Abstract
SILVA (lat. forest) is a comprehensive web resource, providing services around up to date, high-quality datasets of aligned ribosomal RNA gene (rDNA) sequences from the Bacteria, Archaea, and Eukaryota domains. SILVA dates back to the year 1991 when Dr. Wolfgang Ludwig from the Technical University Munich started the integrated software workbench ARB (lat. tree) to support high-quality phylogenetic inference and taxonomy based on the SSU and LSU rDNA marker genes. At that time, the ARB project maintained both, the sequence reference datasets and the software package for data analysis. In 2005, with the massive increase of DNA sequence data, the maintenance of the software system ARB and the corresponding rRNA databases SILVA was split between Munich and the Microbial Genomics and Bioinformatics Research Group in Bremen. ARB has been continuously developed to include new features and improve the usability of the workbench. Thousands of users worldwide appreciate the seamless integration of common analysis tools under a central graphical user interface, in combination with its versatility.The first SILVA release was deployed in February 2007 based on the EMBL-EBI/ENA release 89. Since then, full SILVA releases offering the database content in various flavours are published at least annually, complemented by intermediate web-releases where only the SILVA web dataset is updated. SILVA is the only rDNA database project worldwide where special emphasis is given to the consistent naming of clades of uncultivated (environmental) sequences, where no validly described cultivated representatives are available. Also exclusive for SILVA is the maintenance of both comprehensive aligned 16S/18S rDNA and 23S/28S rDNA sequence datasets. Furthermore, the SILVA alignments and trees were designed to include Eukaryota, another unique feature among rDNA databases. With the termination of the European Ribosomal RNA Database Project in 2007, the SILVA database has become the authoritative rDNA database project for Europe. The application spectrum of ARB and SILVA ranges from biodiversity analysis, medical diagnostics, to biotechnology and quality control for academia and industry.
Highlights
Pioneered by Fox et al (1977) more than 40 years ago and propagated by Giovannoni et al (1988), Olsen et al (1986), Pace et al (1985) and Ward et al (1990), the use of ribosomal RNA molecule has become the “gold-standard” for nucleic acid-based investigations of microbial diversity, their taxonomic assignment and phylogenetic reconstructions (Amann et al, 1995; Fuhrman et al, 2015; Pace, 1997)
The two major objectives that were formulated at the beginning of the ARB project and were followed until today are: (1) the maintenance of a structured integrative secondary database of high-quality sequences, combining processed primary structures and any type of additional data assigned to the individual sequence entries, and (2) a comprehensive selection of directly interacting software tools, as well as a central database controlled via a common graphical user interface
Sequences are rejected based on the quality values or based on the alignment quality to achieve specificity of the SILVA datasets, thereby correcting over-prediction by the RNAmmer models as well as removing sequences wrongly annotated as rDNA
Summary
Pioneered by Fox et al (1977) more than 40 years ago and propagated by Giovannoni et al (1988), Olsen et al (1986), Pace et al (1985) and Ward et al (1990), the use of ribosomal RNA (rRNA) molecule has become the “gold-standard” for nucleic acid-based investigations of microbial diversity, their taxonomic assignment and phylogenetic reconstructions (Amann et al, 1995; Fuhrman et al, 2015; Pace, 1997). The resulting millions of small and large subunit (SSU and LSU) rRNA gene sequences in the public archives require specialised tools and databases for alignment, analysis, phylogenetic inference, and classification. In 2005, the decision was made to split the workload by separating the maintenance of the ARB software package from the production and dissemination of the rDNA datasets. This laid the foundation of the SILVA ribosomal RNA database project in the Microbial Genomics and Bioinformatics Group in Bremen. SILVA maintains manually curated and non-public reference alignments of 75,000 16S/ 18S and 23S/28S ribosomal RNA genes (the SEED) in order to re-align all sequences for each SILVA release. The complete history of all releases is available on the SILVA website under ‘Documentation’ and ‘Archive’
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