Release information: SILVA 128

Release information of the SILVA SSU and LSU databases 128 as of Sept 29, 2016

SSU 128 LSU 128
Parc

5,616,941

(+ 632,275)

735,238

(+ 171,906)

Ref 1,922,213

(+ 164,598)

154,297

(+ 57,655)

Ref NR 99
645,151 (+ 46,681) since release 115, only SSU 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

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 using the UCLUST tool was applied. 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 123.1. 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 is available Opens internal link in current windowhere.

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, a guide tree was calculated based on the LSU Ref tree of SILVA release 123, and basic filters have been added. The tree was 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.

Please take into account that the LSU SEED consists only of around 5590 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. Based on the curated SILVA Ref 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 greengenes (May 2013), RDP II (May 2015) and Opens internal link in current windowLTP (Sept 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_gg, tax_rdp and tax_ltp for SILVA, EMBL-EBI/ENA, greengenes, 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. For the LSU datasets only SILVA, LTP and EMBL-EBI/ENA taxonomies are available.

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 "Nomenclature up to date" catalogue as of April 2016.

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 2016), The Ribosomal Database Project II (May 2015) and the Living Tree Project (release 123) which provides manually curated information compliant with Euzebys "Opens external link in new windowList 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 windowEMBL-EBI/ENA and added to the field strain. It is indicated by e[G].

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 70,512 rRNA sequences for SSU and 5590 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 128 LSU 128
candidates (total) 8,430,487 1,134,275
RNAmmer124,45085,381
< 300 bases 2,144,997 284,200
> 2% ambiguities 28,433 8228
> 2% homopolymers 151,533 33,388
> 2% vector contamination 2151 1351
low alignment identity 597,823 100,760

total rejected by QC

2,800,910

389,836

Sequences have been retrieved from EMBL-EBI/ENA Opens external link in new windowRelease 128 (June 16) 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 SSUParc sequences

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Blue: raw data, red: the quality checked & aligned LSUParc sequences

Basic statistics for the SILVA databases

    SSURef   SSURef NR   LSUParc   LSURef  
Version   128   128   128   128  
Total   1,922,213   645,151   735,238   154,297  
Bacteria   1,719,541   552,377   176,194   130,965  
Archaea   64,390   24,315   1528   1271  
Eukaryota   140,020   68,996   557,769   22,105  
Cultured   36,747   36,747   24,664   8232  
Typestrains   22,334   22,334   5809   4675  
                   

Strain Identifiers

Source Information Tag Datasets
EMBL-EBI/ENA Typestrains (t) SSU, LSU
EMBL-EBI/ENA Genomes e[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 128

  • Webpage
    • All SILVA sequences are automatically taxonomically classified based on LSURef and SSURef NR 99.
    • Opens internal link in current windowLTP updated to release 123.
    • Links to BacDive, DSMZ Catalogue and LPSN have been added where possible.
    • The Opens external link in new windowSILVA Treeviewer 1.1 has been released.
  • ARB files
    • The guide tree is only available for SSU Ref NR 99 and LSU Ref.
  • Exports
    • Mapping files for the SILVA taxonomy and ranks are now available for SSU and LSU.
    • Opens external link in new window Megan compatible files are now available.
  • Pipeline
    • Several improvements and bug fixing.
    • Added more than 1000 sequences to the blacklist after manual inspection.
  • Seed
    • The SSU Seed was extended with the latest LTP version (123).
    • The SSU Seed now contains 70,512 sequences (+1305).
    • The LSU Seed was extended with the latest LTP version (123).
    • The LSU Seed now contains 5590 sequences (+2722).
  • SILVA
  • Taxonomy
    • Several errors in the bacterial, archaeal and eukaryotic taxonomy have been corrected.
    • Many taxonomic clusters have been evaluated for their stability.
    • Clean up of suspect bad quality/chimeric sequences.
    • The Fungi taxonomy has been significantly revised.
    • Eukaryotic taxonomy is currently under revision by the UniEuk project.

Known Bugs

  • SSUParc: 98,364 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