Ref (Web database & ARB file), all sequences below 1,200 bases for Bacteria and Eukarya and below 900 bases for Archaea or an alignment identity below 70 or an alignment quality value below 50 have been removed from SSU Parc. All sequences with a Pintail value < 50 or an alignment quality value < 75 have been assigned to color group 1 in ARB (red). All Living Tree Project or StrainInfo typestrains have been assigned to color group 2 in ARB (light blue).

To create SSU Ref NR 99 (Web database & ARB file), a 99% identity criterion to remove highly identical sequences was applied using the vsearch tool with a custom sequence order first based on presence in the last release's Ref NR 99 and second based on combination of sequence length (weighted twofold) and quality. For the sorting, the quality of a sequence is determinded by ambiguties (50%), overall alignment quality (45%), and homopolymers (5%). The overall alignment quality of the sequence is calculated from its alignment score, alignment identity, and alignment percentage (all equally weighted). Sequences from cultivated species have been preserved in all cases.

A guide tree was calculated by adding all sequences to the SSU Ref tree of SILVA release 132. For tree calculation, highly variable positions were removed for Bacteria, Archaea, and Eukarya with the respective position variability filters. Position variability filters for Bacteria, Archaea and Eukarya have been calculated and added to the dataset. The tree was extensively manually curated taking into account the latest taxonomic information. More information about the SILVA and LTP taxonomic frameworks can be found in the respective Opens external link in new windowpaper. Detailed information about the SSU Ref NR dataset will be made available later.

Remark: Before using the alignment for extensive phylogenetic reconstructions all sequences should be checked carefully.

Large Subunit rRNA Databases

LSU Parc (Web database & ARB file) contains all aligned sequences with an alignment identity value equal and above 40 and an alignment quality value, a basepair score or a sequence quality equal and above 30. All sequences with an alignment quality value < 75 have been assigned to color group 1 in ARB (red). All Living Tree Project or StrainInfo typestrains have been assigned to color group 2 in ARB (light blue). No further curation has been applied. 

Additionally, for LSU Ref (Web database & ARB file) all sequences below 1,900 bases or an alignment identity below 60 have been removed. The process to create LSU Ref NR 99 (Web database & ARB file) from the LSU Ref is analogous to the creation of the SSU Ref NR99 (see above).

Please take into account that the LSU SEED consists only of around 4508 sequences and there is no guaranty that well aligned close relatives have always been available. We would recommend additional manual curation before using it for extensive phylogenetic reconstructions.

Taxonomies, Names, Type Strain & Genome Information

Taxonomy

With SILVA release 102 the default taxonomy shown on the webpage (browser/search) is the Opens external link in new windowSILVA taxonomy. Briefly, the tree for Bacteria and Archaea has been organized based on the Bergey's taxonomic outline, LPSN and the literature. Starting with SILVA release 111, extensive care has been taken to also improve the Opens internal link in current windoweukaryotic taxonomy. From SILVA release 138 on, the Opens external link in new windowGenome Taxonomy Database (GTDB) and Opens external link in new windowUniEuk taxonomies are used as additional resources for the curation. Based on the curated SILVA Ref NR taxonomy all sequences in SILVA (Parc) have been automatically classified.

Alternative Taxonomies

Besides the SILVA and EMBL-EBI/ENA taxonomy, alternative classifications taken from the GTDB (June 2019), RDP II (July 2017) and Opens internal link in current windowLTP (SSU June 2017, LSU September 2015) projects are also available in SILVA. On the webpage, the user can switch using the taxonomy menu. In ARB, the different taxonomies can be found in the fields: tax_slv, tax_embl, tax_gtdb, tax_rdp and tax_ltp for SILVA, EMBL-EBI/ENA, GTDB, RDP II and LTP, respectively. The corresponding *_name fields shows the respective sequence name for each entry.  Please take into account that greengenes, RDP II and LTP provide only a subset of the sequences hosted by SILVA. If no taxonomic mapping to greengenes, RDP II or LTP was available they are assigned as "unclassified" and the respective sequence name equals EMBL-EBI/ENA.

Altenative Names

All names of validly described species in the SSU and LSU databases have been checked for changes (basonyms, synonyms and orthographical corrections) against the DSMZ "Bacterial Nomenclature up to date (PNU)" service as of June 2019.

Cultured and Type strains

The information if a sequence originates from a cultured or type strain has been added to the field strain and is indicated by [T] and [C]. Several sources have been used to compile the information: The Opens external link in new windowStrainInfo.net bioportal (July 2017), The Ribosomal Database Project II (July 2017) and the Living Tree Project (SSU release 132, LSU release 123) which provides manually curated information compliant with Euzebys Opens external link in new window"List of Prokaryotic names with Standing in Nomenclature".

Genomes

The information if a sequence originates from a genome project has been taken from Opens external link in new windowNBCI and added to the field strain. It is indicated by n[G] and w[G] for genomic entries reported in the WGS section of INSDC.

Detailed information about the corresponding identifiers and target databases can be found in the table to the right.

The identifiers can be used for data retrieval by searching in the strain field see Opens internal link in current windowFAQ.

Quality Values

The length and colours of the bars give a first indication on the sequence and alignment quality as well as the risk for sequence anomalies based on Pintail analysis. After downloading the sequences as an ARB file, sequences that need attention can be selected by searching for low quality (alignment, sequence) or Pintail values in the corresponding ARB database fields. A full description of the colour code and all database fields available in the ARB files can be found in the Opens internal link in current windowFAQ section. Taking into account the rich set of sequence associated information that comes along with every SILVA sequence, user designed sub-databases can be easily generated.

SEEDs

All rRNA sequences have been aligned based on a completely manually re-checked SEED alignment of 67,342 rRNA sequences for SSU and 4508 rRNA sequences for LSU. The SSU alignment is based on the official ssu_jan04 release of the ARB Project. The SSU SEED alignment has been considerably improved for Archaea by manual addition of more than 1,000 sequences as well as Fungi (10,000 sequences). All SSU Eukaryotic sequences (18S) have been cross-checked by Wolfgang Ludwig before their addition to the SEED. Most of the bacterial sequences have also undergone a curation process carried out by the SILVA Team. We would rate our SSU SEED alignment for all Bacteria and Archaea as good and for Eukarya as reasonable.

The LSU alignment was provided by Wolfgang Ludwig and has not been released before SILVA. It was cross-checked by the SILVA Team before using it as the SEED for automatic alignment.  Bacteria and Archaea could be rated as good. The Eukaryotes need definitely further attention. With SILVA release 128 the LSU SEED has been significantly expanded by the integration of the LSU LTP sequences (1217) and curated sequences from Fungi (1587) thanks to Katrin Panzer and Marlis Reich. 

Statistics

Sequence Retrieval and Processing

SSU 138 LSU 138
candidates (total) 13,044,369 1,890,403
RNAmmer2,952,346346,642
< 300 bases 2,659,189 400,577
> 2% ambiguities 36,696 15,760
> 2% homopolymers 191,630 40,150
> 2% vector contamination 2,206 1,515
low alignment identity 810,792 146,677

total rejected by QC

3,573,934

577,730

Sequences have been retrieved from EMBL-EBI/ENA Opens external link in new windowRelease 138 (November 2018) using a complex keyword search procedure and sequence based search with Opens external link in new windowRNAmmer profiles. Cross checks with RDP II indicated no loss of primary data. Most of the sequences rejected by a low identity value after alignment with SINA were classified as not ribosomal RNA sequences by manual inspection.

1. Growth of the ribosomal RNA databases since 1992

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Blue: RDP II, orange: SILVA SSUParc based on EMBL releases

2. Length Distribution (SSU & LSU)

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Blue: raw data, red: the quality checked & aligned SSU Parc

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Blue: raw data, red: the quality checked & aligned LSU Parc

Basic statistics for the SILVA databases

SSU Ref SSU Ref NR LSU Ref LSU Ref NR
Version 138 138 138 138
Total 4,945,070 659,046 357,845 123,524
Bacteria tbd tbd tbd tbd
Archaea tbd tbd tbd tbd
Eukaryota tbd tbd tbd tbd
Cultured 39,322 39,322 8,106 8,106
Typestrains 24,444 24,444 4,706 4,706

Strain Identifiers

Source Information Tag Datasets
NCBI Genomes n[G] SSU, LSU
NCBI WGS genomes w[G]  SSU, LSU
Straininfo.net Cultured s[C] SSU, LSU
Straininfo.net Typestrains s[T] SSU, LSU
Living Tree Project  Typestrains (curated)  l[T] SSU
RDP II Typestrains r[T] SSU

RNAmmer

RNAmmer is a computational predictor for the major rRNA species (SSU, LSU) from all three domains of life. The program uses hidden Markov models trained on data from the European ribosomal RNA database project. SILVA runs the profiles of RNAmmer on all sequence entries of the EMBL-EBI/ENA archive to complement the existing predictions. All predictions are marked with RNAmmer in the ann_src_field. More information about RNAmmer can be found in the Opens external link in new windowpaper.

New in Release 138

  • Webpage
    • the new LSU Ref Nr 99 dataset is available for all tools
    • Opens internal link in current windowTestProbe and Opens internal link in current windowTestPrime now use the non-redundant versions of the SILVA Parc datasets if run on the Parc
    • fixed an issue in Opens internal link in current windowTestProbe and Opens internal link in current windowTestPrime that would report inconsistent results based on the allowed number of mismatches
  • ARB files
    • new LSU Ref Nr 99 ARB file
  • Exports
    • Opens external link in new windowMGnify/Opens external link in new windowMAPSeq compatible files are now available
    • LSU Ref Nr 99
  • Pipeline
    • several improvements and bug fixing
    • changed clustering tool to vsearch
    • use quality-based sorting for clustering
    • genome information is now imported from NCBI (was EMBL)
    • Opens external link in new windowGTDB taxonomy is imported as alternative taxonomy
    • Opens external link in new windowUniEuk taxonomy is imported as alternative taxonomy
  • Taxonomy
    • on-going

Known Bugs

  • SSU Parc: 211,240 sequences have no Pintail values

Citations

Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Opens external link in new windowNucl. Acids Res. 41 (D1): D590-D596.

Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, Schweer T, Peplies J, Ludwig W, Glöckner FO (2014) The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Opens external link in new windowNucl. Acids Res. 42:D643-D648

If you use SINA please cite:

Pruesse, E, Peplies, J and Glöckner, FO (2012) SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Opens external link in new windowBioinformatics, 28, 1823-1829